|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-994 |
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: 1011.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 1 MVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----AMIRPKWKTRGPGYTQYGVSMHCV 76
Cdd:cd00653 102 MLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsKGKRIYTKTSIPSYSPYRGSWLEV 181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 77 REEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikgkeddsflrnsvsqmlrivmeegc 155
Cdd:cd00653 182 KSDKKkDRIYVRIDLKR--------------------------------------------------------------- 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 156 stQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 235
Cdd:cd00653 199 --QEEALKYIGK-----------------------------------RFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 236 LTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIFTMGIDLTKPFEYLFATGNLRSKTGLglLQDSGLC 315
Cdd:cd00653 242 RLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIKEFLATGNWGSKRFL--MQRSGLS 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 316 VVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVtqfvytasipall 395
Cdd:cd00653 315 QVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------- 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 396 cnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrhfkvlrekrippwmevvlipmtgkpslypglflft 475
Cdd:cd00653 --------------------------------------------------------------------------------
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 476 tpcrlvrpvqnlalgkeeliGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQ 555
Cdd:cd00653 382 --------------------GRIERPYRIVE--------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQ 433
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 556 TMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVY 635
Cdd:cd00653 434 AVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHY 513
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 636 KSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFV--------------MY 701
Cdd:cd00653 514 KKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTpifgekardvrdtsLK 593
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 702 YKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGF 781
Cdd:cd00653 594 YPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGF 673
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 782 PSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTERLYSGISGLELEADIFIGVVYYQ 861
Cdd:cd00653 674 PSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQ 749
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 862 RLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPl 941
Cdd:cd00653 750 RLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSA- 828
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|...
gi 544346144 942 lekpppswsamrnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 994
Cdd:cd00653 829 ---------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
424-482 |
1.37e-23 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
:
Pssm-ID: 462028 Cd Length: 58 Bit Score: 94.47 E-value: 1.37e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 544346144 424 VGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 482
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_2 super family |
cl37712 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
47-236 |
9.20e-11 |
|
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).
The actual alignment was detected with superfamily member pfam04561:
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 61.98 E-value: 9.20e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 47 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 124
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 125 IFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIH 196
Cdd:pfam04561 69 ILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 544346144 197 LKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 236
Cdd:pfam04561 146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-994 |
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: 1011.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 1 MVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----AMIRPKWKTRGPGYTQYGVSMHCV 76
Cdd:cd00653 102 MLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsKGKRIYTKTSIPSYSPYRGSWLEV 181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 77 REEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikgkeddsflrnsvsqmlrivmeegc 155
Cdd:cd00653 182 KSDKKkDRIYVRIDLKR--------------------------------------------------------------- 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 156 stQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 235
Cdd:cd00653 199 --QEEALKYIGK-----------------------------------RFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 236 LTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIFTMGIDLTKPFEYLFATGNLRSKTGLglLQDSGLC 315
Cdd:cd00653 242 RLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIKEFLATGNWGSKRFL--MQRSGLS 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 316 VVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVtqfvytasipall 395
Cdd:cd00653 315 QVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------- 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 396 cnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrhfkvlrekrippwmevvlipmtgkpslypglflft 475
Cdd:cd00653 --------------------------------------------------------------------------------
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 476 tpcrlvrpvqnlalgkeeliGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQ 555
Cdd:cd00653 382 --------------------GRIERPYRIVE--------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQ 433
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 556 TMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVY 635
Cdd:cd00653 434 AVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHY 513
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 636 KSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFV--------------MY 701
Cdd:cd00653 514 KKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTpifgekardvrdtsLK 593
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 702 YKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGF 781
Cdd:cd00653 594 YPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGF 673
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 782 PSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTERLYSGISGLELEADIFIGVVYYQ 861
Cdd:cd00653 674 PSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQ 749
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 862 RLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPl 941
Cdd:cd00653 750 RLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSA- 828
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|...
gi 544346144 942 lekpppswsamrnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 994
Cdd:cd00653 829 ---------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
1-995 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 572.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 1 MVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML--IMPRRnfpiamIRPKWKTRGPGYTqygvsmhcvre 78
Cdd:PRK08565 113 MVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedLAPNR------VLVDKGEAGSSIT----------- 175
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 79 eHSA----------VNMNLHYLENGTVMLNF--IYRKelffLPLGFALKAL-----------VSfSDYQIFQELIKGKED 135
Cdd:PRK08565 176 -HTAkvissragyrAQVTVERRKDGTIYVSFpaVPGK----IPFVILMRALgletdrdivyaVS-LDPEIQQELLPSLEQ 249
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 136 dsflrnsVSQMLRivmeegcsTQKQVLNYLGEcfRVKLNVPDWYPNEQAAEFLFNQCIcIHLKSNTE----KFYMLCLMT 211
Cdd:PRK08565 250 -------ASSIAA--------TVEDALDYIGK--RVAIGQPREYRIERAEQILDKYLL-PHLGTSPEdrikKAYFLGQMA 311
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 212 RKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSvSMNTDNLMRiftMGIdLTKPF 291
Cdd:PRK08565 312 SKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGR-KLDLRAIVR---PDI-ITERI 386
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 292 EYLFATGN-LRSKTGLG-LLqdsglcvvaDKLNFIRYLSHFRCV----HRG-ADFAkmrtttVRRLLPESWGFLCPVHTP 364
Cdd:PRK08565 387 RHALATGNwVGGRTGVSqLL---------DRTNYLSTLSHLRRVvsplSRGqPHFE------ARDLHGTQWGRICPFETP 451
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 365 DGEPCGLMNHLTAVCEVvTQFVYTASIPALLCNLGVTPIDGAPHRSYSECYPVLLDGVMVGWVDKDLApgIADSLRHFKv 444
Cdd:PRK08565 452 EGPNCGLVKNLALMAQI-SVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEE--LAEKIRELR- 527
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 445 lREKRIPPWMEVVLIPMTGKPSLYpglfLFTTPCRLVRPVQNLALGKEELIGTM-EQIFMNVAIFEDEVFAGV------- 516
Cdd:PRK08565 528 -RSGKISDEVNVAYIETGEINEVY----VNCDSGRVRRPLIVVENGKPKLTREHvEKLKKGELTFDDLVKMGVieyldae 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 517 -----------------TTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQ 579
Cdd:PRK08565 603 eeenayvaldpedltpeHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQ 682
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 580 SPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAhgsvyKSEFIDL--SEKIK----QGD--- 650
Cdd:PRK08565 683 RPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA-----RSTFFRTyeTEERKypggQEDkie 757
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 651 --SSLVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD------------PYYSYLNLNTGE----SFVMyyKSKENCVVDN 712
Cdd:PRK08565 758 ipEPNVRGYRG--EEYYRKLDEDGIVSPEVEVKGGDvligktspprflEELEELSLGLQErrdtSVTV--RHGEKGIVDT 833
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 713 IKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE 792
Cdd:PRK08565 834 VLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLE 910
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 793 SMAGKSAALHGLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQ 872
Cdd:PRK08565 911 SIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIH 986
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 873 VRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSllspllekppPSWSAM 952
Cdd:PRK08565 987 ARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH----------IAWYDR 1056
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|...
gi 544346144 953 RNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 995
Cdd:PRK08565 1057 RKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
531-890 |
1.33e-180 |
|
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: 528.25 E-value: 1.33e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 531 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 610
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 611 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 689
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 690 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 754
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 755 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 834
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 544346144 835 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 890
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
417-995 |
3.00e-146 |
|
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: 448.32 E-value: 3.00e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 417 VLLDGVMVGWVDKdlAPGIADSLRhfKVLREKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGK 491
Cdd:TIGR03670 1 VYLNGRLIGYHDD--PEELVEEVR--KLRRSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTR 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 492 EELigtmEQIFMNVAIFEDEVFAGVT------------------------THQELFPHSLLSVIANFIPFSDHNQSPRNM 547
Cdd:TIGR03670 71 EHV----EKLKEGELTWDDLVKQGVIeyldaeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 548 YQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWER 627
Cdd:TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 628 GFAHGS---VYKSEFID----LSEKIKQGDSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYL 690
Cdd:TIGR03670 227 GLARSTffrTYEAEERRypggQEDRFEIPEPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELR 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 691 NLNTGE------SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMP 764
Cdd:TIGR03670 304 EFGLVTerrrdtSVTV--RHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMP 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 765 FTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGI 844
Cdd:TIGR03670 379 FTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGI 454
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 845 SGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 924
Cdd:TIGR03670 455 TGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 534
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544346144 925 RSVAHVCVKCGSLlspllekpppSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 995
Cdd:TIGR03670 535 KYVVYVCENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
518-993 |
8.62e-104 |
|
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: 347.48 E-value: 8.62e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 518 THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG-----FPLLTY---------QDRSDNklyrlqtpQSPLV 583
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN--------QRPIV 582
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 584 R--------------PSMydyyDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFIDLSE----K 645
Cdd:COG0085 583 RvgdrvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIEEYEiearD 653
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 646 IKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFIGAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSK---- 705
Cdd:COG0085 654 TKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGAEVKGGDilvgkvtpkgeteltPEERLLRAIFGE------KARevrd 726
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 706 --------ENCVVDNIKVCSNDTGS----GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPD 773
Cdd:COG0085 727 tslrvphgEKGKVIDVKVFSREEGDelppGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVD 806
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 774 ILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEAD 852
Cdd:COG0085 807 IVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGRTGEPFDNP 881
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 853 IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCV 932
Cdd:COG0085 882 VTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV 961
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544346144 933 kcgsllsplLEkpppswsamRNRKynctlcsrSDTIDTVSVPYVFRYFVAELAAMNIKVKL 993
Cdd:COG0085 962 ---------YE---------AIVK--------GENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
424-482 |
1.37e-23 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
Pssm-ID: 462028 Cd Length: 58 Bit Score: 94.47 E-value: 1.37e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 544346144 424 VGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 482
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
47-236 |
9.20e-11 |
|
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: 61.98 E-value: 9.20e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 47 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 124
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 125 IFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIH 196
Cdd:pfam04561 69 ILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 544346144 197 LKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 236
Cdd:pfam04561 146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-994 |
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: 1011.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 1 MVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----AMIRPKWKTRGPGYTQYGVSMHCV 76
Cdd:cd00653 102 MLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsKGKRIYTKTSIPSYSPYRGSWLEV 181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 77 REEHS-AVNMNLHYLENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikgkeddsflrnsvsqmlrivmeegc 155
Cdd:cd00653 182 KSDKKkDRIYVRIDLKR--------------------------------------------------------------- 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 156 stQKQVLNYLGEcfrvklnvpdwypneqaaeflfnqcicihlksnteKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEV 235
Cdd:cd00653 199 --QEEALKYIGK-----------------------------------RFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 236 LTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMntdnlMRIFTMGIDLTKPFEYLFATGNLRSKTGLglLQDSGLC 315
Cdd:cd00653 242 RLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIKEFLATGNWGSKRFL--MQRSGLS 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 316 VVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVtqfvytasipall 395
Cdd:cd00653 315 QVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------- 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 396 cnlgvtpidgaphrsysecypvlldgvmvgwvdkdlapgiadslrhfkvlrekrippwmevvlipmtgkpslypglflft 475
Cdd:cd00653 --------------------------------------------------------------------------------
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 476 tpcrlvrpvqnlalgkeeliGTMEQIFMNVAifedevfaGVTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQ 555
Cdd:cd00653 382 --------------------GRIERPYRIVE--------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQ 433
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 556 TMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVY 635
Cdd:cd00653 434 AVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHY 513
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 636 KSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFV--------------MY 701
Cdd:cd00653 514 KKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTpifgekardvrdtsLK 593
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 702 YKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGF 781
Cdd:cd00653 594 YPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGF 673
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 782 PSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTERLYSGISGLELEADIFIGVVYYQ 861
Cdd:cd00653 674 PSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQ 749
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 862 RLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPl 941
Cdd:cd00653 750 RLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSA- 828
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|...
gi 544346144 942 lekpppswsamrnrkYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLD 994
Cdd:cd00653 829 ---------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
1-995 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 572.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 1 MVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML--IMPRRnfpiamIRPKWKTRGPGYTqygvsmhcvre 78
Cdd:PRK08565 113 MVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedLAPNR------VLVDKGEAGSSIT----------- 175
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 79 eHSA----------VNMNLHYLENGTVMLNF--IYRKelffLPLGFALKAL-----------VSfSDYQIFQELIKGKED 135
Cdd:PRK08565 176 -HTAkvissragyrAQVTVERRKDGTIYVSFpaVPGK----IPFVILMRALgletdrdivyaVS-LDPEIQQELLPSLEQ 249
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 136 dsflrnsVSQMLRivmeegcsTQKQVLNYLGEcfRVKLNVPDWYPNEQAAEFLFNQCIcIHLKSNTE----KFYMLCLMT 211
Cdd:PRK08565 250 -------ASSIAA--------TVEDALDYIGK--RVAIGQPREYRIERAEQILDKYLL-PHLGTSPEdrikKAYFLGQMA 311
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 212 RKLFALAKGECMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSvSMNTDNLMRiftMGIdLTKPF 291
Cdd:PRK08565 312 SKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGR-KLDLRAIVR---PDI-ITERI 386
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 292 EYLFATGN-LRSKTGLG-LLqdsglcvvaDKLNFIRYLSHFRCV----HRG-ADFAkmrtttVRRLLPESWGFLCPVHTP 364
Cdd:PRK08565 387 RHALATGNwVGGRTGVSqLL---------DRTNYLSTLSHLRRVvsplSRGqPHFE------ARDLHGTQWGRICPFETP 451
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 365 DGEPCGLMNHLTAVCEVvTQFVYTASIPALLCNLGVTPIDGAPHRSYSECYPVLLDGVMVGWVDKDLApgIADSLRHFKv 444
Cdd:PRK08565 452 EGPNCGLVKNLALMAQI-SVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEE--LAEKIRELR- 527
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 445 lREKRIPPWMEVVLIPMTGKPSLYpglfLFTTPCRLVRPVQNLALGKEELIGTM-EQIFMNVAIFEDEVFAGV------- 516
Cdd:PRK08565 528 -RSGKISDEVNVAYIETGEINEVY----VNCDSGRVRRPLIVVENGKPKLTREHvEKLKKGELTFDDLVKMGVieyldae 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 517 -----------------TTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQ 579
Cdd:PRK08565 603 eeenayvaldpedltpeHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQ 682
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 580 SPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAhgsvyKSEFIDL--SEKIK----QGD--- 650
Cdd:PRK08565 683 RPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA-----RSTFFRTyeTEERKypggQEDkie 757
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 651 --SSLVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD------------PYYSYLNLNTGE----SFVMyyKSKENCVVDN 712
Cdd:PRK08565 758 ipEPNVRGYRG--EEYYRKLDEDGIVSPEVEVKGGDvligktspprflEELEELSLGLQErrdtSVTV--RHGEKGIVDT 833
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 713 IKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE 792
Cdd:PRK08565 834 VLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLE 910
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 793 SMAGKSAALHGLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQ 872
Cdd:PRK08565 911 SIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIH 986
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 873 VRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSllspllekppPSWSAM 952
Cdd:PRK08565 987 ARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGH----------IAWYDR 1056
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|...
gi 544346144 953 RNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 995
Cdd:PRK08565 1057 RKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
531-890 |
1.33e-180 |
|
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: 528.25 E-value: 1.33e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 531 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYT 610
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 611 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKIKQGDSSLVFGIKPGDPR-VLQKLDDDGLPFIGAKLQYGDPYYSY 689
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 690 L---------------NLNTGESFVMYYKSKENCVVDNIKVCsnDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGIL 754
Cdd:pfam00562 158 VgpteltkllraifgeKARDVKDTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 755 SRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 834
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 544346144 835 YGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGR 890
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
417-995 |
3.00e-146 |
|
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: 448.32 E-value: 3.00e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 417 VLLDGVMVGWVDKdlAPGIADSLRhfKVLREKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN--LALGK 491
Cdd:TIGR03670 1 VYLNGRLIGYHDD--PEELVEEVR--KLRRSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPlivVENgkPKLTR 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 492 EELigtmEQIFMNVAIFEDEVFAGVT------------------------THQELFPHSLLSVIANFIPFSDHNQSPRNM 547
Cdd:TIGR03670 71 EHV----EKLKEGELTWDDLVKQGVIeyldaeeeenayialdpeeltpehTHLEIDPSAILGIIASTIPYPEHNQSPRNT 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 548 YQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWER 627
Cdd:TIGR03670 147 MGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 628 GFAHGS---VYKSEFID----LSEKIKQGDSSlVFGIKPgdPRVLQKLDDDGLPFIGAKLQYGD--------P--YYSYL 690
Cdd:TIGR03670 227 GLARSTffrTYEAEERRypggQEDRFEIPEPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDvligktspPrfLEELR 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 691 NLNTGE------SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMP 764
Cdd:TIGR03670 304 EFGLVTerrrdtSVTV--RHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMP 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 765 FTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGI 844
Cdd:TIGR03670 379 FTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGI 454
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 845 SGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 924
Cdd:TIGR03670 455 TGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 534
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544346144 925 RSVAHVCVKCGSLlspllekpppSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 995
Cdd:TIGR03670 535 KYVVYVCENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
416-995 |
1.24e-130 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 407.81 E-value: 1.24e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 416 PVLLDGVMVGWVDKdlAPGIADSLRhfKVLREKRIPPWMEVVLIPMTGKpslypgLFLFTTPCRLVRP---VQN------ 486
Cdd:PRK07225 6 KVYVNGKLIGTHDD--PEELVEEIR--EARRSGEISEEVNVSYKEETNE------VIINTDAGRARRPlivVENgepllt 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 487 -----------------LALGKEELIGTMEQIFMNVAIFEDEVFAGvTTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQ 549
Cdd:PRK07225 76 eehieklkngeltfddlVKQGVIEYLDAEEEENAYIAVYEEDLTEE-HTHLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 550 CQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGF 629
Cdd:PRK07225 155 AGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 630 AHGSVYKSefIDLSEKIKQGDSSLVFGIKPGDPR------VLQKLDDDGLPFIGAKLQYGD--------PyySYLNLNTG 695
Cdd:PRK07225 235 GRSHFFRT--YEGEERRYPGGQEDRFEIPDKDVRgyrgeeAYRHLDEDGLVNPETEVKEGDvligktspP--RFLEEPDD 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 696 E----------SFVMyyKSKENCVVDNIKVCSNDTGSgkfKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPF 765
Cdd:PRK07225 311 FgispekrretSVTM--RSGEEGIVDTVILTETEEGS---RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPF 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 766 TESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENSalEYFGEMLKAAGYNFYGTERLYSGIS 845
Cdd:PRK07225 386 TESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAF--SGEDE--EDLREALEKLGFEHTGKEVMYDGIT 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 846 GLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDR 925
Cdd:PRK07225 462 GEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDK 541
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544346144 926 SVAHVCVKCGSLlspllekpppswsAMRNRKYN---CTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDV 995
Cdd:PRK07225 542 VEIYVCAKCGMI-------------AIYDKKRNrkyCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
518-993 |
8.62e-104 |
|
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: 347.48 E-value: 8.62e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 518 THQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMG-----FPLLTY---------QDRSDNklyrlqtpQSPLV 583
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN--------QRPIV 582
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 584 R--------------PSMydyyDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFIDLSE----K 645
Cdd:COG0085 583 RvgdrvekgdvladgPAT----DNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIEEYEiearD 653
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 646 IKQGDSSLVFGI-KPGDpRVLQKLDDDGLPFIGAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSK---- 705
Cdd:COG0085 654 TKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGAEVKGGDilvgkvtpkgeteltPEERLLRAIFGE------KARevrd 726
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 706 --------ENCVVDNIKVCSNDTGS----GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPD 773
Cdd:COG0085 727 tslrvphgEKGKVIDVKVFSREEGDelppGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVD 806
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 774 ILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEAD 852
Cdd:COG0085 807 IVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGRTGEPFDNP 881
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 853 IFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCV 932
Cdd:COG0085 882 VTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV 961
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544346144 933 kcgsllsplLEkpppswsamRNRKynctlcsrSDTIDTVSVPYVFRYFVAELAAMNIKVKL 993
Cdd:COG0085 962 ---------YE---------AIVK--------GENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
598-924 |
8.06e-50 |
|
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: 191.80 E-value: 8.06e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 598 IGTNAIVAVISYTGYDMEDAMIVNkaswERGF---AHGSVYKSEFIDLSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 674
Cdd:TIGR02013 673 LGRNVLVAFMPWNGYNYEDAILIS----ERLVkddVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIV 748
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 675 FIGAKLQYGD---------------PYYSYLNLNTGEsfvmyyKSKEncVVDN--------------IKVCSNDTGS--- 722
Cdd:TIGR02013 749 RIGAEVKAGDilvgkvtpkgeteltPEEKLLRAIFGE------KARD--VRDTslrvppgvegtvidVKVFSREQGDelp 820
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 723 -GKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKS 798
Cdd:TIGR02013 821 pGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAGKR 900
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 799 AALHGLCHdATPfIFseENSALEYFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGA 878
Cdd:TIGR02013 901 LGRKGVPI-ATP-VF--DGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGP 976
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 544346144 879 RDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 924
Cdd:TIGR02013 977 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
1-277 |
5.29e-49 |
|
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: 179.11 E-value: 5.29e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 1 MVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVRE-E 79
Cdd:pfam04563 111 MLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPdS 190
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 80 HSAVNMnLHYLENGTVMLNFIYRKELFflPLGFALKALVSFSDYQIFqELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQK 159
Cdd:pfam04563 191 TSWVNV-LEYLSNGTIYFKFPYIKKEI--PIVIILRALGFTSDREIF-ELICYDVNDQQLQEELLPSLEEGFKIRIQTQE 266
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 160 QVLNYLGECFRVKLNV-PDWYPNEQAAEFLFNQCICIHLK----SNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQE 234
Cdd:pfam04563 267 QALDYIGGRGRAIFRMgRPREPRIKYAEEILQKEVLPHLGtyelDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKR 346
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 544346144 235 VLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQK-----TSVSMNTDNL 277
Cdd:pfam04563 347 LRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSpddlmLQLLVNAKPI 394
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
319-924 |
1.31e-43 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 172.20 E-value: 1.31e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 319 DKLNFIRYLSH-FRCVHRGAD-FAKMRTTT-VRRLLPESWGFLCPVHTPDGEPCGLMNHLTaVCEVVTQFvytasipall 395
Cdd:CHL00207 371 DQTNPLSELTHkRRISILGPGgLDKDRISFaVRDIHPSHYGRICPIETPEGPNCGLIGSLA-TNARINKF---------- 439
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 396 cNLGVTPidgaphrsyseCYPVLldgvmVGWVDKDLAPGI--ADSLRHFKVLrekrippwmevvlipmtgkpslyPGlfl 473
Cdd:CHL00207 440 -GFIETP-----------FYKVI-----NGKVKKFGNPIYltADSEDLYRIA-----------------------PN--- 476
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 474 fttpcrlvrpvqNLALGKEELIgtmeqIFMNVAIFEDEVFAGVTTHQELF----PHSLLSVIANFIPFSDHNQSPRnmyq 549
Cdd:CHL00207 477 ------------DINLNKNNYF-----KKNIIPVRYKQEFKTVNPSKVDFiaisPIQVFSIAESLIPFLEHNDANR---- 535
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 550 CQMGK--QTMGFPLL---------------------------------------TYQDRSDNKL-YRLQ----------T 577
Cdd:CHL00207 536 ALMGSnmQRQAVPLLypekpivgtgyekqialdsgmtiisltegivvsvsaykiIIQDDNNRYIhYYLQkyqrsnqntcI 615
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 578 PQSPLVRPS--------MYDYYDMDN--YPIGTNAIVAVISYTGYDMEDAMIVNKAswergFAHGSVYKSEFIDLSEKI- 646
Cdd:CHL00207 616 NYRPIVWVGekinigqiLADGSDIDNseLALGQNVLVAYMPWEGYNFEDAILINKR-----LVYEDLFTSIHIEKYEIEl 690
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 647 ---KQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGD-------PYYSYLNLNTGESFVMYYKSKENCVVDN---- 712
Cdd:CHL00207 691 rqtKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDilvgkitPKGESDQLPEGKLLRAIFGEKAKDVKDTslrm 770
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 713 ----------IKVCSNDTGSGKFKCVCITMRV----PRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNP 778
Cdd:CHL00207 771 pnggygrvikVEIFSRSKGDELKFGYYLKIRVfiaqIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNP 850
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 779 HGFPSRMTIGMLIESMAGKSAalHGLCHDATPFIFSEENSALE---YFGEMLKAAG--------YNFY--GTERLYSGIS 845
Cdd:CHL00207 851 LGVPSRMNVGQLFECLLGLAG--DNLNKRFKILPFDEMYGSEYsriLINNKLNQASiknneywlFNSYhpGKMVLRDGRT 928
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544346144 846 GLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 924
Cdd:CHL00207 929 GYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD 1007
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
739-915 |
2.13e-36 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 149.10 E-value: 2.13e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 739 TIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIES---MAGKsaalhGL-CHDATPfIF- 813
Cdd:PRK00405 881 QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAAK-----GLgIKFATP-VFd 954
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 814 --SEENsaleyFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRN 891
Cdd:PRK00405 955 gaKEEE-----IKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKA 1029
|
170 180
....*....|....*....|....
gi 544346144 892 VQGGIRFGEMERDALLAHGTSFLL 915
Cdd:PRK00405 1030 QFGGQRFGEMEVWALEAYGAAYTL 1053
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
316-380 |
6.81e-32 |
|
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: 118.40 E-value: 6.81e-32
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544346144 316 VVADKLNFIRYLSHFRCVH--RGADFAKMRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCE 380
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNspRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
599-924 |
1.86e-31 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 133.49 E-value: 1.86e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 599 GTNAIVAVISYTGYDMEDAMIVNkaswERgFAHGSVYKSEFIDLSE----KIKQGDSSLVFGIKPGDPRVLQKLDDDGLP 674
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLIS----ER-LVYEDIYTSFHIRKYEiqthVTSQGPERITKEIPHLEAHLLRNLDKNGIV 726
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 675 FIGAKLQYGD-------PYYSYLNLNTGESFVMY-------YKSKENC----------VVDNIKVCSNDTGSGKFKCVCI 730
Cdd:CHL00001 727 MLGSWVETGDilvgkltPQEAEESSYAPEGRLLRaifgiqvSTSKETClklpiggrgrVIDVRWIQKKGGSSYNPETIHV 806
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 731 TMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATP 810
Cdd:CHL00001 807 YILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAP 886
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 811 F--IFSEENSALEYFGEMLKA---AGY------NFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGAR 879
Cdd:CHL00001 887 FdeRYEQEASRKLVFSELYEAskqTANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPY 966
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 544346144 880 DRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 924
Cdd:CHL00001 967 ALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
722-924 |
3.94e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 123.11 E-value: 3.94e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 722 SGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIE---SMAGK- 797
Cdd:PRK09603 1072 NGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEmhlGLVGKe 1151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 798 ----------------------------------------------SAALHGLCHD-------ATPfIFseENSALEYFG 824
Cdd:PRK09603 1152 fgkqiasmledktkdfakelrakmleianainekdpltihalencsDEELLEYAKDwskgvkmAIP-VF--EGISQEKFY 1228
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 825 EMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERD 904
Cdd:PRK09603 1229 KLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308
|
250 260
....*....|....*....|
gi 544346144 905 ALLAHGTSFLLHDRLFNCSD 924
Cdd:PRK09603 1309 ALEAYGAAHTLKEMLTIKSD 1328
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
424-482 |
1.37e-23 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
Pssm-ID: 462028 Cd Length: 58 Bit Score: 94.47 E-value: 1.37e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 544346144 424 VGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPMTgKPSLYPGLFLFTTPCRLVR 482
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
1-405 |
7.62e-23 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 103.49 E-value: 7.62e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 1 MVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIRML-------IMPRRNFPIAMIRPKWKTrgpgYTQY-GVS 72
Cdd:PRK09606 118 MVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLedlapnkILVEKDERYGDRIEVAKV----FSQRrGYR 193
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 73 MHCVREEHSavnmnlhyleNGTVMLNFIY-RKELFFLPLgfaLKALVSFSDyqifQELIKGKEDDsflRNSVSQMLRIVM 151
Cdd:PRK09606 194 ALVTVERNR----------DGLLEVSFPSvPGSIPFVIL---MRALGLETD----EEIVEAVSDD---PEIVKFMLENLE 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 152 EEGCSTQKQVLNYLGEcfRVKLNVPDWYPNEQaAEFLFNQCICIHLKSNTEKF----YMLCLMTRKLFALAKGECMEDNP 227
Cdd:PRK09606 254 EAEVDTQEEALEYIGK--RVAPGQTKEYRIKR-AEYVIDRYLLPHLGVEPEVRrakaHYLGRMAEACFELALGRREEDDK 330
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 228 DSLVNQEVLTPGQLFlmflkEKLegwlvsIKIAF-----DKKAQKTSVSM-NTDNLMRIFTMGIDLTKPFEYLFATGNLR 301
Cdd:PRK09606 331 DHYANKRLKLAGDLM-----EDL------FRVAFnrlarDVKYQLERANMrNRELSIKTAVRSDVLTERLEHAMATGNWV 399
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 302 S-KTGLGLLqdsglcvvADKLNFIRYLSHFRCV---------HRGAdfakmrtttvRRLLPESWGFLCPVHTPDGEPCGL 371
Cdd:PRK09606 400 GgRTGVSQL--------LDRTDYMATLSHLRRVvsplsrsqpHFEA----------RDLHPTQWGRICPSETPEGPNCGL 461
|
410 420 430
....*....|....*....|....*....|....
gi 544346144 372 MNHLTAVCEVVTQFVYTASIPaLLCNLGVTPIDG 405
Cdd:PRK09606 462 VKNFAQMVEISTGEDEEEVKE-ILKELGVEPERG 494
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
894-996 |
4.55e-22 |
|
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 91.11 E-value: 4.55e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 894 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGsllspllekpppswsAMRNRKYnCTLCSRSDTIDTVSV 973
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCG---------------LYAAYNK-CPICKGETDISPGYI 64
|
90 100
....*....|....*....|...
gi 544346144 974 PYVFRYFVAELAAMNIKVKLDVV 996
Cdd:pfam04560 65 PESFKLLFQELQSLGIDPRLLLE 87
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
741-924 |
2.00e-20 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 98.16 E-value: 2.00e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 741 GDKFASRHGQKGILSRLWPAEDMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAG--------------------KSAA 800
Cdd:PRK14844 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgekvgnildeinkiKSAF 1163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 801 LHGL--------------------------------------------------------CHDATPFIFS---------- 814
Cdd:PRK14844 1164 CKGIrslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenylnsCKSAYSNLRNflievyscgs 1243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 815 -----------EENSALEY----------------------FGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQ 861
Cdd:PRK14844 1244 nvsicnnirdiSDNNLIEFarklrdgipvaapvfegpkdeqIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYML 1323
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544346144 862 RLRHMVSDKFQVRTTGARDRVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 924
Cdd:PRK14844 1324 KLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
47-236 |
9.20e-11 |
|
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: 61.98 E-value: 9.20e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 47 RRNFPIAMIRPKWKTRGPGYTQYgvsmhcvreEHSAVNMnLHYLEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 124
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSS---------LISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544346144 125 IFQELIKGKEDDSFLrnsVSQMLRIVMEEGCSTQKQVLNYLGECFRVKLNVPDWYPNEQAA------EFLFNQCI--CIH 196
Cdd:pfam04561 69 ILDRLCYDFNDPQML---ELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 544346144 197 LKSNTEKFYMLCLMTRKLFALAKGECMEDNPDSLVNQEVL 236
Cdd:pfam04561 146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
