|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
2-654 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 601.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 2 VKADIPIVVVFRALGVVSDEDILNHICydrNDTPMLEMLKPCIEEGF-VIQDREVALDFIAKR---GSSQSNlnhdrRVR 77
Cdd:PRK08565 208 VPGKIPFVILMRALGLETDRDIVYAVS---LDPEIQQELLPSLEQASsIAATVEDALDYIGKRvaiGQPREY-----RIE 279
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 78 YARDIMQKELLPHISQSDGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTKDLQR 157
Cdd:PRK08565 280 RAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKY 359
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 158 YVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKkaattkAGVSQVLSRYTFASSLSHLRRTNTPIGRDGKIAK 237
Cdd:PRK08565 360 QLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFE 433
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 238 PRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPAEPIVDfmIQRNMEV--LEEFEPQVTPNATKVFVNGVWVG 315
Cdd:PRK08565 434 ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLNGRLIG 511
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 316 IHRDPSHLVTTMQNLRRRNMISHEVSL--IRDIREREFKIFTDTGRVCRPLFVIDNdpksensGGLVLNKDHIRKLESDK 393
Cdd:PRK08565 512 YHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLKKGE 584
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 394 dlptdlgpeerreqyFGWDGLVRSGAVEYVDAEEEETIMIVMTPEDLeisrqlqagyaLPEdetgdpnkrvrsilsqraH 473
Cdd:PRK08565 585 ---------------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL-----------TPE------------------H 620
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 474 twTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFSQRMETMANILYYPQKPLATTRSMEFLRFRE 553
Cdd:PRK08565 621 --THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYND 698
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 554 LPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYADTEK--MVGLQvvERFEKPMRiDTLGMR-KGTYDKL 630
Cdd:PRK08565 699 RPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERkyPGGQE--DKIEIPEP-NVRGYRgEEYYRKL 775
|
650 660
....*....|....*....|....
gi 2770801248 631 DEDGIVAPGVRVSGEDIIIGKTAP 654
Cdd:PRK08565 776 DEDGIVSPEVEVKGGDVLIGKTSP 799
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
100-655 |
4.30e-156 |
|
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: 472.05 E-value: 4.30e-156
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 100 RKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTKDLQRYVQRCVETNREIYLNIGIKAST 179
Cdd:cd00653 208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKP 287
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 180 LTGGLKYALATGNWGeQKKAATTKAGVSQVLSRYTFASSLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 258
Cdd:cd00653 288 ITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGE 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 259 ACGLVKNLALMCYITvgtpaepivdfmiqrnmevleefepqvtpnatkvfvngvwvgihrdpshlvttmqnlrrrnmish 338
Cdd:cd00653 367 NCGLVKNLALMARIS----------------------------------------------------------------- 381
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 339 evslirdirerefkiftdtGRVCRPLFVIDNDpksensgglvlnkdhirklesdkdlptdlgpeerreqyfgwdglvrsg 418
Cdd:cd00653 382 -------------------GRIERPYRIVEKE------------------------------------------------ 394
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 419 aveyvdaeeeetimivmtpedleisrqlqagyalpedetgdpnkrvrsilsqrahtWTHCEIHPSMILGVCASIIPFPDH 498
Cdd:cd00653 395 --------------------------------------------------------VTHIEISPSQILSVAASLIPFPEH 418
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 499 NQSPRNTYQSAMGKQAMGVFLTNFSQRMETMANILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIATYSGYNQEDSVIM 578
Cdd:cd00653 419 NQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIII 498
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2770801248 579 NQSSIDRGLFRSLFYRTYADTEKMVGLQVVERFekpmRIDTLGMRKGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPL 655
Cdd:cd00653 499 NKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPK 571
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
307-654 |
2.45e-106 |
|
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: 334.69 E-value: 2.45e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 307 VFVNGVWVGIHRDPSHLVTTMQNLRRRNMISHEVSLIRDIREREFKIFTDTGRVCRPLFVIDNdpksensGGLVLNKDHI 386
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 387 RKLesdkdlptdlgpeerREQYFGWDGLVRSGAVEYVDAEEEETIMIVMTPEDLeisrqlqagyaLPEdetgdpnkrvrs 466
Cdd:TIGR03670 74 EKL---------------KEGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL-----------TPE------------ 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 467 ilsqraHTwtHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFSQRMETMANILYYPQKPLATTRSM 546
Cdd:TIGR03670 116 ------HT--HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVL 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 547 EFLRFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYADTEKMVGLQVVERFEKPMRiDTLGMR-KG 625
Cdd:TIGR03670 188 ELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEP-DVRGYRgEE 266
|
330 340
....*....|....*....|....*....
gi 2770801248 626 TYDKLDEDGIVAPGVRVSGEDIIIGKTAP 654
Cdd:TIGR03670 267 AYKHLDEDGIVYPEVEVKGGDVLIGKTSP 295
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
1-654 |
6.98e-84 |
|
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: 284.31 E-value: 6.98e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 1 YVKAD----IPIVVVFRALGVVSDEDILNHIcydrNDTPMLEMLKPCIEEGfVIQDREVALDFIAKR---G------SSQ 67
Cdd:COG0085 168 YVRIDrkrkIPVTVLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpGepptieRAE 242
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 68 SNLNH----DRRVRYA---RDIMQKELLPHISQSDGseTRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLL 140
Cdd:COG0085 243 QLLDNlffdPKRYDLAhvgRYKINKKLGLDVPPEDR--VLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELL 320
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 141 ASLFRTLFTRVTKDLqRYvQRCVETNREIYLNIGIKASTLTGGLKYALATGnwgeqkkaattkaGVSQVLSRYTFASSLS 220
Cdd:COG0085 321 QNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELT 385
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 221 HLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITvgtpaepivdfmiqrnmev 292
Cdd:COG0085 386 HKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------------------- 442
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 293 leefepqvtpnatkvfvngvwvgihrdpshlvttmqnlrrrnmishevslirdirerEFkiftdtGRVCRPLFVIDNdpk 372
Cdd:COG0085 443 ---------------------------------------------------------EY------GFIETPYRKVEN--- 456
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 373 sensgGLVLNKdhirklesdkdlptdlgpeerreqyfgwdglvrsgaVEYVDAEEEETIMIVmtpedleisrqlQAGYAL 452
Cdd:COG0085 457 -----GKVTDE------------------------------------IEYLTADEEENYYIA------------QANAPL 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 453 PED----ETGDPNKRVRSILSQRAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNfsqrmet 528
Cdd:COG0085 484 DEDgnflEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE------- 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 529 mANILYYP--------------QKPLAttRSMEFLR------------FRELPAGQNAIVAIATYSGYNQEDSVIMNQSS 582
Cdd:COG0085 557 -APLLHYPlqkfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERL 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 583 IDRGLFRSLFYRTYadtekmvglQVVERfekpmriDT-LGMRKGT----------YDKLDEDGIVAPGVRVSGEDIIIGK 651
Cdd:COG0085 634 VKDDVLTSIHIEEY---------EIEAR-------DTkLGPEEITrdipnvseeaLRNLDEDGIIRIGAEVKGGDILVGK 697
|
...
gi 2770801248 652 TAP 654
Cdd:COG0085 698 VTP 700
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
1-181 |
4.45e-73 |
|
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: 241.13 E-value: 4.45e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 1 YVKADIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFVI--QDREVALDFIAKRGSSQSNLNHDR--RV 76
Cdd:pfam04563 211 YIKKEIPIVIILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIFRMGRPRepRI 290
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 77 RYARDIMQKELLPHISQSDGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTKDLQ 156
Cdd:pfam04563 291 KYAEEILQKEVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVR 370
|
170 180
....*....|....*....|....*
gi 2770801248 157 RYVQRCVETNREIYLNIGIKASTLT 181
Cdd:pfam04563 371 ERLQKVLGSPDDLMLQLLVNAKPIT 395
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
2-654 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 601.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 2 VKADIPIVVVFRALGVVSDEDILNHICydrNDTPMLEMLKPCIEEGF-VIQDREVALDFIAKR---GSSQSNlnhdrRVR 77
Cdd:PRK08565 208 VPGKIPFVILMRALGLETDRDIVYAVS---LDPEIQQELLPSLEQASsIAATVEDALDYIGKRvaiGQPREY-----RIE 279
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 78 YARDIMQKELLPHISQSDGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTKDLQR 157
Cdd:PRK08565 280 RAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKY 359
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 158 YVQRCVETNREIYLNIGIKASTLTGGLKYALATGNWGEQKkaattkAGVSQVLSRYTFASSLSHLRRTNTPIGRDGKIAK 237
Cdd:PRK08565 360 QLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFE 433
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 238 PRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPAEPIVDfmIQRNMEV--LEEFEPQVTPNATKVFVNGVWVG 315
Cdd:PRK08565 434 ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWSRVYLNGRLIG 511
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 316 IHRDPSHLVTTMQNLRRRNMISHEVSL--IRDIREREFKIFTDTGRVCRPLFVIDNdpksensGGLVLNKDHIRKLESDK 393
Cdd:PRK08565 512 YHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLKKGE 584
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 394 dlptdlgpeerreqyFGWDGLVRSGAVEYVDAEEEETIMIVMTPEDLeisrqlqagyaLPEdetgdpnkrvrsilsqraH 473
Cdd:PRK08565 585 ---------------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL-----------TPE------------------H 620
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 474 twTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFSQRMETMANILYYPQKPLATTRSMEFLRFRE 553
Cdd:PRK08565 621 --THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYND 698
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 554 LPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYADTEK--MVGLQvvERFEKPMRiDTLGMR-KGTYDKL 630
Cdd:PRK08565 699 RPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERkyPGGQE--DKIEIPEP-NVRGYRgEEYYRKL 775
|
650 660
....*....|....*....|....
gi 2770801248 631 DEDGIVAPGVRVSGEDIIIGKTAP 654
Cdd:PRK08565 776 DEDGIVSPEVEVKGGDVLIGKTSP 799
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
100-655 |
4.30e-156 |
|
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: 472.05 E-value: 4.30e-156
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 100 RKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTKDLQRYVQRCVETNREIYLNIGIKAST 179
Cdd:cd00653 208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKP 287
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 180 LTGGLKYALATGNWGeQKKAATTKAGVSQVLSRYTFASSLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 258
Cdd:cd00653 288 ITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGE 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 259 ACGLVKNLALMCYITvgtpaepivdfmiqrnmevleefepqvtpnatkvfvngvwvgihrdpshlvttmqnlrrrnmish 338
Cdd:cd00653 367 NCGLVKNLALMARIS----------------------------------------------------------------- 381
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 339 evslirdirerefkiftdtGRVCRPLFVIDNDpksensgglvlnkdhirklesdkdlptdlgpeerreqyfgwdglvrsg 418
Cdd:cd00653 382 -------------------GRIERPYRIVEKE------------------------------------------------ 394
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 419 aveyvdaeeeetimivmtpedleisrqlqagyalpedetgdpnkrvrsilsqrahtWTHCEIHPSMILGVCASIIPFPDH 498
Cdd:cd00653 395 --------------------------------------------------------VTHIEISPSQILSVAASLIPFPEH 418
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 499 NQSPRNTYQSAMGKQAMGVFLTNFSQRMETMANILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIATYSGYNQEDSVIM 578
Cdd:cd00653 419 NQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIII 498
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2770801248 579 NQSSIDRGLFRSLFYRTYADTEKMVGLQVVERFekpmRIDTLGMRKGTYDKLDEDGIVAPGVRVSGEDIIIGKTAPL 655
Cdd:cd00653 499 NKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPK 571
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
307-654 |
2.45e-106 |
|
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: 334.69 E-value: 2.45e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 307 VFVNGVWVGIHRDPSHLVTTMQNLRRRNMISHEVSLIRDIREREFKIFTDTGRVCRPLFVIDNdpksensGGLVLNKDHI 386
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 387 RKLesdkdlptdlgpeerREQYFGWDGLVRSGAVEYVDAEEEETIMIVMTPEDLeisrqlqagyaLPEdetgdpnkrvrs 466
Cdd:TIGR03670 74 EKL---------------KEGELTWDDLVKQGVIEYLDAEEEENAYIALDPEEL-----------TPE------------ 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 467 ilsqraHTwtHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFSQRMETMANILYYPQKPLATTRSM 546
Cdd:TIGR03670 116 ------HT--HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVL 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 547 EFLRFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYADTEKMVGLQVVERFEKPMRiDTLGMR-KG 625
Cdd:TIGR03670 188 ELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEP-DVRGYRgEE 266
|
330 340
....*....|....*....|....*....
gi 2770801248 626 TYDKLDEDGIVAPGVRVSGEDIIIGKTAP 654
Cdd:TIGR03670 267 AYKHLDEDGIVYPEVEVKGGDVLIGKTSP 295
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
305-654 |
5.62e-98 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 313.05 E-value: 5.62e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 305 TKVFVNGVWVGIHRDPSHLVTTMQNLRRRNMISHEVSLIRDIREREFKIFTDTGRVCRPLFVIDNdpksensGGLVLNKD 384
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 385 HIRKLESDKdlptdlgpeerreqyFGWDGLVRSGAVEYVDAEEEETIMIVMTPEDLEisrqlqagyalPEdetgdpnkrv 464
Cdd:PRK07225 78 HIEKLKNGE---------------LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLT-----------EE---------- 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 465 rsilsqraHTwtHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFSQRMETMANILYYPQKPLATTR 544
Cdd:PRK07225 122 --------HT--HLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQ 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 545 SMEFLRFRELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYADTEKMVGLQVVERFEKPMRiDTLGMR- 623
Cdd:PRK07225 192 TQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDK-DVRGYRg 270
|
330 340 350
....*....|....*....|....*....|.
gi 2770801248 624 KGTYDKLDEDGIVAPGVRVSGEDIIIGKTAP 654
Cdd:PRK07225 271 EEAYRHLDEDGLVNPETEVKEGDVLIGKTSP 301
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
1-654 |
6.98e-84 |
|
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: 284.31 E-value: 6.98e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 1 YVKAD----IPIVVVFRALGVVSDEDILNHIcydrNDTPMLEMLKPCIEEGfVIQDREVALDFIAKR---G------SSQ 67
Cdd:COG0085 168 YVRIDrkrkIPVTVLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpGepptieRAE 242
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 68 SNLNH----DRRVRYA---RDIMQKELLPHISQSDGseTRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLL 140
Cdd:COG0085 243 QLLDNlffdPKRYDLAhvgRYKINKKLGLDVPPEDR--VLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELL 320
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 141 ASLFRTLFTRVTKDLqRYvQRCVETNREIYLNIGIKASTLTGGLKYALATGnwgeqkkaattkaGVSQVLSRYTFASSLS 220
Cdd:COG0085 321 QNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELT 385
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 221 HLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITvgtpaepivdfmiqrnmev 292
Cdd:COG0085 386 HKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------------------- 442
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 293 leefepqvtpnatkvfvngvwvgihrdpshlvttmqnlrrrnmishevslirdirerEFkiftdtGRVCRPLFVIDNdpk 372
Cdd:COG0085 443 ---------------------------------------------------------EY------GFIETPYRKVEN--- 456
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 373 sensgGLVLNKdhirklesdkdlptdlgpeerreqyfgwdglvrsgaVEYVDAEEEETIMIVmtpedleisrqlQAGYAL 452
Cdd:COG0085 457 -----GKVTDE------------------------------------IEYLTADEEENYYIA------------QANAPL 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 453 PED----ETGDPNKRVRSILSQRAHTWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNfsqrmet 528
Cdd:COG0085 484 DEDgnflEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE------- 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 529 mANILYYP--------------QKPLAttRSMEFLR------------FRELPAGQNAIVAIATYSGYNQEDSVIMNQSS 582
Cdd:COG0085 557 -APLLHYPlqkfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERL 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 583 IDRGLFRSLFYRTYadtekmvglQVVERfekpmriDT-LGMRKGT----------YDKLDEDGIVAPGVRVSGEDIIIGK 651
Cdd:COG0085 634 VKDDVLTSIHIEEY---------EIEAR-------DTkLGPEEITrdipnvseeaLRNLDEDGIIRIGAEVKGGDILVGK 697
|
...
gi 2770801248 652 TAP 654
Cdd:COG0085 698 VTP 700
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
1-181 |
4.45e-73 |
|
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: 241.13 E-value: 4.45e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 1 YVKADIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFVI--QDREVALDFIAKRGSSQSNLNHDR--RV 76
Cdd:pfam04563 211 YIKKEIPIVIILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIFRMGRPRepRI 290
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 77 RYARDIMQKELLPHISQSDGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTKDLQ 156
Cdd:pfam04563 291 KYAEEILQKEVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVR 370
|
170 180
....*....|....*....|....*
gi 2770801248 157 RYVQRCVETNREIYLNIGIKASTLT 181
Cdd:pfam04563 371 ERLQKVLGSPDDLMLQLLVNAKPIT 395
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
1-285 |
2.14e-70 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 237.16 E-value: 2.14e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 1 YVKADIPIVVVFRALGVVSDEDILNHICYDRNdtPMLEMLkPCIEEGfVIQDREVALDFIAKRGSSqsNLNHDRRVRYAR 80
Cdd:PRK09606 212 SVPGSIPFVILMRALGLETDEEIVEAVSDDPE--IVKFML-ENLEEA-EVDTQEEALEYIGKRVAP--GQTKEYRIKRAE 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 81 DIMQKELLPHISQSDGSETRKAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTKDLQRYVQ 160
Cdd:PRK09606 286 YVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLE 365
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 161 RCVETNREIYLNIGIKASTLTGGLKYALATGNWgeqkkaATTKAGVSQVLSRYTFASSLSHLRRTNTPIGRDGKIAKPRQ 240
Cdd:PRK09606 366 RANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARD 439
|
250 260 270 280
....*....|....*....|....*....|....*....|....*
gi 2770801248 241 LHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPAEPIVDFM 285
Cdd:PRK09606 440 LHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL 484
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
489-654 |
2.19e-67 |
|
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: 225.10 E-value: 2.19e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 489 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNFSQRMETMANILYYPQKPLATTRSMEFLRFRELPAGQNAIVAIATYS 568
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 569 GYNQEDSVIMNQSSIDRGLFRSLFYRTYaDTEKMVGLQVVERFEKPmridtLGMRKGTYDKLDEDGIVAPGVRVSGEDII 648
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEI-EARKTKLGPIEEITRDI-----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
....*.
gi 2770801248 649 IGKTAP 654
Cdd:pfam00562 155 VGKVGP 160
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
1-134 |
2.05e-44 |
|
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: 157.12 E-value: 2.05e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 1 YVKADIPIVVVFRALGVVSDEDILNHICYDRNDTPMLEMLKPCIEEGFVIQDREVALDFIAK----RGSSQSNLNHDRRV 76
Cdd:pfam04561 47 SKKRKIPIVIFLKALGLVSDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGKgfalRRGEEPRLQRAREI 126
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 77 RYARDiMQKELLPHISQSDGSETR--KAFFLGYMVHRLLQCALGRRDVDDRDHFGKKRLD 134
Cdd:pfam04561 127 LYSRD-PKYNLNKHLGLNEPFENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
307-368 |
7.35e-30 |
|
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: 112.07 E-value: 7.35e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2770801248 307 VFVNGVWVGIHRDPSHLVTTMQNLRRRNMISHEVSLIRDIREREFKIFTDTGRVCRPLFVID 368
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
208-271 |
7.76e-30 |
|
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 112.23 E-value: 7.76e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2770801248 208 QVLSRYTFASSLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 271
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
411-482 |
4.36e-23 |
|
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: 92.60 E-value: 4.36e-23
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2770801248 411 WDGLVRSGAVEYVDAEEEETIMIVMTPEDLEISRQLQAGYAlpedetgdpnkrvrsilsqRAHTWTHCEIHP 482
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREGP-------------------YAHTYTHCEIHP 53
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
109-654 |
3.37e-12 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 70.34 E-value: 3.37e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 109 VHRLLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTKDLQRyvqrcvetnreiylnigiKASTLTGGLKYAL 188
Cdd:PRK09603 441 VKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKD------------------KLTTMSGAFDSLM 502
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 189 ATGNWGEQKKAAT-----TKAGVSQVLSRYTFASSLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQ 258
Cdd:PRK09603 503 PHDLVNSKMITSTimeffMGGQLSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQ 581
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 259 ACGLVKNLALMCYIT----VGTPAEPIVDFMIQRNMEVLEEFEPQ---VTPNATKVFVNGvwvgihrdpsHLVTTMQNLR 331
Cdd:PRK09603 582 NIGLINTLSTFTRVNdlgfIEAPYKKVVDGKVVGETIYLTAIQEDshiIAPASTPIDEEG----------NILGDLIETR 651
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 332 RRNMI----SHEVSLIrDIREREFkiftdTGRVCRPLFVIDNDPKSENSGGLVLNKDHIRKLESDKDLpTDLGPEE--RR 405
Cdd:PRK09603 652 VEGEIvlneKSKVTLM-DLSSSML-----VGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPI-VGTGIEKiiAR 724
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 406 EqyfGWDGL--VRSGAVEYVDAEEEetimivmtpedleisrqlqagYALPEDETGdpnkrvrsilsqrahtwthceihps 483
Cdd:PRK09603 725 D---SWGAIkaNRAGVVEKIDSKNI---------------------YILGEGKEE------------------------- 755
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 484 milgvcasiiPFPDHNQSPRN--TYQSamgkqamgvflTNFSQRMETMANILYYPQKPLATTRSMEFlrfRELPAGQNAI 561
Cdd:PRK09603 756 ----------AYIDAYSLQKNlrTNQN-----------TSFNQVPIVKVGDKVEAGQIIADGPSMDR---GELALGKNVR 811
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 562 VAIATYSGYNQEDSVIMNQSSIDRGLFRSL-FYRTYADTEKMV-GLQVVERfekpmriDTLGMRKGTYDKLDEDGIVAPG 639
Cdd:PRK09603 812 VAFMPWNGYNFEDAIVVSERITKDDIFTSThIYEKEVDARELKhGVEEFTA-------DIPDVKEEALAHLDESGIVKVG 884
|
570
....*....|....*
gi 2770801248 640 VRVSGEDIIIGKTAP 654
Cdd:PRK09603 885 TYVSAGMILVGKTSP 899
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
118-654 |
2.85e-10 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 63.87 E-value: 2.85e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 118 GRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRvtkdLQRYVQRCVETNR--EIYLNIGIKASTLTGGLKYALATGNwge 195
Cdd:PRK14844 459 GQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLK----LERAVVDSMSTSSldKVSPSDFINPKVLTNVLRDFFNSSQ--- 531
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 196 qkkaattkagVSQVLSRYTFASSLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 271
Cdd:PRK14844 532 ----------LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYAR 601
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 272 IT----VGTPAEPIVDFMIQRNMEVLEEFEPqvtpnatkvfvngvwvGIHrdpsHLVTTMQNLRRRNMishevslirdir 347
Cdd:PRK14844 602 INkygfIESPYRKVVNRVVTDQIEYLSAIDE----------------GLY----YIADTSAKLDENNC------------ 649
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 348 erefkiFTDTGRVCRplfvidndpksensgglvlnkdhirklesdkdlptdlgpeerreqYFGWDGLVRSGAVEYVDAEE 427
Cdd:PRK14844 650 ------FVDDMLYCR---------------------------------------------YAGSFVMVSSDQVSYIDVSP 678
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 428 EETIMIvmtpedleisrqlqAGYALPEDETGDPNKRVRSILSQRAHTWTHCEIHP---------------SMILGVCASI 492
Cdd:PRK14844 679 KQVISV--------------AASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPlvatgmesfvasgsgAVVLAKRDGI 744
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 493 IPFPDHNQSPRNTYQSAmGKQAMGVFLTNFSQRMETMANILyYPQKPLA----------TTRSMEFLRFRELPAGQNAIV 562
Cdd:PRK14844 745 VDSSDSNSIVIRAFDKE-RVNYLDVDIYHLRKFQRSNHNTC-INQKPLVcvgdyvkegdVIADGPAINSGELALGQNLLV 822
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 563 AIATYSGYNQEDSVIMNQSSIDRGLFRSLFyrtyadtekmvglqvVERFEKPMRIDTLGMRKGTYD----------KLDE 632
Cdd:PRK14844 823 AFMSWQGYNFEDSIIISSEVVKKDLFTSIH---------------IEEFECVVHDTPLGSEKITRAipgvneenlyHLDD 887
|
570 580
....*....|....*....|..
gi 2770801248 633 DGIVAPGVRVSGEDIIIGKTAP 654
Cdd:PRK14844 888 SGIVKIGTRVGPGYILVGKVTP 909
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
112-267 |
3.53e-10 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 63.57 E-value: 3.53e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 112 LLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVTKDLQRYVQRCVETNREIYLNIGIKastltgglkyalatg 191
Cdd:CHL00207 287 LINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPK--------------- 351
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 192 nwgeqKKAATTKA--GVSQvLSRYT----FASSLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACG 261
Cdd:CHL00207 352 -----PLIALIREffGSSQ-LSQYMdqtnPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCG 425
|
....*.
gi 2770801248 262 LVKNLA 267
Cdd:CHL00207 426 LIGSLA 431
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
553-657 |
4.94e-06 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 49.90 E-value: 4.94e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 553 ELPAGQNAIVAIATYSGYNQEDSVIMNQSSIDRGLFRSLFYRTYaDTEKMVGLQVVERFEKPM-RIDTLGMRKgtydkLD 631
Cdd:CHL00001 648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERITKEIpHLEAHLLRN-----LD 721
|
90 100
....*....|....*....|....*.
gi 2770801248 632 EDGIVAPGVRVSGEDIIIGKTAPLAA 657
Cdd:CHL00001 722 KNGIVMLGSWVETGDILVGKLTPQEA 747
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-267 |
1.46e-05 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 48.56 E-value: 1.46e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 1 YVKAD----IPIVVVFRALGVvSDEDILNHICYDRNDTPMLEMLKPCIEEGFVIQDrEVALDFIAKRGSSQSNLNHDRRV 76
Cdd:PRK00405 188 YVRIDrrrkLPVTVLLRALGY-SDEEILDLFYEKEEFGKEIEVPVEYLLGKVLAED-IVDEETGEVLAEANDEITEELDG 265
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 77 RYARDIMQKEllPHISQSDG---------------SETRKAFF-----------LG----YMVHR--------------- 111
Cdd:PRK00405 266 PYIRNTLEKD--PTSSREEAlveiyrrlrpgepptVEAARSLLenlffdpkrydLSkvgrYKLNKklgldededvrvltk 343
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 112 ---------LLQCALGRRDVDDRDHFGKKRLDLAGPLLASLFRTLFTRVtkdlQRYVqrcvetnREiYLNIG-------- 174
Cdd:PRK00405 344 ediiatikyLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRM----ERAV-------RE-RMSLQdldtltpq 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 175 --IKASTLTGGLKYALATgnwgeqkkaattkagvSQvLSRytF------ASSLSHLRRTNT--PIG----------RDgk 234
Cdd:PRK00405 412 dlINAKPVVAAIKEFFGS----------------SQ-LSQ--FmdqtnpLSELTHKRRLSAlgPGGltreragfevRD-- 470
|
330 340 350
....*....|....*....|....*....|...
gi 2770801248 235 iakprqLHNTHWGLVCPAETPEGQACGLVKNLA 267
Cdd:PRK00405 471 ------VHPTHYGRICPIETPEGPNIGLINSLA 497
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
3-267 |
2.65e-05 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 47.59 E-value: 2.65e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 3 KADIPIVVVFRALGVvSDEDILNHICY----------------DRNDTPMLEMLK--PCIEEGFVIQD---REVALDFIA 61
Cdd:CHL00001 175 KQKISILVLLSAMGL-NLREILDNVCYpeiflsflndkekkkiGSKENAILEFYQqfACVGGDPVFSEslcKELQKKFFQ 253
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 62 KR----GSSQSNLNhdRRVRYarDIMQKE--LLPH--ISQSDgsetrkafflgymvhRLLQCALGRRDVDDRDHFGKKRL 133
Cdd:CHL00001 254 QRcelgRIGRRNMN--RKLNL--DIPENNtfLLPQdvLAAAD---------------YLIGMKFGMGTLDDIDHLKNKRI 314
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2770801248 134 DLAGPLLASLFRTLFTRVTKDLQRYVQRCVETNREIYLNIGIKASTLTGGLK-----YALatgnwgeqkkaattkagvSQ 208
Cdd:CHL00001 315 RSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYEsffgsHPL------------------SQ 376
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2770801248 209 VLSRYTFASSLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKNLA 267
Cdd:CHL00001 377 FLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLA 439
|
|
| |
