|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
11-1056 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1957.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 11 LPDLVEIQRASFCWFL-------NEGLAEEIQSFSPIVNYTGNLELHlFGDqYTLRYPKHNINECKRRDTTYSVQIYVPA 83
Cdd:PRK00405 24 LPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLE-FVS-YELGEPKYDVEECKERGLTYSAPLRVKL 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 84 QLINRETGVIKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELDKQ--GRRTYSSSLISNRGAWVKFET 161
Cdd:PRK00405 102 RLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKTssGKLLYSARIIPYRGSWLEFEF 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 162 DRNDLVWVRIDKTRKIPAHVFLKAMGLSDTDIYN---------------------------------------------G 196
Cdd:PRK00405 182 DPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDlfyekeefgkeievpveyllgkvlaedivdeetgevlaeandeitE 261
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 197 LRHPEYLKKTFRFEGNYTTETALIQMYNKLRPGEPATVTGGQQLLYSRFFDPKRYDLGKVGRYKLNKKLNLSVPENVRVL 276
Cdd:PRK00405 262 ELDGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVL 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 277 TPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRERMTICDITSLTPNTLVNPKPIIA 356
Cdd:PRK00405 342 TKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVA 421
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 357 SIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLATHAR 436
Cdd:PRK00405 422 AIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYAR 501
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 437 INTYGFIEAPFFKVQDGQVYNhsQPIYLTADQEDKYRIAPGDITLDETNRIATKIVPIKYRQEFTTTKPNQVDFIAVSPI 516
Cdd:PRK00405 502 VNEYGFIETPYRKVVDGKVTD--EIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPK 579
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 517 QVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPESPLVGTGLEAQAARDSGMVVVSIEDGQVTFVSGDKICVTNKK 596
Cdd:PRK00405 580 QVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEE 659
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 597 GDEIA-----YYLQKYQRSNQDTCINQRPTVWLGEDVIEGQVIADGAATEGGELALGQNILVAYLPWEGYNYEDAFLINE 671
Cdd:PRK00405 660 LDPGEdgvdiYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISE 739
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 672 RLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNVGEAALRKLDENGIIVIGSWVEAGDILIGKVTPKGESDQPPEGK 751
Cdd:PRK00405 740 RLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEK 819
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 752 LLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTR-EKGDELPTGANIVIRVYIAQSRKIQVGDKMAGRHGNKGIISRI 830
Cdd:PRK00405 820 LLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRI 899
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 831 LPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFDEMHGAEasrvlVNEKLNEAKIKTge 910
Cdd:PRK00405 900 LPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEE-----IKELLEEAGLPE-- 972
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 911 nwlfdlrhPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWAL 990
Cdd:PRK00405 973 --------DGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1044
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11467690 991 EAFGASYTLQELLTVKSDDMQGRNETLNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIGAYKIEN 1056
Cdd:PRK00405 1045 EAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDEDG 1110
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
11-1049 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 1787.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 11 LPDLVEIQRASFCWFLNEGLAEEIQSFSPIVNYTGNLELHlFGDqYTLRYPKHNINECKRRDTTYSVQIYVPAQLINRET 90
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLE-FGD-YRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKET 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 91 GVIKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELDKQGRRTYSSSLISNRGAWVKFETDRNDLVWVR 170
Cdd:COG0085 91 GEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDGTIYVR 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 171 IDKTRKIPAHVFLKAMGL-SDTDIYNGLRH---PEYLKKTFRFEGNYTTETALIQMYNKLRPGEPATVTGGQQLLYSRFF 246
Cdd:COG0085 171 IDRKRKIPVTVLLRALGLeTDEEILEAFGDdpiQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFF 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 247 DPKRYDLGKVGRYKLNKKLNLSVPENVRVLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVRIGLNR 326
Cdd:COG0085 251 DPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSR 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 327 LERIIRERMTICDITSLTPNTLVNPKPIIASIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLNRDRAGFGVRDI 406
Cdd:COG0085 331 MERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDV 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 407 HPSHYGRICPIETPEGPNAGLIGVLATHARINTYGFIEAPFFKVQDGQVYNhsQPIYLTADQEDKYRIAPGDITLDETNR 486
Cdd:COG0085 411 HPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTD--EIEYLTADEEENYYIAQANAPLDEDGN 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 487 IATKIVPIKYRQEFTTTKPNQVDFIAVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPESPLvgtgleaqa 566
Cdd:COG0085 489 FLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL--------- 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 567 ardsgmvvvsiedgqvtfvsgdkicvtnkkgdeIAYYLQKYQRSNQDTCINQRPTVWLGEDVIEGQVIADGAATEGGELA 646
Cdd:COG0085 560 ---------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELA 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 647 LGQNILVAYLPWEGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNVGEAALRKLDENGIIVIGS 726
Cdd:COG0085 607 LGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGA 686
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 727 WVEAGDILIGKVTPKGESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTREKGDELPTGANIVIRVYIA 806
Cdd:COG0085 687 EVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVA 766
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 807 QSRKIQVGDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFDE 886
Cdd:COG0085 767 QKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDG 846
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 887 MHGAEasrvlVNEKLNEAKIKtgenwlfdlrHPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLV 966
Cdd:COG0085 847 APEEE-----IRELLEKAGLP----------PDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLI 911
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 967 TQQPLGGRAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSDDMQGRNETLNAIVKGKPIPRPGTPESFKVLMRELQSLG 1046
Cdd:COG0085 912 TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLG 991
|
...
gi 11467690 1047 LDI 1049
Cdd:COG0085 992 LDV 994
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1049 |
0e+00 |
|
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: 1763.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 10 TLPDLVEIQRASFCWFL----------NEGLAEEIQSFSPIVNYTGNLELHLFGdqYTLRYPKHNINECKRRDTTYSVQI 79
Cdd:TIGR02013 16 EVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYLS--YRLGEPKYSVEECKERGLTYSAPL 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 80 YVPAQLINRE---TGVIKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELD--KQGRRTYSSSLISNRG 154
Cdd:TIGR02013 94 KVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSGKVLFSARIIPYRG 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 155 AWVKFETDRNDLVWVRIDKTRKIPAHVFLKAMGLS-DTDIYNGLRHPEYLKKTFRFEGNYTTETALIQMYNKLRPGEPAT 233
Cdd:TIGR02013 174 SWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTiDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPT 253
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 234 VTGGQQLLYSRFFDPKRYDLGKVGRYKLNKKLNLSVPENVRVLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVG 313
Cdd:TIGR02013 254 VEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVG 333
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 314 ELLQNQVRIGLNRLERIIRERMTICDITSLTPNTLVNPKPIIASIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG 393
Cdd:TIGR02013 334 ELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG 413
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 394 LNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLATHARINTYGFIEAPFFKVQDGQVYNHSQPIYLTADQEDKYR 473
Cdd:TIGR02013 414 LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTDEIDYLTADEEDNYV 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 474 IAPGDITLDETNRIATKIVPIKYRQEFTTTKPNQVDFIAVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYP 553
Cdd:TIGR02013 494 IAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRS 573
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 554 ESPLVGTGLEAQAARDSGMVVVSIEDGQVTFVSGDKICVTNK------KGDEIAYYLQKYQRSNQDTCINQRPTVWLGED 627
Cdd:TIGR02013 574 EAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDedeeepDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDR 653
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 628 VIEGQVIADGAATEGGELALGQNILVAYLPWEGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPN 707
Cdd:TIGR02013 654 VEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPN 733
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 708 VGEAALRKLDENGIIVIGSWVEAGDILIGKVTPKGESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTR 787
Cdd:TIGR02013 734 VSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSR 813
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 788 EKGDELPTGANIVIRVYIAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECL 867
Cdd:TIGR02013 814 EQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETH 893
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 868 LGLAAENLNKRFK--ITP-FDemhGAEASRvlVNEKLNEAKIKTGenwlfdlrhpGKITLYDGRTGEAFDNPVTIGVSYM 944
Cdd:TIGR02013 894 LGWAGKRLGRKGVpiATPvFD---GASEEE--IKEYLEKAGLPRD----------GKVRLYDGRTGEQFDRPVTVGYMYM 958
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 945 LKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSDDMQGRNETLNAIVKGK 1024
Cdd:TIGR02013 959 LKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGE 1038
|
1050 1060
....*....|....*....|....*
gi 11467690 1025 PIPRPGTPESFKVLMRELQSLGLDI 1049
Cdd:TIGR02013 1039 NVPEPGIPESFNVLIKELQSLGLDI 1063
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
14-1049 |
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: 1039.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 14 LVEIQRASFCWFLNEGLAEEIQSFSPIVNYTGNLELHLFGDQYTLRYPKHN---------INECKRRDTTYSVQIYVPAQ 84
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEeggvtrkltPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 85 LINRETGVIKEQEVFIGDLPLMTD------------------------RGTFIINGAERVIVNQIVRSPGIYYKSelDKQ 140
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 141 GRRTYS----SSLISNRGAWVKFETD-RNDLVWVRIDKTRKipahvflkamglsdtdiynglrhpeylkktfrfegnytt 215
Cdd:cd00653 159 GKRIYTktsiPSYSPYRGSWLEVKSDkKKDRIYVRIDLKRQ--------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 216 ETALIQMYNKLRpgepatvtggqqllysrffdpkrydlgkvgryklnkklnlsvpenvrvltpqDTLAAIDYLINLKFEI 295
Cdd:cd00653 200 EEALKYIGKRFE----------------------------------------------------DLIYMIRKLILLVLGK 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 296 GETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRERMTICDITS--LTPNTLVNPKPIIASIREFFGSSQ------- 366
Cdd:cd00653 228 GKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwgskrfl 307
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 367 -----LSQFMDQTNPLAELTHKRRISAlgpGGLNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLATHARINtyG 441
Cdd:cd00653 308 mqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--G 382
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 442 FIEAPFFKVQdgqvynhsqpiyltadqedkyriapgditldetnriatkivpikyrqeftttkpNQVDFIAVSPIQVISI 521
Cdd:cd00653 383 RIERPYRIVE------------------------------------------------------KEVTHIEISPSQILSV 408
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 522 ATSLIPFLEHDDANRALMGSNMQRQAVP----------------LLYPESPLVGTGLEAQAARDsgmvvvsiedgqvtfv 585
Cdd:cd00653 409 AASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG---------------- 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 586 sgdkicvtnkkgdeiayylqkyqrsnqdtcinqrptvwlgedviegqviadgaateggELALGQNILVAYLPWEGYNYED 665
Cdd:cd00653 473 ----------------------------------------------------------ELPLGQNAIVAVMSYSGYNFED 494
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 666 AFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITR-ELPNVGEAALRKLDENGIIVIGSWVEAGDILIGKVTPKGES 744
Cdd:cd00653 495 AIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGET 574
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 745 DQPPegkllraIFGEKARDVRDTSLRVPNGGRGRILDVRIFTREkgdeLPTGANIVIRVYIAQSRKIQVGDKMAGRHGNK 824
Cdd:cd00653 575 ESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQK 643
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 825 GIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFDEMHGAEASRVLVNEKLNea 904
Cdd:cd00653 644 GVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLN-- 721
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 905 kiktgenwlfdlrHPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQHGGQRLGE 984
Cdd:cd00653 722 -------------YYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGE 788
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11467690 985 MEVWALEAFGASYTLQELLTVKSDDMQGRNETLNAIV----------KGKPIPRPGTPESFKVLMRELQSLGLDI 1049
Cdd:cd00653 789 MERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDP 863
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
523-976 |
1.43e-169 |
|
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: 502.83 E-value: 1.43e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 523 TSLIPFLEHDDANRALMGSNMQRQAVPLlypesplvgtgleaqaardsgmvvvsiedgqvtfvsgdkicvtnkkgdeiaY 602
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGI---------------------------------------------------Y 30
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 603 YLQKYQRSNQDT---CINQRPTVWLGedVIEgqviadgaATEGGELALGQNILVAYLPWEGYNYEDAFLINERLVYNDVY 679
Cdd:pfam00562 31 TLNKFYRSDQNTyvlCYPQKPLVKTG--AVE--------AGGFGELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFF 100
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 680 TSVHIEkyEIEARQTKLG-SEEITRELPNVGEAALRKLDENGIIVIGSWVEAGDILIGKVTPkgesdqPPEGKLLRAIFG 758
Cdd:pfam00562 101 TSIHIK--EIEARKTKLGpIEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGP------TELTKLLRAIFG 172
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 759 EKARDVRDTSLRVPNGGRGRILDVRIFTrekgdeLPTGANIVIRVYIAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPY 838
Cdd:pfam00562 173 EKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPF 246
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 839 LPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFDemhGAEASRVLVNEKLNEAKiktgenwlfdLRH 918
Cdd:pfam00562 247 TEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAG----------YNY 313
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*...
gi 11467690 919 PGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQ 976
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
11-1056 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1957.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 11 LPDLVEIQRASFCWFL-------NEGLAEEIQSFSPIVNYTGNLELHlFGDqYTLRYPKHNINECKRRDTTYSVQIYVPA 83
Cdd:PRK00405 24 LPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLE-FVS-YELGEPKYDVEECKERGLTYSAPLRVKL 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 84 QLINRETGVIKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELDKQ--GRRTYSSSLISNRGAWVKFET 161
Cdd:PRK00405 102 RLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKTssGKLLYSARIIPYRGSWLEFEF 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 162 DRNDLVWVRIDKTRKIPAHVFLKAMGLSDTDIYN---------------------------------------------G 196
Cdd:PRK00405 182 DPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDlfyekeefgkeievpveyllgkvlaedivdeetgevlaeandeitE 261
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 197 LRHPEYLKKTFRFEGNYTTETALIQMYNKLRPGEPATVTGGQQLLYSRFFDPKRYDLGKVGRYKLNKKLNLSVPENVRVL 276
Cdd:PRK00405 262 ELDGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVL 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 277 TPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRERMTICDITSLTPNTLVNPKPIIA 356
Cdd:PRK00405 342 TKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVA 421
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 357 SIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLATHAR 436
Cdd:PRK00405 422 AIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYAR 501
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 437 INTYGFIEAPFFKVQDGQVYNhsQPIYLTADQEDKYRIAPGDITLDETNRIATKIVPIKYRQEFTTTKPNQVDFIAVSPI 516
Cdd:PRK00405 502 VNEYGFIETPYRKVVDGKVTD--EIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPK 579
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 517 QVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPESPLVGTGLEAQAARDSGMVVVSIEDGQVTFVSGDKICVTNKK 596
Cdd:PRK00405 580 QVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEE 659
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 597 GDEIA-----YYLQKYQRSNQDTCINQRPTVWLGEDVIEGQVIADGAATEGGELALGQNILVAYLPWEGYNYEDAFLINE 671
Cdd:PRK00405 660 LDPGEdgvdiYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISE 739
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 672 RLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNVGEAALRKLDENGIIVIGSWVEAGDILIGKVTPKGESDQPPEGK 751
Cdd:PRK00405 740 RLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEK 819
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 752 LLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTR-EKGDELPTGANIVIRVYIAQSRKIQVGDKMAGRHGNKGIISRI 830
Cdd:PRK00405 820 LLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRI 899
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 831 LPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFDEMHGAEasrvlVNEKLNEAKIKTge 910
Cdd:PRK00405 900 LPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEE-----IKELLEEAGLPE-- 972
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 911 nwlfdlrhPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWAL 990
Cdd:PRK00405 973 --------DGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1044
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11467690 991 EAFGASYTLQELLTVKSDDMQGRNETLNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIGAYKIEN 1056
Cdd:PRK00405 1045 EAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDEDG 1110
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
5-1077 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1852.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 5 TFANRTLPDLVEIQRASFCWFLNEGLAEEIQSFSPIVNYTGNLELHLFGDQYTLRYPKHNINECKRRDTTYSVQIYVPAQ 84
Cdd:CHL00207 1 INMNFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFGKNYKLKYPKYNLLSAKSYDSNYSIQIYLPLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 85 LINRETGVIKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELDKQGRRTYSSSLISNRGAWVKFETDRN 164
Cdd:CHL00207 81 FINLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATLIPNRGSWIKFELDKN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 165 DLVWVRIDKTRKIPAHVFLKAMGLSDTDIYNGLR---HPEYLKKTFRFEGNYTTETALIQMYNKLRPGEPATVTGGQQLL 241
Cdd:CHL00207 161 KEIWIRIDKNRKKPLIIFLKALGLTDQDIYSRLTkseFLKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQNL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 242 YSRFFDPKRYDLGKVGRYKLNKKLNLSVPENVRVLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVR 321
Cdd:CHL00207 241 FSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFR 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 322 IGLNRLERIIRERMTICDITSLTPNTLVNPKPIIASIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLNRDRAGF 401
Cdd:CHL00207 321 IGLKRLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISF 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 402 GVRDIHPSHYGRICPIETPEGPNAGLIGVLATHARINTYGFIEAPFFKVQDGQVYNHSQPIYLTADQEDKYRIAPGDITL 481
Cdd:CHL00207 401 AVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFGNPIYLTADSEDLYRIAPNDINL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 482 DETNRIATKIVPIKYRQEFTTTKPNQVDFIAVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPESPLVGTG 561
Cdd:CHL00207 481 NKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTG 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 562 LEAQAARDSGMVVVSIEDGQVTFVSGDKICVTNKKGDEIAYYLQKYQRSNQDTCINQRPTVWLGEDVIEGQVIADGAATE 641
Cdd:CHL00207 561 YEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDID 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 642 GGELALGQNILVAYLPWEGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNVGEAALRKLDENGI 721
Cdd:CHL00207 641 NSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGI 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 722 IVIGSWVEAGDILIGKVTPKGESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTREKGDELPTGANIVI 801
Cdd:CHL00207 721 ISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKI 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 802 RVYIAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKI 881
Cdd:CHL00207 801 RVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKI 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 882 TPFDEMHGAEASRVLVNEKLNEAKIKTGENWLFDLRHPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTG 961
Cdd:CHL00207 881 LPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTG 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 962 PYSLVTQQPLGGRAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSDDMQGRNETLNAIVKGKPIPRPGTPESFKVLMRE 1041
Cdd:CHL00207 961 PYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRE 1040
|
1050 1060 1070
....*....|....*....|....*....|....*.
gi 11467690 1042 LQSLGLDIGAYKIENLPDGQTRGIEVDLMMNYQQSR 1077
Cdd:CHL00207 1041 LQSLGLDIEAYKIENFLEGQRLEIEINLMENYKYFR 1076
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
11-1049 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 1787.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 11 LPDLVEIQRASFCWFLNEGLAEEIQSFSPIVNYTGNLELHlFGDqYTLRYPKHNINECKRRDTTYSVQIYVPAQLINRET 90
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLE-FGD-YRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKET 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 91 GVIKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELDKQGRRTYSSSLISNRGAWVKFETDRNDLVWVR 170
Cdd:COG0085 91 GEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDGTIYVR 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 171 IDKTRKIPAHVFLKAMGL-SDTDIYNGLRH---PEYLKKTFRFEGNYTTETALIQMYNKLRPGEPATVTGGQQLLYSRFF 246
Cdd:COG0085 171 IDRKRKIPVTVLLRALGLeTDEEILEAFGDdpiQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFF 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 247 DPKRYDLGKVGRYKLNKKLNLSVPENVRVLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVRIGLNR 326
Cdd:COG0085 251 DPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSR 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 327 LERIIRERMTICDITSLTPNTLVNPKPIIASIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLNRDRAGFGVRDI 406
Cdd:COG0085 331 MERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDV 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 407 HPSHYGRICPIETPEGPNAGLIGVLATHARINTYGFIEAPFFKVQDGQVYNhsQPIYLTADQEDKYRIAPGDITLDETNR 486
Cdd:COG0085 411 HPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTD--EIEYLTADEEENYYIAQANAPLDEDGN 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 487 IATKIVPIKYRQEFTTTKPNQVDFIAVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPESPLvgtgleaqa 566
Cdd:COG0085 489 FLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL--------- 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 567 ardsgmvvvsiedgqvtfvsgdkicvtnkkgdeIAYYLQKYQRSNQDTCINQRPTVWLGEDVIEGQVIADGAATEGGELA 646
Cdd:COG0085 560 ---------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELA 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 647 LGQNILVAYLPWEGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNVGEAALRKLDENGIIVIGS 726
Cdd:COG0085 607 LGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGA 686
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 727 WVEAGDILIGKVTPKGESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTREKGDELPTGANIVIRVYIA 806
Cdd:COG0085 687 EVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVA 766
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 807 QSRKIQVGDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFDE 886
Cdd:COG0085 767 QKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDG 846
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 887 MHGAEasrvlVNEKLNEAKIKtgenwlfdlrHPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLV 966
Cdd:COG0085 847 APEEE-----IRELLEKAGLP----------PDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLI 911
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 967 TQQPLGGRAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSDDMQGRNETLNAIVKGKPIPRPGTPESFKVLMRELQSLG 1046
Cdd:COG0085 912 TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLG 991
|
...
gi 11467690 1047 LDI 1049
Cdd:COG0085 992 LDV 994
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1049 |
0e+00 |
|
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: 1763.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 10 TLPDLVEIQRASFCWFL----------NEGLAEEIQSFSPIVNYTGNLELHLFGdqYTLRYPKHNINECKRRDTTYSVQI 79
Cdd:TIGR02013 16 EVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYLS--YRLGEPKYSVEECKERGLTYSAPL 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 80 YVPAQLINRE---TGVIKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELD--KQGRRTYSSSLISNRG 154
Cdd:TIGR02013 94 KVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSGKVLFSARIIPYRG 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 155 AWVKFETDRNDLVWVRIDKTRKIPAHVFLKAMGLS-DTDIYNGLRHPEYLKKTFRFEGNYTTETALIQMYNKLRPGEPAT 233
Cdd:TIGR02013 174 SWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTiDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPT 253
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 234 VTGGQQLLYSRFFDPKRYDLGKVGRYKLNKKLNLSVPENVRVLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVG 313
Cdd:TIGR02013 254 VEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVG 333
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 314 ELLQNQVRIGLNRLERIIRERMTICDITSLTPNTLVNPKPIIASIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGG 393
Cdd:TIGR02013 334 ELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGG 413
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 394 LNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLATHARINTYGFIEAPFFKVQDGQVYNHSQPIYLTADQEDKYR 473
Cdd:TIGR02013 414 LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTDEIDYLTADEEDNYV 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 474 IAPGDITLDETNRIATKIVPIKYRQEFTTTKPNQVDFIAVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYP 553
Cdd:TIGR02013 494 IAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRS 573
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 554 ESPLVGTGLEAQAARDSGMVVVSIEDGQVTFVSGDKICVTNK------KGDEIAYYLQKYQRSNQDTCINQRPTVWLGED 627
Cdd:TIGR02013 574 EAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDedeeepDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDR 653
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 628 VIEGQVIADGAATEGGELALGQNILVAYLPWEGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPN 707
Cdd:TIGR02013 654 VEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPN 733
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 708 VGEAALRKLDENGIIVIGSWVEAGDILIGKVTPKGESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTR 787
Cdd:TIGR02013 734 VSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSR 813
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 788 EKGDELPTGANIVIRVYIAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECL 867
Cdd:TIGR02013 814 EQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETH 893
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 868 LGLAAENLNKRFK--ITP-FDemhGAEASRvlVNEKLNEAKIKTGenwlfdlrhpGKITLYDGRTGEAFDNPVTIGVSYM 944
Cdd:TIGR02013 894 LGWAGKRLGRKGVpiATPvFD---GASEEE--IKEYLEKAGLPRD----------GKVRLYDGRTGEQFDRPVTVGYMYM 958
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 945 LKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSDDMQGRNETLNAIVKGK 1024
Cdd:TIGR02013 959 LKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGE 1038
|
1050 1060
....*....|....*....|....*
gi 11467690 1025 PIPRPGTPESFKVLMRELQSLGLDI 1049
Cdd:TIGR02013 1039 NVPEPGIPESFNVLIKELQSLGLDI 1063
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
10-1054 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1671.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 10 TLPDLVEIQRASFCWFLNEGLAEEIQSFSPIVNYTGNLELHLFGDQYTLRYPKHNINECKRRDTTYSVQIYVPAQLINRE 89
Cdd:CHL00001 11 TIPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVPAGLIWKK 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 90 TGVIKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELDKQGRRTYSSSLISNRGAWVKFETDRNDLVWV 169
Cdd:CHL00001 91 SRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKARIWA 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 170 RIDKTRKIPAHVFLKAMGLSDTDIYNGLRHPEYLKKTFRFEGN---YTTETALIQMYNKL--RPGEPATVTGGQQLLYSR 244
Cdd:CHL00001 171 RVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLNDKEKkkiGSKENAILEFYQQFacVGGDPVFSESLCKELQKK 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 245 FFDpKRYDLGKVGRYKLNKKLNLSVPENVRVLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVRIGL 324
Cdd:CHL00001 251 FFQ-QRCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLAL 329
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 325 NRLERIIRErmTICDITS----LTPNTLVNPKPIIASIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLNRDRAG 400
Cdd:CHL00001 330 NRLENAVRG--TICGAIRrkliPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTAS 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 401 FGVRDIHPSHYGRICPIETPEGPNAGLIGVLATHARINTYGFIEAPFFKVqdGQVYNHSQPIYLTADQEDKYRIAPGDiT 480
Cdd:CHL00001 408 FRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEI--SERSKEERMVYLSPSEDEYYMIAAGN-S 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 481 LDETNRIATK-IVPIKYRQEFTTTKPNQVDFIAVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPESPLVG 559
Cdd:CHL00001 485 LALNQGIQEEqVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVG 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 560 TGLEAQAARDSGMVVVSIEDGQVTFVSGDKICVTNKkGDEIAYYLQKYQRSNQDTCINQRPTVWLGEDVIEGQVIADGAA 639
Cdd:CHL00001 565 TGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGN-GDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAA 643
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 640 TEGGELALGQNILVAYLPWEGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNVGEAALRKLDEN 719
Cdd:CHL00001 644 TVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKN 723
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 720 GIIVIGSWVEAGDILIGKVTPK--GESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTREKGDELPTGa 797
Cdd:CHL00001 724 GIVMLGSWVETGDILVGKLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNPE- 802
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 798 niVIRVYIAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNK 877
Cdd:CHL00001 803 --TIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNR 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 878 RFKITPFDEMHGAEASRVLVNEKLNEAKIKTGENWLFDLRHPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHA 957
Cdd:CHL00001 881 HYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHA 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 958 RSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSDDMQGRNETLNAIVKGKPIPRP-GTPESFK 1036
Cdd:CHL00001 961 RSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKPeDAPESFR 1040
|
1050
....*....|....*...
gi 11467690 1037 VLMRELQSLGLDIGAYKI 1054
Cdd:CHL00001 1041 LLVRELRSLALELNHFLV 1058
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
14-1049 |
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: 1039.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 14 LVEIQRASFCWFLNEGLAEEIQSFSPIVNYTGNLELHLFGDQYTLRYPKHN---------INECKRRDTTYSVQIYVPAQ 84
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEeggvtrkltPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 85 LINRETGVIKEQEVFIGDLPLMTD------------------------RGTFIINGAERVIVNQIVRSPGIYYKSelDKQ 140
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 141 GRRTYS----SSLISNRGAWVKFETD-RNDLVWVRIDKTRKipahvflkamglsdtdiynglrhpeylkktfrfegnytt 215
Cdd:cd00653 159 GKRIYTktsiPSYSPYRGSWLEVKSDkKKDRIYVRIDLKRQ--------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 216 ETALIQMYNKLRpgepatvtggqqllysrffdpkrydlgkvgryklnkklnlsvpenvrvltpqDTLAAIDYLINLKFEI 295
Cdd:cd00653 200 EEALKYIGKRFE----------------------------------------------------DLIYMIRKLILLVLGK 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 296 GETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRERMTICDITS--LTPNTLVNPKPIIASIREFFGSSQ------- 366
Cdd:cd00653 228 GKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwgskrfl 307
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 367 -----LSQFMDQTNPLAELTHKRRISAlgpGGLNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLATHARINtyG 441
Cdd:cd00653 308 mqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--G 382
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 442 FIEAPFFKVQdgqvynhsqpiyltadqedkyriapgditldetnriatkivpikyrqeftttkpNQVDFIAVSPIQVISI 521
Cdd:cd00653 383 RIERPYRIVE------------------------------------------------------KEVTHIEISPSQILSV 408
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 522 ATSLIPFLEHDDANRALMGSNMQRQAVP----------------LLYPESPLVGTGLEAQAARDsgmvvvsiedgqvtfv 585
Cdd:cd00653 409 AASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG---------------- 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 586 sgdkicvtnkkgdeiayylqkyqrsnqdtcinqrptvwlgedviegqviadgaateggELALGQNILVAYLPWEGYNYED 665
Cdd:cd00653 473 ----------------------------------------------------------ELPLGQNAIVAVMSYSGYNFED 494
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 666 AFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITR-ELPNVGEAALRKLDENGIIVIGSWVEAGDILIGKVTPKGES 744
Cdd:cd00653 495 AIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGET 574
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 745 DQPPegkllraIFGEKARDVRDTSLRVPNGGRGRILDVRIFTREkgdeLPTGANIVIRVYIAQSRKIQVGDKMAGRHGNK 824
Cdd:cd00653 575 ESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQK 643
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 825 GIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFDEMHGAEASRVLVNEKLNea 904
Cdd:cd00653 644 GVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLN-- 721
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 905 kiktgenwlfdlrHPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQHGGQRLGE 984
Cdd:cd00653 722 -------------YYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGE 788
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11467690 985 MEVWALEAFGASYTLQELLTVKSDDMQGRNETLNAIV----------KGKPIPRPGTPESFKVLMRELQSLGLDI 1049
Cdd:cd00653 789 MERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDP 863
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
2-1067 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1011.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 2 FNTTFANRTLPDLVEIQRASFCWFL------NEGLAEEIQSFSPIVNYTGNLELHLFGDQYTlrYPKHNINECKRRDTTY 75
Cdd:PRK09603 15 FTKTPTDLEVPNLLLLQRDSYDSFLyskdgkESGIEKVFKSIFPIQDEHNRITLEYAGCEFG--KSKYTVREAMERGITY 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 76 SVQIYVPAQLI----NRETGV------IKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELDK--QGRR 143
Cdd:PRK09603 93 SIPLKIKVRLIlwekDTKSGEkngikdIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESStsLNKL 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 144 TYSSSLISNRGAWVKFETDRNDLVWVRIDKTRKIPAHVFLKAMGLSDTDIY----------------------------- 194
Cdd:PRK09603 173 IYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIkmfyplvkvryendkylipfasldanqrm 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 195 -----------------------------NGLRHPEY------------------------------------------- 202
Cdd:PRK09603 253 efdlkdpqgkiillagkkltsrkikelkeNHLEWVEYpmdillnrhlaepvmvgkevlldmltqldknklekihdlgvqe 332
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 203 ----------------------------LKKTFRFEGNytTETALIQMYNKLRPGEPATVTGGQQLLYSRFFDPKRYDLG 254
Cdd:PRK09603 333 fviindlalghdasiihsfsadseslklLKQTEKIDDE--NALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLT 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 255 KVGRYKLNKKLNLSVPENVRVLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRER 334
Cdd:PRK09603 411 MVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDK 490
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 335 MTICDIT--SLTPNTLVNPKPIIASIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLNRDRAGFGVRDIHPSHYG 412
Cdd:PRK09603 491 LTTMSGAfdSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYG 570
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 413 RICPIETPEGPNAGLIGVLATHARINTYGFIEAPFFKVQDGQVYNhsQPIYLTADQEDKYRIAPGDITLDETNRIATKIV 492
Cdd:PRK09603 571 RICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVG--ETIYLTAIQEDSHIIAPASTPIDEEGNILGDLI 648
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 493 PIKYRQEFTTTKPNQVDFIAVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPESPLVGTGLEAQAARDSGM 572
Cdd:PRK09603 649 ETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWG 728
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 573 VVVSIEDGQVTFVSGDKICV--TNKKGDEI-AYYLQKYQRSNQDTCINQRPTVWLGEDVIEGQVIADGAATEGGELALGQ 649
Cdd:PRK09603 729 AIKANRAGVVEKIDSKNIYIlgEGKEEAYIdAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGK 808
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 650 NILVAYLPWEGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNVGEAALRKLDENGIIVIGSWVE 729
Cdd:PRK09603 809 NVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVS 888
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 730 AGDILIGKVTPKGESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTR---------------------- 787
Cdd:PRK09603 889 AGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKkgyekdarvlsayeeekakldm 968
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 --------------------------------------------------------------------------------
Cdd:PRK09603 969 ehfdrltmlnreellrvssllsqaileepfshngkdykegdqipkeeiasinrftlaslvkkyskevqnhyeitknnfle 1048
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 788 ----------------EKGDELPTGANIVIRVYIAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNP 851
Cdd:PRK09603 1049 qkkvlgeeheeklsilEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNP 1128
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 852 LGVPSRMNVGQIFECLLGLAAENLNK-----------------RFKITPFDEMHGAEASRV--LVNEKLNEAKIKTGENW 912
Cdd:PRK09603 1129 LGVPSRMNIGQILEMHLGLVGKEFGKqiasmledktkdfakelRAKMLEIANAINEKDPLTihALENCSDEELLEYAKDW 1208
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 913 ---------------------LFDLRH---PGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQ 968
Cdd:PRK09603 1209 skgvkmaipvfegisqekfykLFELAKiamDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTH 1288
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 969 QPLGGRAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSDDMQGRNETLNAIVKGKPIPRPGTPESFKVLMRELQSLGLD 1048
Cdd:PRK09603 1289 QPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALD 1368
|
1370
....*....|....*....
gi 11467690 1049 IGAYKIENLPDGQTRGIEV 1067
Cdd:PRK09603 1369 INIFGDDVDEDGAPKPIVI 1387
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
10-1049 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 934.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 10 TLPDLVEIQRASFCWFL-----NEGLAEEIQSFSPIvnytgNLELHLFGDQYT---LRYPKHNINECKRRDTTYSVQIYV 81
Cdd:PRK14844 28 SLLDLVKVQKESYDSFTpknkgNERLEVIFHTIFPI-----NDPLHRATIEFIscrVDDPKYDESECIKRGITFSAQVIA 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 82 PAQLINRETGV-----------------------IKEQEVFIGDLPLMTDRGTFIINGAERVIVNQIVRSPGIYYKSELD 138
Cdd:PRK14844 103 SIRLVIMQDGIsldeyksikesgdhsklatviksIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKG 182
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 139 K---QGRRTYSSSLISNRGAWVKFETDRNDLVWVRIDKTRKIPAHVFLKAMGLSDTDI---------------------- 193
Cdd:PRK14844 183 KtynSGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDIldrfyekikyikhkdgwkvpfv 262
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 194 ---YNGLRHP--------------------------------EYL----------------------------------- 203
Cdd:PRK14844 263 pdkFKGVRLPfdlmdvegnvllkanvritsrlakklydnelkEYLvpfdsicglflaedlidsasstkilsagesikled 342
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 204 -KK-------------------------TFRFEGNYTTETALIQMYNKLRPGEPATVTGGQQLLYSRFFDPKRYDLGKVG 257
Cdd:PRK14844 343 iKKlellsideisvlnidnlsvgpyilnTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIG 422
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 258 RYKLNKKLNLSVPENVRVLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRERMTI 337
Cdd:PRK14844 423 RLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMST 502
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 338 CDITSLTPNTLVNPKPIIASIREFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLNRDRAGFGVRDIHPSHYGRICPI 417
Cdd:PRK14844 503 SSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPI 582
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 418 ETPEGPNAGLIGVLATHARINTYGFIEAPFFKVQDGQVYNHSQpiYLTADQEDKYRIAPGDITLDETNRIATKIVPIKYR 497
Cdd:PRK14844 583 ETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIE--YLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYA 660
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 498 QEFTTTKPNQVDFIAVSPIQVISIATSLIPFLEHDDANRALMGSNMQRQAVPLLYPESPLVGTGLEAQAARDSGMVVVSI 577
Cdd:PRK14844 661 GSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAK 740
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 578 EDGQVTFVSGDKICV-------TNKKGDEIaYYLQKYQRSNQDTCINQRPTVWLGEDVIEGQVIADGAATEGGELALGQN 650
Cdd:PRK14844 741 RDGIVDSSDSNSIVIrafdkerVNYLDVDI-YHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQN 819
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 651 ILVAYLPWEGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSEEITRELPNVGEAALRKLDENGIIVIGSWVEA 730
Cdd:PRK14844 820 LLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGP 899
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 731 GDILIGKVTPKGESDQPPEGKLLRAIFGEKARDVRDTSLRVPNGGRGRILDVRIFTR----------------------- 787
Cdd:PRK14844 900 GYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRrgveenerallikqkeindfeke 979
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 788 ------------------------------------------------------------------------------EK 789
Cdd:PRK14844 980 rdyiinvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklHE 1059
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 790 GDELPTGANIVIRVYIAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLG 869
Cdd:PRK14844 1060 GYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVG 1139
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 870 LAAENLNKR----------------------------------FKITPFDEMHGAEASRVLVN----EKLNEAKIKTGEN 911
Cdd:PRK14844 1140 WACKKLGEKvgnildeinkiksafckgirslnddnftkfaaayLDNKKIENIDDDEITASVLNtpnkNALNDELNELVEN 1219
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 912 WL-------FDLRH---------------------------------------------------------------PGK 921
Cdd:PRK14844 1220 YLnscksaySNLRNflievyscgsnvsicnnirdisdnnliefarklrdgipvaapvfegpkdeqiaklfelagldnSGQ 1299
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 922 ITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWALEAFGASYTLQE 1001
Cdd:PRK14844 1300 AVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQE 1379
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|....*...
gi 11467690 1002 LLTVKSDDMQGRNETLNAIVKGKPIPRPGTPESFKVLMRELQSLGLDI 1049
Cdd:PRK14844 1380 MLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNV 1427
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
523-976 |
1.43e-169 |
|
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: 502.83 E-value: 1.43e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 523 TSLIPFLEHDDANRALMGSNMQRQAVPLlypesplvgtgleaqaardsgmvvvsiedgqvtfvsgdkicvtnkkgdeiaY 602
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGI---------------------------------------------------Y 30
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 603 YLQKYQRSNQDT---CINQRPTVWLGedVIEgqviadgaATEGGELALGQNILVAYLPWEGYNYEDAFLINERLVYNDVY 679
Cdd:pfam00562 31 TLNKFYRSDQNTyvlCYPQKPLVKTG--AVE--------AGGFGELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFF 100
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 680 TSVHIEkyEIEARQTKLG-SEEITRELPNVGEAALRKLDENGIIVIGSWVEAGDILIGKVTPkgesdqPPEGKLLRAIFG 758
Cdd:pfam00562 101 TSIHIK--EIEARKTKLGpIEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGP------TELTKLLRAIFG 172
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 759 EKARDVRDTSLRVPNGGRGRILDVRIFTrekgdeLPTGANIVIRVYIAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPY 838
Cdd:pfam00562 173 EKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPF 246
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 839 LPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFDemhGAEASRVLVNEKLNEAKiktgenwlfdLRH 918
Cdd:pfam00562 247 TEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAG----------YNY 313
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*...
gi 11467690 919 PGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQ 976
Cdd:pfam00562 314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
14-1048 |
2.23e-118 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 392.01 E-value: 2.23e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 14 LVEIQRASFCWFLNEGLAEEIQSFSPIVNYTGNLELhLFGDqytLRYPKHNI------------NECKRRDTTYSVQIYV 81
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKI-VLGK---IRVGEPEIkeadgserpitpMEARLRNLTYAAPLYL 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 82 PAQLINrETGVIKEQEVFIGDLPLM------------TDR------------GTFIINGAERVIVNQIVRSPG--IYYKS 135
Cdd:PRK08565 90 TMIPVE-NGIEYEPEEVKIGDLPIMvkskicplsglsPDElieigedpkdpgGYFIINGSERVIVSQEDLAPNrvLVDKG 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 136 EldKQGRRTYSSSLISNRG---AWVKFETDRNDLVWVRIDKTR-KIPAHVFLKAMGL-SDTDIYNGLR-HPEYLKKTF-R 208
Cdd:PRK08565 169 E--AGSSITHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAVPgKIPFVILMRALGLeTDRDIVYAVSlDPEIQQELLpS 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 209 FEG----NYTTETALIQMYNKLRPGEPATV--TGGQQLLYSRFFdPKrydLGKVGRYKLNKKLNLSvpenvrvltpqdtl 282
Cdd:PRK08565 247 LEQassiAATVEDALDYIGKRVAIGQPREYriERAEQILDKYLL-PH---LGTSPEDRIKKAYFLG-------------- 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 283 AAIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRERM--TICDITSLTPNTLVNPKPIIASIRE 360
Cdd:PRK08565 309 QMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLekSYARGRKLDLRAIVRPDIITERIRH 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 361 FF-------GSSQLSQFMDQTNPLAELTHKRRIsaLGPggLNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLAT 433
Cdd:PRK08565 389 ALatgnwvgGRTGVSQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLAL 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 434 HARINT-----------YGFIEAPFFKVQD------GQVY-N------HSQPIYLTADQEDKYRiaPGDITlDETN---- 485
Cdd:PRK08565 465 MAQISVgvdeeeveeilYELGVVPVEEAREeeyiswSRVYlNgrligyHPDGEELAEKIRELRR--SGKIS-DEVNvayi 541
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 486 ---------------RIATKIVPIKY--------------RQEFTTT---KPNQVDF----------IAVSPIQVIS--- 520
Cdd:PRK08565 542 etgeinevyvncdsgRVRRPLIVVENgkpkltrehveklkKGELTFDdlvKMGVIEYldaeeeenayVALDPEDLTPeht 621
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 521 -----------IATSLIPFLEHDDANRALMGSNMQRQAVP----------------LLYPESPLVGT-GLEAqaardsgm 572
Cdd:PRK08565 622 hleiwppailgITASIIPYPEHNQSPRNTYQAAMAKQSLGlyaanfrirtdtrghlLHYPQRPLVQTrALEI-------- 693
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 573 vvvsiedgqvtfvsgdkicvtnkkgdeIAYylqkyqrsnqdtciNQRPTvwlgedviegqviadgaateggelalGQNIL 652
Cdd:PRK08565 694 ---------------------------IGY--------------NDRPA--------------------------GQNAV 706
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 653 VAYLPWEGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSE-EITRELPNV----GEAALRKLDENGIIVIGSW 727
Cdd:PRK08565 707 VAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEdKIEIPEPNVrgyrGEEYYRKLDEDGIVSPEVE 786
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 728 VEAGDILIGKVTPkgesdqP---PEGKLLRAIFGEKardvRDTSLRVPNGGRGRILDVRIFTREKGDELptganivIRVY 804
Cdd:PRK08565 787 VKGGDVLIGKTSP------PrflEELEELSLGLQER----RDTSVTVRHGEKGIVDTVLITESPEGNKL-------VKVR 849
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 805 IAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPF 884
Cdd:PRK08565 850 VRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF 929
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 885 DEMHgaeasrvlvNEKLNEAKIKTGenwlfdLRHPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYS 964
Cdd:PRK08565 930 YGEP---------EEELRKELLKLG------YKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQ 994
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 965 LVTQQPLGGRAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSD-------DMQGRNETLNAIvKGKPI-PRPG------ 1030
Cdd:PRK08565 995 ILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDkttiyvcELCGHIAWYDRR-KNKYVcPIHGdkgnis 1073
|
1210 1220
....*....|....*....|.
gi 11467690 1031 ---TPESFKVLMRELQSLGLD 1048
Cdd:PRK08565 1074 pveVSYAFKLLLQELMSMGIS 1094
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
515-1048 |
2.15e-77 |
|
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: 266.51 E-value: 2.15e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 515 PIQVISIATSLIPFLEHDDANRALMGSNMQRQA--VP--------------LLYPESPLVGTgleaqaardsgmvvvsie 578
Cdd:TIGR03670 123 PSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSlgLYaanyrirldtrghlLHYPQKPLVKT------------------ 184
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 579 dgqvtfvsgdkicvtnKKGDEIAYylqkyqrsnqdtciNQRPTvwlgedviegqviadgaateggelalGQNILVAYLPW 658
Cdd:TIGR03670 185 ----------------RVLELIGY--------------DDRPA--------------------------GQNFVVAVMSY 208
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 659 EGYNYEDAFLINERLVYNDVYTSVHIEKYEIEARQTKLGSE-EITRELPNV----GEAALRKLDENGIIVIGSWVEAGDI 733
Cdd:TIGR03670 209 EGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDV 288
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 734 LIGKVTPkgesdqpPEGKLLRAIFGEKARDVRDTSLRVPNGGRGrILDVRIFTrekgdELPTGANIViRVYIAQSRKIQV 813
Cdd:TIGR03670 289 LIGKTSP-------PRFLEELREFGLVTERRRDTSVTVRHGEKG-IVDKVIIT-----ETEEGNKLV-KVRVRDLRIPEL 354
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 814 GDKMAGRHGNKGIISRILPRQDMPYLPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFDEMHgaeas 893
Cdd:TIGR03670 355 GDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEP----- 429
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 894 rvlvNEKLNEAKIKTGenwlfdLRHPGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQQPLGG 973
Cdd:TIGR03670 430 ----EEELRKELLKLG------FKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEG 499
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 974 RAQHGGQRLGEMEVWALEAFGASYTLQELLTVKSD-------DMQGRNETLNAIvKGKPI-PRPG---------TPESFK 1036
Cdd:TIGR03670 500 RAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDkyvvyvcENCGHIAWEDKR-KGTAYcPVCGetgdispveMSYAFK 578
|
570
....*....|..
gi 11467690 1037 VLMRELQSLGLD 1048
Cdd:TIGR03670 579 LLLDELKSLGIS 590
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
463-1048 |
8.17e-69 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 242.56 E-value: 8.17e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 463 YLTADQEDKYRIA--PGDITLDETNriatkivpikyrqeftttkpnqvdfIAVSPIQVISIATSLIPFLEHDDANRALMG 540
Cdd:PRK07225 100 YLDAEEEENAYIAvyEEDLTEEHTH-------------------------LEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 541 SNMQRQA--VP--------------LLYPESPLVGTgleaqaardsgmvvvsiedgQVTfvsgdkicvtnkkgDEIAYyl 604
Cdd:PRK07225 155 AGMIKQSlgLPaanyklrpdtrghlLHYPQVPLVKT--------------------QTQ--------------EIIGF-- 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 605 qkyqrsnqdtciNQRPTvwlgedviegqviadgaateggelalGQNILVAYLPWEGYNYEDAFLINERLVYNDVYTSVHI 684
Cdd:PRK07225 199 ------------DERPA--------------------------GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFF 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 685 EKYEIEARQTKLGSE-EITRELPNV----GEAALRKLDENGIIVIGSWVEAGDILIGKVTPKGESDQPPEgkllraiFGE 759
Cdd:PRK07225 241 RTYEGEERRYPGGQEdRFEIPDKDVrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLEEPDD-------FGI 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 760 KARDVRDTSLRVPNGGRGrILDVRIFTR-EKGDELptganivIRVYIAQSRKIQVGDKMAGRHGNKGIISRILPRQDMPY 838
Cdd:PRK07225 314 SPEKRRETSVTMRSGEEG-IVDTVILTEtEEGSRL-------VKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPF 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 839 LPDGTPVDLVLNPLGVPSRMNVGQIFECLLGLAAENLNKRFKITPFdemHGAEasrvlvNEKLNEAKIKTGenwlfdLRH 918
Cdd:PRK07225 386 TESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAF---SGED------EEDLREALEKLG------FEH 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 919 PGKITLYDGRTGEAFDNPVTIGVSYMLKLVHLVDDKIHARSTGPYSLVTQQPLGGRAQHGGQRLGEMEVWALEAFGASYT 998
Cdd:PRK07225 451 TGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAML 530
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11467690 999 LQELLTVKSDDMQ-------GRNETLNAIVKGKPIPRPGTPES---------FKVLMRELQSLGLD 1048
Cdd:PRK07225 531 LKERLLDESDKVEiyvcakcGMIAIYDKKRNRKYCPICGEETDiypvemsyaFKLLLDELKSLGIA 596
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
127-310 |
2.33e-57 |
|
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: 196.03 E-value: 2.33e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 127 RSPGIYYKSELDKQGR-RTYSSSLISNRGAWVKFETDRNDLVWVRIDKTRKIPAHVFLKAMGL-SDTDIYNGLRH----- 199
Cdd:pfam04561 1 RSNGIYVEKELDKNGIiATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLvSDREILDRLCYdfndp 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 200 ---PEYLKKTFRFEGNYTTETALIQMYN--KLRPGEPATVTGGQQLLYSRFfdpkrydlgkvGRYKLNKKLNLSVPENVR 274
Cdd:pfam04561 81 qmlELLKPELEEAENIYTQEEALDYIGKgfALRRGEEPRLQRAREILYSRD-----------PKYNLNKHLGLNEPFENE 149
|
170 180 190
....*....|....*....|....*....|....*.
gi 11467690 275 VLTPQDTLAAIDYLINLKFEIGETDDIDHLGNRRVR 310
Cdd:pfam04561 150 RLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
14-354 |
1.69e-38 |
|
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: 148.68 E-value: 1.69e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 14 LVEIQRASFCWFLNEGLAEEI------QSFSPIVNYTGNLE-LHLFGDQYTLRYPKHN----------INECKRRDTTYS 76
Cdd:pfam04563 2 LVRQQLDSFNEFVDNDLQKIIdenaliESEFEIQHPGENGDkLSLKFGQIRLGKPMFDetdgstreiyPQECRLRNLTYS 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 77 VQIYVPAQLINRETGVIKEQEVFIGDLPLMTD------------------------RGTFIINGAERVIVNQIVRS---P 129
Cdd:pfam04563 82 APLYVDLELSVYNGEDIKPIEVFIGRLPIMLRsnacilsgateselvklgecpldpGGYFIINGSEKVIVAQEHRSrnhP 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 130 GIYYKSEldkQGRRTYSSSLISN--------RGAWVKF-ETDRNDLVWVRIDKTRK-IPAHVFLKAMG-LSDTDIYNGL- 197
Cdd:pfam04563 162 IVFKKAD---PKKRGSVASVRSSaeisvrpdSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGfTSDREIFELIc 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 198 ---RHPEY-------LKKTFRfEGNYTTETALiqmynklrpgepatvtggqQLLYSRFFDPKRYDLGKVGRYKLNKKL-- 265
Cdd:pfam04563 239 ydvNDQQLqeellpsLEEGFK-IRIQTQEQAL-------------------DYIGGRGRAIFRMGRPREPRIKYAEEIlq 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 266 -NLSVPENVRVLTPQDTLAAIDYLINLKFEI----GETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIRERMTIC-- 338
Cdd:pfam04563 299 kEVLPHLGTYELDETKKAYFIGYMIRRLLLLalgrREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVlg 378
|
410
....*....|....*.
gi 11467690 339 DITSLTPNTLVNPKPI 354
Cdd:pfam04563 379 SPDDLMLQLLVNAKPI 394
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
13-439 |
2.84e-35 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 141.24 E-value: 2.84e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 13 DLVEIQRASFCWFLNEGLAEEIQSFSPIVNYTGNLELHLFGD-------------QYTLRYPkhniNECKRRDTTYSVQI 79
Cdd:PRK09606 17 RLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKirvgkpvvkeadgSEREIYP----MEARLRNLTYSAPL 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 80 YVPAQLInrETGVIKEQ-EVFIGDLPLM-----------TDR-------------GTFIINGAERVIVNQIVRSPGIYYK 134
Cdd:PRK09606 93 YLEMSPV--EGGEEEEPeEVYIGELPVMvgskicnlyglSEEelievgedpldpgGYFIVNGSERVLMTLEDLAPNKILV 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 135 SELDKQGRRTYSSSLISNRG---AWVKFETDRNDLVWVRIDK-TRKIPAHVFLKAMGL-SDTDIYNGL-RHPEYLKKTFR 208
Cdd:PRK09606 171 EKDERYGDRIEVAKVFSQRRgyrALVTVERNRDGLLEVSFPSvPGSIPFVILMRALGLeTDEEIVEAVsDDPEIVKFMLE 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 209 ---FEGNYTTETALIQMYNKLRPGEPatvtggqqllysrffdpKRYDLgKVGRYKLNKKL--NLSVPENVRVLTPQDTLA 283
Cdd:PRK09606 251 nleEAEVDTQEEALEYIGKRVAPGQT-----------------KEYRI-KRAEYVIDRYLlpHLGVEPEVRRAKAHYLGR 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 284 AIDYLINLKFEIGETDDIDHLGNRRVRSVGELLQNQVRIGLNRLERIIR---ERMTICDiTSLTPNTLVNPKPIIASIRE 360
Cdd:PRK09606 313 MAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKyqlERANMRN-RELSIKTAVRSDVLTERLEH 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 361 FF-------GSSQLSQFMDQTNPLAELTHKRRISAlgPggLNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLAT 433
Cdd:PRK09606 392 AMatgnwvgGRTGVSQLLDRTDYMATLSHLRRVVS--P--LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQ 467
|
....*.
gi 11467690 434 HARINT 439
Cdd:PRK09606 468 MVEIST 473
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
369-436 |
2.63e-34 |
|
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: 125.33 E-value: 2.63e-34
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11467690 369 QFMDQTNPLAELTHKRRISAlGPGGLNRDRAGFGVRDIHPSHYGRICPIETPEGPNAGLIGVLATHAR 436
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
978-1049 |
1.08e-31 |
|
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: 118.84 E-value: 1.08e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11467690 978 GGQRLGEMEVWALEAFGASYTLQELLTVKSD----DMQGRNETLNA-----IVKGKPIPRPGT-PESFKVLMRELQSLGL 1047
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGYiPESFKLLFQELQSLGI 80
|
..
gi 11467690 1048 DI 1049
Cdd:pfam04560 81 DP 82
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
447-514 |
1.61e-20 |
|
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.
Pssm-ID: 463067 [Multi-domain] Cd Length: 66 Bit Score: 86.27 E-value: 1.61e-20
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11467690 447 FFKVQDGQVYNhsQPIYLTADQEDKYRIAPGDITLDETNRIATKIVPIKYRQEFTTTKPNQVDFIAVS 514
Cdd:pfam10385 1 YRKVEDGKVTD--EIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| |
