|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
47-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 858.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 47 ENHKGGfgqTVKATLPYVKTDVPIGIVFRGLGIVSDEDILNHICydrNDTQMLEKLKPCIEEAF-VIQDREVALDWIGSR 125
Cdd:PRK08565 194 ERRKDG---TIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVS---LDPEIQQELLPSLEQASsIAATVEDALDYIGKR 267
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 126 gNSQSLSRPKRVKYARDIMQKELLPHISQTDGSETKKAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLDLAGPLLAGLF 205
Cdd:PRK08565 268 -VAIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELF 346
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 206 RMLFNKLTKDVFKYLQKCVENNREFNLTLGVKSTTLTNGLKYSLATGNWGDQKkaasskAGVSQVLNRYTFASTLSHLRR 285
Cdd:PRK08565 347 RVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRR 420
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 286 TNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPCEPIIDFMNQRNMEMLEEYEPLRSPNA 365
Cdd:PRK08565 421 VVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISW 500
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 366 TKVFVNGVWVGVHRDPAHLVSNVQDLRRGHIISHEVSlVRDIRDREFK---IFTDAGRVCRPLFVIDNdtrsmnyGNLVL 442
Cdd:PRK08565 501 SRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKL 572
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 443 TKEHITRLeedkeaaigmDRDELEarqmgWDGLVNQGVVEYVDAEEEETVMIVMTPGDLetsrqiqlgkaVPENaedepn 522
Cdd:PRK08565 573 TREHVEKL----------KKGELT-----FDDLVKMGVIEYLDAEEEENAYVALDPEDL-----------TPEH------ 620
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 523 krvnamshrsaqtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMA 602
Cdd:PRK08565 621 --------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLV 686
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 603 TTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPmrTDTLR 682
Cdd:PRK08565 687 QTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVR 764
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 683 LKHG--TYEKLDDDGIVAPGVRVSGEDMIIGKTAPiP---PDSEELGQRTKMhiKRDASTPLRSTENGIVDQVLLTTNAE 757
Cdd:PRK08565 765 GYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PrflEELEELSLGLQE--RRDTSVTVRHGEKGIVDTVLITESPE 841
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 758 GLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRG 837
Cdd:PRK08565 842 GNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEG 921
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*...
gi 45545341 838 FEGDATPFTEVTVDSVSKILRAHGYQSRGFEVMYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:PRK08565 922 RFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHH 979
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
161-895 |
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: 764.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 161 KKAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLDLAGPLLAGLFRMLFNKLTKDVFKYLQKCVENNREFNLTLGVKSTT 240
Cdd:cd00653 208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKP 287
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 241 LTNGLKYSLATGNWGDQKKAaSSKAGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 319
Cdd:cd00653 288 ITSGIKEFLATGNWGSKRFL-MQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGE 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 320 ACGLVKNLALMCYITvgtpcepiidfmnqrnmemleeyeplrspnatkvfvngvwvgvhrdpahlvsnvqdlrrghiish 399
Cdd:cd00653 367 NCGLVKNLALMARIS----------------------------------------------------------------- 381
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 400 evslvrdirdrefkiftdaGRVCRPLFVIDNDTrsmnygnlvltkehitrleedkeaaigmdrdelearqmgwdglvnqg 479
Cdd:cd00653 382 -------------------GRIERPYRIVEKEV----------------------------------------------- 395
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 480 vveyvdaeeeetvmivmtpgdletsrqiqlgkavpenaedepnkrvnamshrsaqtwTHCEIHPSMILGICASIIPFPDH 559
Cdd:cd00653 396 ---------------------------------------------------------THIEISPSQILSVAASLIPFPEH 418
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 560 NQSPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 639
Cdd:cd00653 419 NQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIII 498
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 640 NQSSIDRGLFRSLFYRSYTDQEKRIGmsivEQFEKPMRTDTLRLKHGTYEKLDDDGIVAPGVRVSGEDMIIGKTAPIPPD 719
Cdd:cd00653 499 NKSSVDRGFFRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGET 574
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 720 SEELGQRTKMHIKRDASTPLRSTENGIVDQVLLTT---NAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQED 796
Cdd:cd00653 575 ESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQED 654
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 797 MPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTEVTVDSVSKILRAHGYQSRGFEVMYNAHTG 876
Cdd:cd00653 655 MPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTG 734
|
730
....*....|....*....
gi 45545341 877 QKLVAQVFLGPTYYQRLRH 895
Cdd:cd00653 735 EPLEAPIFVGPVYYQRLKH 753
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
368-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 574.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 368 VFVNGVWVGVHRDPAHLVSNVQDLRRGHIISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNdtrsmnyGNLVLTKEHI 447
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 448 TRLEEDkeaaigmdrdELEarqmgWDGLVNQGVVEYVDAEEEETVMIVMTPGDLetsrqiqlgkaVPENaedepnkrvna 527
Cdd:TIGR03670 74 EKLKEG----------ELT-----WDDLVKQGVIEYLDAEEEENAYIALDPEEL-----------TPEH----------- 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 528 mshrsaqtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMATTRSM 607
Cdd:TIGR03670 117 ---------THLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVL 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 608 EFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPmrTDTLRLKHG- 686
Cdd:TIGR03670 188 ELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGe 265
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 687 -TYEKLDDDGIVAPGVRVSGEDMIIGKTAPiPPDSEELGQ-RTKMHIKRDASTPLRSTENGIVDQVLLTTNAEGLRFVKV 764
Cdd:TIGR03670 266 eAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-PRFLEELREfGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKV 344
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 765 RMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATP 844
Cdd:TIGR03670 345 RVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTP 424
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|.
gi 45545341 845 FTEVTVDSVSKILRAHGYQSRGFEVMYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:TIGR03670 425 FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
550-895 |
1.28e-154 |
|
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: 458.53 E-value: 1.28e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 550 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMATTRSMEFLKFRELPAGQNAIVAIACYS 629
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 630 GYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIvEQFEKPmrtDTLRLKHgtYEKLDDDGIVAPGVRVSGEDMI 709
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPIE-EITRDI---PNVSEEA--LKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 710 IGKTAPIPPDSE---ELGQRTKmhIKRDASTPLRSTENGIVDQVLL-TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 785
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGEKAR--DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 786 GTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTEVT--VDSVSKILRAHGYQ 863
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYN 312
|
330 340 350
....*....|....*....|....*....|..
gi 45545341 864 SRGFEVMYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
63-895 |
3.77e-144 |
|
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: 452.64 E-value: 3.77e-144
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 63 YVKTD----VPIGIVFRGLGIVSDEDILNHIcydrNDTQMLEKLKPCIEEAfVIQDREVALDWIGSR---G------NSQ 129
Cdd:COG0085 168 YVRIDrkrkIPVTVLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpGepptieRAE 242
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 130 SL-----SRPKRVKYA---RDIMQKELLPHISQTDGseTKKAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLDLAGPLL 201
Cdd:COG0085 243 QLldnlfFDPKRYDLAhvgRYKINKKLGLDVPPEDR--VLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELL 320
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 202 AGLFRMLFNKLTKDVfKYlQKCVENNREFNLTLGVKSTTLTNGLKYSLATGnwgdqkkaasskaGVSQVLNRYTFASTLS 281
Cdd:COG0085 321 QNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELT 385
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 282 HLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITvgtpcepiidfmnqrnmem 353
Cdd:COG0085 386 HKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------------------- 442
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 354 leEYeplrspnatkvfvngvwvgvhrdpahlvsnvqdlrrghiishevslvrdirdrefkiftdaGRVCRPLFVIDNdtr 433
Cdd:COG0085 443 --EY-------------------------------------------------------------GFIETPYRKVEN--- 456
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 434 smnyGnlVLTKEhitrleedkeaaigmdrdelearqmgwdglvnqgvVEYVDAEEEETVMIVMTPGDLETSRQIqLGKAV 513
Cdd:COG0085 457 ----G--KVTDE-----------------------------------IEYLTADEEENYYIAQANAPLDEDGNF-LEERV 494
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 514 PENAEDEPnKRVNAMSHrsaqtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNydqrmdtmANI 593
Cdd:COG0085 495 LVRYRGEE-VLVPPEEV------DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APL 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 594 LYYP--------------QKPMAttRSMEFLK------------FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 647
Cdd:COG0085 560 LHYPlqkfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 648 LFRSLFYRSYTDQEKR--IGMSIVeQFEKPmrtdtlrlKHG--TYEKLDDDGIVAPGVRVSGEDMIIGKTAP---IPPDS 720
Cdd:COG0085 638 VLTSIHIEEYEIEARDtkLGPEEI-TRDIP--------NVSeeALRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTP 708
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 721 EELGQR----TKMHIKRDASTPLRSTENGIVDQVLLTTNAEG-------LRFVKVRMRTTKIPQIGDKFASRHGQKGTIG 789
Cdd:COG0085 709 EERLLRaifgEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVIS 788
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 790 ITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTEVTVDSVSKILRAHGYQSRGFEV 869
Cdd:COG0085 789 RILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEV 868
|
890 900
....*....|....*....|....*.
gi 45545341 870 MYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:COG0085 869 LYDGRTGEPFDNPVTVGYMYYLKLHH 894
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
47-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 858.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 47 ENHKGGfgqTVKATLPYVKTDVPIGIVFRGLGIVSDEDILNHICydrNDTQMLEKLKPCIEEAF-VIQDREVALDWIGSR 125
Cdd:PRK08565 194 ERRKDG---TIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVS---LDPEIQQELLPSLEQASsIAATVEDALDYIGKR 267
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 126 gNSQSLSRPKRVKYARDIMQKELLPHISQTDGSETKKAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLDLAGPLLAGLF 205
Cdd:PRK08565 268 -VAIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELF 346
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 206 RMLFNKLTKDVFKYLQKCVENNREFNLTLGVKSTTLTNGLKYSLATGNWGDQKkaasskAGVSQVLNRYTFASTLSHLRR 285
Cdd:PRK08565 347 RVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRR 420
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 286 TNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPCEPIIDFMNQRNMEMLEEYEPLRSPNA 365
Cdd:PRK08565 421 VVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISW 500
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 366 TKVFVNGVWVGVHRDPAHLVSNVQDLRRGHIISHEVSlVRDIRDREFK---IFTDAGRVCRPLFVIDNdtrsmnyGNLVL 442
Cdd:PRK08565 501 SRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKL 572
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 443 TKEHITRLeedkeaaigmDRDELEarqmgWDGLVNQGVVEYVDAEEEETVMIVMTPGDLetsrqiqlgkaVPENaedepn 522
Cdd:PRK08565 573 TREHVEKL----------KKGELT-----FDDLVKMGVIEYLDAEEEENAYVALDPEDL-----------TPEH------ 620
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 523 krvnamshrsaqtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMA 602
Cdd:PRK08565 621 --------------THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLV 686
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 603 TTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPmrTDTLR 682
Cdd:PRK08565 687 QTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVR 764
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 683 LKHG--TYEKLDDDGIVAPGVRVSGEDMIIGKTAPiP---PDSEELGQRTKMhiKRDASTPLRSTENGIVDQVLLTTNAE 757
Cdd:PRK08565 765 GYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-PrflEELEELSLGLQE--RRDTSVTVRHGEKGIVDTVLITESPE 841
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 758 GLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRG 837
Cdd:PRK08565 842 GNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEG 921
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*...
gi 45545341 838 FEGDATPFTEVTVDSVSKILRAHGYQSRGFEVMYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:PRK08565 922 RFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHH 979
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
161-895 |
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: 764.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 161 KKAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLDLAGPLLAGLFRMLFNKLTKDVFKYLQKCVENNREFNLTLGVKSTT 240
Cdd:cd00653 208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKP 287
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 241 LTNGLKYSLATGNWGDQKKAaSSKAGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQ 319
Cdd:cd00653 288 ITSGIKEFLATGNWGSKRFL-MQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGE 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 320 ACGLVKNLALMCYITvgtpcepiidfmnqrnmemleeyeplrspnatkvfvngvwvgvhrdpahlvsnvqdlrrghiish 399
Cdd:cd00653 367 NCGLVKNLALMARIS----------------------------------------------------------------- 381
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 400 evslvrdirdrefkiftdaGRVCRPLFVIDNDTrsmnygnlvltkehitrleedkeaaigmdrdelearqmgwdglvnqg 479
Cdd:cd00653 382 -------------------GRIERPYRIVEKEV----------------------------------------------- 395
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 480 vveyvdaeeeetvmivmtpgdletsrqiqlgkavpenaedepnkrvnamshrsaqtwTHCEIHPSMILGICASIIPFPDH 559
Cdd:cd00653 396 ---------------------------------------------------------THIEISPSQILSVAASLIPFPEH 418
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 560 NQSPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIM 639
Cdd:cd00653 419 NQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIII 498
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 640 NQSSIDRGLFRSLFYRSYTDQEKRIGmsivEQFEKPMRTDTLRLKHGTYEKLDDDGIVAPGVRVSGEDMIIGKTAPIPPD 719
Cdd:cd00653 499 NKSSVDRGFFRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGET 574
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 720 SEELGQRTKMHIKRDASTPLRSTENGIVDQVLLTT---NAEGLRFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQED 796
Cdd:cd00653 575 ESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQED 654
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 797 MPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTEVTVDSVSKILRAHGYQSRGFEVMYNAHTG 876
Cdd:cd00653 655 MPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTG 734
|
730
....*....|....*....
gi 45545341 877 QKLVAQVFLGPTYYQRLRH 895
Cdd:cd00653 735 EPLEAPIFVGPVYYQRLKH 753
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
368-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 574.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 368 VFVNGVWVGVHRDPAHLVSNVQDLRRGHIISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNdtrsmnyGNLVLTKEHI 447
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 448 TRLEEDkeaaigmdrdELEarqmgWDGLVNQGVVEYVDAEEEETVMIVMTPGDLetsrqiqlgkaVPENaedepnkrvna 527
Cdd:TIGR03670 74 EKLKEG----------ELT-----WDDLVKQGVIEYLDAEEEENAYIALDPEEL-----------TPEH----------- 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 528 mshrsaqtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMATTRSM 607
Cdd:TIGR03670 117 ---------THLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVL 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 608 EFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPmrTDTLRLKHG- 686
Cdd:TIGR03670 188 ELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGe 265
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 687 -TYEKLDDDGIVAPGVRVSGEDMIIGKTAPiPPDSEELGQ-RTKMHIKRDASTPLRSTENGIVDQVLLTTNAEGLRFVKV 764
Cdd:TIGR03670 266 eAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-PRFLEELREfGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKV 344
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 765 RMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATP 844
Cdd:TIGR03670 345 RVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTP 424
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|.
gi 45545341 845 FTEVTVDSVSKILRAHGYQSRGFEVMYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:TIGR03670 425 FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
366-895 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 543.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 366 TKVFVNGVWVGVHRDPAHLVSNVQDLRRGHIISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNdtrsmnyGNLVLTKE 445
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 446 HITRLEEDkeaaigmdrdELEarqmgWDGLVNQGVVEYVDAEEEETVMIVMTPGDLEtsrqiqlgkavPENaedepnkrv 525
Cdd:PRK07225 78 HIEKLKNG----------ELT-----FDDLVKQGVIEYLDAEEEENAYIAVYEEDLT-----------EEH--------- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 526 namshrsaqtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMATTR 605
Cdd:PRK07225 123 -----------THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQ 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 606 SMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIVEQFEKPmrTDTLRLKH 685
Cdd:PRK07225 192 TQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIP--DKDVRGYR 269
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 686 G--TYEKLDDDGIVAPGVRVSGEDMIIGKTAPipP----DSEELGQRTKMhiKRDASTPLRSTENGIVDQVLLTTNAEGL 759
Cdd:PRK07225 270 GeeAYRHLDEDGLVNPETEVKEGDVLIGKTSP--PrfleEPDDFGISPEK--RRETSVTMRSGEEGIVDTVILTETEEGS 345
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 760 RFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFE 839
Cdd:PRK07225 346 RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRR 425
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*.
gi 45545341 840 GDATPFTEVTVDSVSKILRAHGYQSRGFEVMYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:PRK07225 426 VDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHH 481
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
550-895 |
1.28e-154 |
|
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: 458.53 E-value: 1.28e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 550 CASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYDQRMDTMANILYYPQKPMATTRSMEFLKFRELPAGQNAIVAIACYS 629
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 630 GYNQEDSVIMNQSSIDRGLFRSLFYRSYTDQEKRIGMSIvEQFEKPmrtDTLRLKHgtYEKLDDDGIVAPGVRVSGEDMI 709
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPIE-EITRDI---PNVSEEA--LKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 710 IGKTAPIPPDSE---ELGQRTKmhIKRDASTPLRSTENGIVDQVLL-TTNAEGLRFVKVRMRTTKIPQIGDKFASRHGQK 785
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGEKAR--DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 786 GTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTEVT--VDSVSKILRAHGYQ 863
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYN 312
|
330 340 350
....*....|....*....|....*....|..
gi 45545341 864 SRGFEVMYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
63-895 |
3.77e-144 |
|
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: 452.64 E-value: 3.77e-144
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 63 YVKTD----VPIGIVFRGLGIVSDEDILNHIcydrNDTQMLEKLKPCIEEAfVIQDREVALDWIGSR---G------NSQ 129
Cdd:COG0085 168 YVRIDrkrkIPVTVLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRKlrpGepptieRAE 242
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 130 SL-----SRPKRVKYA---RDIMQKELLPHISQTDGseTKKAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLDLAGPLL 201
Cdd:COG0085 243 QLldnlfFDPKRYDLAhvgRYKINKKLGLDVPPEDR--VLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELL 320
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 202 AGLFRMLFNKLTKDVfKYlQKCVENNREFNLTLGVKSTTLTNGLKYSLATGnwgdqkkaasskaGVSQVLNRYTFASTLS 281
Cdd:COG0085 321 QNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELT 385
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 282 HLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITvgtpcepiidfmnqrnmem 353
Cdd:COG0085 386 HKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------------------- 442
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 354 leEYeplrspnatkvfvngvwvgvhrdpahlvsnvqdlrrghiishevslvrdirdrefkiftdaGRVCRPLFVIDNdtr 433
Cdd:COG0085 443 --EY-------------------------------------------------------------GFIETPYRKVEN--- 456
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 434 smnyGnlVLTKEhitrleedkeaaigmdrdelearqmgwdglvnqgvVEYVDAEEEETVMIVMTPGDLETSRQIqLGKAV 513
Cdd:COG0085 457 ----G--KVTDE-----------------------------------IEYLTADEEENYYIAQANAPLDEDGNF-LEERV 494
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 514 PENAEDEPnKRVNAMSHrsaqtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNydqrmdtmANI 593
Cdd:COG0085 495 LVRYRGEE-VLVPPEEV------DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APL 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 594 LYYP--------------QKPMAttRSMEFLK------------FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRG 647
Cdd:COG0085 560 LHYPlqkfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 648 LFRSLFYRSYTDQEKR--IGMSIVeQFEKPmrtdtlrlKHG--TYEKLDDDGIVAPGVRVSGEDMIIGKTAP---IPPDS 720
Cdd:COG0085 638 VLTSIHIEEYEIEARDtkLGPEEI-TRDIP--------NVSeeALRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTP 708
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 721 EELGQR----TKMHIKRDASTPLRSTENGIVDQVLLTTNAEG-------LRFVKVRMRTTKIPQIGDKFASRHGQKGTIG 789
Cdd:COG0085 709 EERLLRaifgEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVIS 788
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 790 ITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGDATPFTEVTVDSVSKILRAHGYQSRGFEV 869
Cdd:COG0085 789 RILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEV 868
|
890 900
....*....|....*....|....*.
gi 45545341 870 MYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:COG0085 869 LYDGRTGEPFDNPVTVGYMYYLKLHH 894
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
1-243 |
2.09e-90 |
|
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: 291.98 E-value: 2.09e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 1 RSAANIVQVFKKAPPSATPYIAEIRSAVEKGSRLISSMQIKLFakgENHKGGfgqTVKATLPYVKTDVPIGIVFRGLGIV 80
Cdd:pfam04563 155 HRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVL---EYLSNG---TIYFKFPYIKKEIPIVIILRALGFT 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 81 SDEDILNHICYDRNDTQMLEKLKPCIEEAFVI--QDREVALDWIGSRGNSQ---SLSRPKRVKYARDIMQKELLPHISQT 155
Cdd:pfam04563 229 SDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQKEVLPHLGTY 308
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 156 DGSETKKAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLDLAGPLLAGLFRMLFNKLTKDVFKYLQKCVENNREFNLTLG 235
Cdd:pfam04563 309 ELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLL 388
|
....*...
gi 45545341 236 VKSTTLTN 243
Cdd:pfam04563 389 VNAKPITS 396
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
47-346 |
1.26e-74 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 252.95 E-value: 1.26e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 47 ENHKGGFgqtVKATLPYVKTDVPIGIVFRGLGIVSDEDILNHICYDRN-DTQMLEKLkpciEEAfVIQDREVALDWIGSR 125
Cdd:PRK09606 199 ERNRDGL---LEVSFPSVPGSIPFVILMRALGLETDEEIVEAVSDDPEiVKFMLENL----EEA-EVDTQEEALEYIGKR 270
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 126 GNSQSlSRPKRVKYARDIMQKELLPHISQTDGSETKKAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLDLAGPLLAGLF 205
Cdd:PRK09606 271 VAPGQ-TKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLF 349
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 206 RMLFNKLTKDVfKY-LQKCVENNREFNLTLGVKSTTLTNGLKYSLATGNWgdqkkaASSKAGVSQVLNRYTFASTLSHLR 284
Cdd:PRK09606 350 RVAFNRLARDV-KYqLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLR 422
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545341 285 RTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPCEPIIDFM 346
Cdd:PRK09606 423 RVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL 484
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
3-195 |
3.80e-47 |
|
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: 166.37 E-value: 3.80e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 3 AANIVQVFKKAPPSATPYIAEIRSAVEKGSRLissmqiklfaKGENhkggFGQTVKATLPYVKTDVPIGIVFRGLGIVSD 82
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGSWL----------KLEI----DGKTLIWSRPSKKRKIPIVIFLKALGLVSD 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 83 EDILNHICYDRNDTQMLEKLKPCIEEAFVIQDREVALDWIGSrGNSQSLSRPKRVKYARDIMQK-----ELLPHISQTDG 157
Cdd:pfam04561 67 REILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 45545341 158 SETK--KAFFLGYMVHRMLQCALGRREVDDRDHFGKKRLD 195
Cdd:pfam04561 146 FENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
63-895 |
8.00e-39 |
|
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: 156.36 E-value: 8.00e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 63 YVKTD----VPIGIVFRGLGIVSDEDILNHICYDRNDTQMLEKLKPCIEEAFVIQ-----------DREVALDWIGSRGN 127
Cdd:TIGR02013 187 YVRIDrkrkLPATVLLRALGYTIDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEiyrklrpgeppTVEAARSLLENLFF 266
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 128 SQ---SLSRPKRVKyardiMQKELLPHISQTDGSETKKAFF--LGYMVhRMLQcalGRREVDDRDHFGKKRLDLAGPLLA 202
Cdd:TIGR02013 267 DPkryDLGRVGRYK-----LNKKLGLDVPESIGVLTKEDIIatIKYLI-KLRN---GKGEIDDIDHLGNRRIRSVGELLQ 337
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 203 GLFRMLFNKLTKDVFKYLqkcveNNREFN-LTLG--VKSTTLTNGLKYSLATGNwgdqkkaasskagVSQVLNRYTFAST 279
Cdd:TIGR02013 338 NQFRVGLARMERIVRERM-----STQDTDtLTPQdlINAKPISAAIKEFFGSSQ-------------LSQFMDQTNPLAE 399
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 280 LSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT----VGTPCEPIIDFM----- 346
Cdd:TIGR02013 400 LTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNeygfIETPYRKVKDGKvvvtd 479
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 347 NQRNMEMLEEYEPLRSPNATKVFVNGVWVGVHrdpahlvsnVQDLRRGHIISHEVSLVrDIRDREFKIFTDAGRVCRPLF 426
Cdd:TIGR02013 480 EIDYLTADEEDNYVIAQANAPLDENGRFVEDL---------VVARYRGEITLVSPDQV-DYMDVSPKQVVSVAASLIPFL 549
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 427 VIDNDTRSMNYGNLvlTKEHITRLEEDKeAAIGMDRDELEARQMGWDGLVNQ-GVVEYVDAEEeetvmIVMTPgdletsr 505
Cdd:TIGR02013 550 EHDDANRALMGSNM--QRQAVPLLRSEA-PLVGTGMEAKVARDSGAVIVAKRgGVVEYVDAKR-----IVIRY------- 614
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 506 qiqlgkavpENAEDEPNKRVNAMS----HRSAQtwthceihpsmilGICasiipfpdHNQSPRntyqsamgkqamgVFLT 581
Cdd:TIGR02013 615 ---------DEDEEEPDGGIDIYRllkyQRSNQ-------------DTC--------INQRPI-------------VSVG 651
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 582 NYDQRMDTMANilyypqKPmATTRSmeflkfrELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFyrsytdqe 661
Cdd:TIGR02013 652 DRVEAGDVLAD------GP-STDLG-------ELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIH-------- 709
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 662 krigmsiVEQFEKPMRtDTlrlKHGTYE--------------KLDDDGIVAPGVRVSGEDMIIGKTAP---IPPDSEE-- 722
Cdd:TIGR02013 710 -------IEEYEVEAR-DT---KLGPEEitrdipnvseealrNLDENGIVRIGAEVKAGDILVGKVTPkgeTELTPEEkl 778
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 723 ----LGQRTKmHIkRDASTPLRSTENGIVDQVLLTTNAEG-------LRFVKVRMRTTKIPQIGDKFASRHGQKGTIGIT 791
Cdd:TIGR02013 779 lraiFGEKAR-DV-RDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKI 856
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 792 YRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKVSALRGFEGD--ATP-FTEVTVDSVSKILRAHGYQSRGFE 868
Cdd:TIGR02013 857 LPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKV 936
|
890 900
....*....|....*....|....*..
gi 45545341 869 VMYNAHTGQKLVAQVFLGPTYYQRLRH 895
Cdd:TIGR02013 937 RLYDGRTGEQFDRPVTVGYMYMLKLHH 963
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
269-332 |
8.60e-31 |
|
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: 115.32 E-value: 8.60e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45545341 269 QVLNRYTFASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 332
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
368-429 |
1.26e-29 |
|
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: 111.69 E-value: 1.26e-29
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545341 368 VFVNGVWVGVHRDPAHLVSNVQDLRRGHIISHEVSLVRDIRDREFKIFTDAGRVCRPLFVID 429
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
63-895 |
3.36e-27 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 119.43 E-value: 3.36e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 63 YVKTD----VPIGIVFRGLGIvSDEDILNHICYDRN-------------------DTQMLEKLKPcIEEAFViqdrEVAL 119
Cdd:CHL00207 164 WIRIDknrkKPLIIFLKALGL-TDQDIYSRLTKSEFlkklkpillnsnsytneeiLLEIYKNLSP-IEPATV----NDAN 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 120 DWIGSR---GNSQSLSRPKRVKYardimQKELLPHISQTDGSETKKAFFLGymVHRMLQCALGRREVDDRDHFGKKRLDL 196
Cdd:CHL00207 238 QNLFSRffdPKNYDLGKVGRYKI-----NNKLNLNIPERVRNLTYEDILSI--IDKLINLKINKGNFDDIDHLKNRRVRS 310
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 197 AGPLLAGLFRMLFNKLTKDVFKYLQKCVENNREfnltlgvKSTTLTNGLKYSLATGNWGdqkkaaSSKagVSQVLNRYTF 276
Cdd:CHL00207 311 VGELLQNQFRIGLKRLERILRNRMTICDIDSLS-------KFNLINPKPLIALIREFFG------SSQ--LSQYMDQTNP 375
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 277 ASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT----VGTPCEPIIDfmnq 348
Cdd:CHL00207 376 LSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINkfgfIETPFYKVIN---- 451
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 349 rnmemleeyeplrspNATKVFVNgvwvgvhrdPAHLVSNVQDLRRghIISHEVSLvrdirdrefkiftdagrvcrplfvi 428
Cdd:CHL00207 452 ---------------GKVKKFGN---------PIYLTADSEDLYR--IAPNDINL------------------------- 480
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 429 dndtRSMNYgnlvLTKEHItrleedkeaaigmdrdELEARQmgwdglvnqgvvEYVDAEEEETVMIVMTPgdletsrqIQ 508
Cdd:CHL00207 481 ----NKNNY----FKKNII----------------PVRYKQ------------EFKTVNPSKVDFIAISP--------IQ 516
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 509 lgkavpenaedepnkrvnamshrsaqtwthceihpsmILGICASIIPFPDHNQSPRNTYQSAMGKQAMGVFL-------T 581
Cdd:CHL00207 517 -------------------------------------VFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYpekpivgT 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 582 NYDQRMDTMAN----------------------------ILYYPQKpmaTTRSMEF------------------------ 609
Cdd:CHL00207 560 GYEKQIALDSGmtiisltegivvsvsaykiiiqddnnryIHYYLQK---YQRSNQNtcinyrpivwvgekinigqiladg 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 610 --LKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYtDQEKRIGMSIVEQFEKPMrtdtlrLKHGT 687
Cdd:CHL00207 637 sdIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY-EIELRQTKLGSEEITRNI------PNVSE 709
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 688 YE--KLDDDGIVAPGVRVSGEDMIIGKTAPiPPDSEELGQ---------RTKMHIKrdaSTPLRSTENG---IVDQVLLT 753
Cdd:CHL00207 710 YSlkNLDENGIISIGSKVLAGDILVGKITP-KGESDQLPEgkllraifgEKAKDVK---DTSLRMPNGGygrVIKVEIFS 785
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 754 TNaEGLR-----FVKVRMRTTKIP--QIGDKFASRHGQKGTIG-ITYRQeDMPFTSEGVVPDLIINPHAIPSRMTIAHLI 825
Cdd:CHL00207 786 RS-KGDElkfgyYLKIRVFIAQIRkiQVGDKLAGRHGNKGIISrILPRQ-DMPYLPDGTPPDIILNPLGVPSRMNVGQLF 863
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 826 ECQLskvsalrGFEGD-------ATPFTEVTVDSVSKILRAHGYQS----RGFEVMYNAH-----------TGQKLVAQV 883
Cdd:CHL00207 864 ECLL-------GLAGDnlnkrfkILPFDEMYGSEYSRILINNKLNQasikNNEYWLFNSYhpgkmvlrdgrTGYKFKNPV 936
|
970
....*....|..
gi 45545341 884 FLGPTYYQRLRH 895
Cdd:CHL00207 937 TVGIAYMLKLIH 948
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
614-895 |
3.08e-24 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 109.81 E-value: 3.08e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 614 ELPAGQNAIVAIACYSGYNQEDSVIMNQSSI--DRglfrslfyrsYTdqekrigmSI-VEQFEKPMRtDTlrlKHGTYE- 689
Cdd:PRK00405 712 ELALGQNVLVAFMPWNGYNFEDAILISERLVkeDV----------FT--------SIhIEEYEIEAR-DT---KLGPEEi 769
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 690 -------------KLDDDGIVAPGVRVSGEDMIIGKTAP---IPPDSEE------LGQRTKMHikRDAStpLR--STENG 745
Cdd:PRK00405 770 trdipnvseealrNLDESGIVRIGAEVKPGDILVGKVTPkgeTELTPEEkllraiFGEKARDV--KDTS--LRvpHGEEG 845
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 746 IV-DQVLLTTNAEG-------LRFVKV-----RmrttKIpQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINP 812
Cdd:PRK00405 846 TViDVKVFTRIEQGdelppgvNKLVKVyiaqkR----KI-QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNP 920
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 813 HAIPSRMTIAHLIECQLSKVSALRG--FegdATP-FTEVTVDSVSKILRAHGYQSRGFEVMYNAHTGQKLVAQVFLGPTY 889
Cdd:PRK00405 921 LGVPSRMNIGQILETHLGWAAKGLGikF---ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMY 997
|
....*.
gi 45545341 890 YQRLRH 895
Cdd:PRK00405 998 MLKLHH 1003
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
472-543 |
1.93e-22 |
|
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: 91.06 E-value: 1.93e-22
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545341 472 WDGLVNQGVVEYVDAEEEETVMIVMTPGDLETSRQIQLgkavpenaedepnkrvnamSHRSAQTWTHCEIHP 543
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREER-------------------EGPYAHTYTHCEIHP 53
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
170-832 |
8.06e-17 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 86.13 E-value: 8.06e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 170 VHRMLQCALGRREVDDRDHFGKKRLDLAGPLLA-----GLFRMlfNKLTKDVFKYLQKCVENNREFNLtlgVKSTTLTNG 244
Cdd:PRK09603 441 VKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLAnelhsGLVKM--QKTIKDKLTTMSGAFDSLMPHDL---VNSKMITST 515
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 245 LKYSLATGNwgdqkkaasskagVSQVLNRYTFASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQ 319
Cdd:PRK09603 516 IMEFFMGGQ-------------LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQ 581
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 320 ACGLVKNLALMCYIT----VGTPCEPIIDFMNQRNMEML---EEYEPLRSPNATKVFVNGvwvgvhrdpaHLVSNVQDLR 392
Cdd:PRK09603 582 NIGLINTLSTFTRVNdlgfIEAPYKKVVDGKVVGETIYLtaiQEDSHIIAPASTPIDEEG----------NILGDLIETR 651
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 393 R-GHIISHEVSLVrDIRDREFKIFTDAGRVCRPLFVIDNDTRSMNYGNLvlTKEHITRLEEDKeAAIGMDRDELEARQmG 471
Cdd:PRK09603 652 VeGEIVLNEKSKV-TLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNM--QRQAVPLLRSDA-PIVGTGIEKIIARD-S 726
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 472 WDGL--VNQGVVEYVDA-------EEEETVMI---------------------VMTPGDLETSRQI------------QL 509
Cdd:PRK09603 727 WGAIkaNRAGVVEKIDSkniyilgEGKEEAYIdayslqknlrtnqntsfnqvpIVKVGDKVEAGQIiadgpsmdrgelAL 806
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 510 GKAV-----PENAEDEPNKRVNAMSHRSAQTWTHCEIHPSMI------LGICASIIPFPDHNQSpRNTYQSAMGKQAMGV 578
Cdd:PRK09603 807 GKNVrvafmPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVdarelkHGVEEFTADIPDVKEE-ALAHLDESGIVKVGT 885
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 579 FLTNydqrmdtmANILYYPQKPMATTRSMEFLKFRELPAGQNA--IVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRS 656
Cdd:PRK09603 886 YVSA--------GMILVGKTSPKGEIKSTPEERLLRAIFGDKAghVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLS 957
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 657 YTDQEKRIgmSIVEQFEKPM---RTDTLRLKHG-TYEKLDDDGIVAPGVRVSGEDMIIGKTAPIPPDSeeLGQRTKmHIK 732
Cdd:PRK09603 958 AYEEEKAK--LDMEHFDRLTmlnREELLRVSSLlSQAILEEPFSHNGKDYKEGDQIPKEEIASINRFT--LASLVK-KYS 1032
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 733 RDASTPLRSTENGIVDQ--VLLTTNAEGL--------------RFVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQED 796
Cdd:PRK09603 1033 KEVQNHYEITKNNFLEQkkVLGEEHEEKLsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVAD 1112
|
730 740 750
....*....|....*....|....*....|....*.
gi 45545341 797 MPFTSEGVVPDLIINPHAIPSRMTIAHLIECQLSKV 832
Cdd:PRK09603 1113 MPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLV 1148
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
614-829 |
1.63e-16 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 84.57 E-value: 1.63e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 614 ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLFYRSYtDQEKRIGMSIVEQFEKPM-RTDTLRLKHgtyekLD 692
Cdd:CHL00001 648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERITKEIpHLEAHLLRN-----LD 721
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 693 DDGIVAPGVRVSGEDMIIGKTAP-IPPDSEE----------LGQRTkmhikRDA-STPLRSTENG---------IVDQVL 751
Cdd:CHL00001 722 KNGIVMLGSWVETGDILVGKLTPqEAEESSYapegrllraiFGIQV-----STSkETCLKLPIGGrgrvidvrwIQKKGG 796
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45545341 752 LTTNAEGLRFVKVRMRttKIpQIGDKFASRHGQKGTIG-ITYRQeDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQL 829
Cdd:CHL00001 797 SSYNPETIHVYILQKR--EI-QVGDKVAGRHGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL 871
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
179-829 |
1.22e-14 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 78.90 E-value: 1.22e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 179 GRREVDDRDHFGKKRLDLAGPLLAGLFRMLFNKLTKDVFKYLQkcVENNREFNLTLGVKSTTLTNGLKYSLatgnwgdqk 258
Cdd:PRK14844 459 GQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMS--TSSLDKVSPSDFINPKVLTNVLRDFF--------- 527
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 259 kaasSKAGVSQVLNRYTFASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT 334
Cdd:PRK14844 528 ----NSSQLSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 335 ----VGTPCEPIIDFMNQRNMEMLEEY-EPLRSPNATKV-------FVN--------GVWVGVHRDPAHLVsnvqDLRRG 394
Cdd:PRK14844 604 kygfIESPYRKVVNRVVTDQIEYLSAIdEGLYYIADTSAkldenncFVDdmlycryaGSFVMVSSDQVSYI----DVSPK 679
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 395 HIISHEVSLVrdirdrefkiftdagrvcrPLFVIDNDTRSMNYGNLvltKEHITRLEEDKEAAIGMDRDELEARQMGWDG 474
Cdd:PRK14844 680 QVISVAASLI-------------------PFLENDDANRALMGSNM---QRQAVPLLKPTAPLVATGMESFVASGSGAVV 737
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 475 LVNQGVVeyVDAEEEETVMIvmtpgdletsrqiqlgkavpeNAEDEpnKRVNAMShrsaqtwthceihpsmilgicASII 554
Cdd:PRK14844 738 LAKRDGI--VDSSDSNSIVI---------------------RAFDK--ERVNYLD---------------------VDIY 771
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 555 PFPDHNQSPRNTYQSamgkQAMGVFLTNYDQRMDTMANilyypqKPMATTRsmeflkfrELPAGQNAIVAIACYSGYNQE 634
Cdd:PRK14844 772 HLRKFQRSNHNTCIN----QKPLVCVGDYVKEGDVIAD------GPAINSG--------ELALGQNLLVAFMSWQGYNFE 833
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 635 DSVIMNQSSIDRGLFRSLFyrsytdqekrigmsiVEQFE-----KPMRTDTL-RLKHGTYEK----LDDDGIVAPGVRVS 704
Cdd:PRK14844 834 DSIIISSEVVKKDLFTSIH---------------IEEFEcvvhdTPLGSEKItRAIPGVNEEnlyhLDDSGIVKIGTRVG 898
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 705 GEDMIIGKTAP-----IPPDSEEL----GQRT----------------------------------KMHIKRDASTPLRS 741
Cdd:PRK14844 899 PGYILVGKVTPkpslsLPPETKLLmtifGEKSfdcadsslytspdvegtvidvqvftrrgveenerALLIKQKEINDFEK 978
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 742 TENGIVD-----------QVLLTTNAE----------------GLR---------------------------------- 760
Cdd:PRK14844 979 ERDYIINvtseyfydelkKLLINSGSQdrekfdsiereqwwgiGLKnqsiseqvkslkkdfdekvshaiaqfkrkveklh 1058
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545341 761 -----------FVKVRMRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGVVPDLIINPHAIPSRMTIAHLIECQL 829
Cdd:PRK14844 1059 egydlpqgvsmSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHV 1138
|
|
| |
