|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
31-1216 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1273.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 31 WAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEdstlileqlaqhTTESDNISRKYEISFGKIYVTKPMVNESDGVTH 110
Cdd:PRK08565 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE------------FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSER 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 111 ALYPQEARLRNLTYSSGLFVDVKkrtyeaIDVPGRELKYEliaeeseddsesgKVFIGRLPIMLRSKNCYLSEATESDLY 190
Cdd:PRK08565 70 PITPMEARLRNLTYAAPLYLTMI------PVENGIEYEPE-------------EVKIGDLPIMVKSKICPLSGLSPDELI 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 191 KLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSAlEKGSRfiSTLQVKlYGREGssarTIK 270
Cdd:PRK08565 131 EIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISS-RAGYR--AQVTVE-RRKDG----TIY 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 271 ATLPYIKQDIPIVIIFRALGIIPDGEILEHIcydVNDWQMLEMLKPCVEDGF-VIQDRETALDFIGRRgTALGIKKEKRI 349
Cdd:PRK08565 203 VSFPAVPGKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRI 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 350 QYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIF 429
Cdd:PRK08565 279 ERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLK 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 430 RYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGeqkkamSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLA 509
Cdd:PRK08565 359 YQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHF 432
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 510 KPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGV 589
Cdd:PRK08565 433 EARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGY 512
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 590 HRNPARLMETLRTLRRKGDINPEVSM--IRDIREKELKIFTDAGRVYRPLFIVEDDEslghkeLKVRKGHIAKLmateyq 667
Cdd:PRK08565 513 HPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGK------PKLTREHVEKL------ 580
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 668 dieggfeDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPaeaneendldvdpakrirvSHhattfTHCEIHPSM 747
Cdd:PRK08565 581 -------KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTP-------------------EH-----THLEIWPPA 629
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 748 ILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAI 827
Cdd:PRK08565 630 ILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAV 709
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 828 ACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPqrTNTLRMKHG--TYDKLDDDGLIAPGVRV 905
Cdd:PRK08565 710 LSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEV 787
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 906 SGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHG 985
Cdd:PRK08565 788 KGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHG 867
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 986 QKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQ 1065
Cdd:PRK08565 868 QKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYK 947
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1066 SRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAS 1145
Cdd:PRK08565 948 PDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAM 1027
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 343781198 1146 FLKERLMEASDAFRVHICGICGLMTVIAKlNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRL 1216
Cdd:PRK08565 1028 LLKERLLDSSDKTTIYVCELCGHIAWYDR-RKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRL 1097
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
43-1217 |
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: 1173.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 43 LVSQQLDSFNQFVDYTLQDIICEDSTLileqlaqhttESDNISRKYEISFGKIYVTKPMVNEsDGVTHALYPQEARLRNL 122
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPI----------TDTDDDGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 123 TYSSGLFVDVKKRTYEaidvpgrelkyeliaeesEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGY 202
Cdd:cd00653 70 TYSAPLYVDIRLTVND------------------KGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGY 131
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 203 FIINGSEKVLIAQERSAGNIVQVFkkaaPSPISHVAEIRSALEKGSRFISTLQVKLYGREGssarTIKATLPYIKQdipi 282
Cdd:cd00653 132 FIINGTEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKKD----RIYVRIDLKRQ---- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 283 viifralgiipdgeilehicydvndwqmlemlkpcvedgfviqdrETALDFIGRRGtalgikkekriqyakdilqkeflp 362
Cdd:cd00653 200 ---------------------------------------------EEALKYIGKRF------------------------ 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 363 hitqlegfesrkaFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDF 442
Cdd:cd00653 211 -------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL 277
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 443 NMKLAINAKTITSGLKYALATGNWGeQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGL 521
Cdd:cd00653 278 TPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGR 356
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 522 VCPAETPEGQACGLVKNLSLMSCISvgtdpmpiitflsewgmepledyvphqspdatrvfvngvwhgvhrnparlmetlr 601
Cdd:cd00653 357 ICPIETPEGENCGLVKNLALMARIS------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 602 tlrrkgdinpevsmirdirekelkiftdaGRVYRPLFIVEDDeslghkelkvrkghiaklmateyqdieggfedveeytw 681
Cdd:cd00653 382 -----------------------------GRIERPYRIVEKE-------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 682 ssllneglveyidaeeeesiliamqpedlepaeaneendldvdpakrirvshhattFTHCEIHPSMILGVAASIIPFPDH 761
Cdd:cd00653 395 --------------------------------------------------------VTHIEISPSQILSVAASLIPFPEH 418
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 762 NQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIM 841
Cdd:cd00653 419 NQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIII 498
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 842 NQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFekpqRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPD 921
Cdd:cd00653 499 NKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGET 574
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 922 EEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTT---NQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRRED 998
Cdd:cd00653 575 ESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQED 654
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 999 MPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTG 1078
Cdd:cd00653 655 MPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTG 734
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1079 KKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAF 1158
Cdd:cd00653 735 EPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDV 814
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*....
gi 343781198 1159 RVHICGICGLMTVIaklnhnqFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLY 1217
Cdd:cd00653 815 VARVCVKCGIILSA-------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
580-1216 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 774.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 580 VFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDEslghkeLKVRKGHIA 659
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGK------PKLTREHVE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 660 KLMateyqdiEGgfedveEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPaeaneendldvdpakrirvSHhattfT 739
Cdd:TIGR03670 75 KLK-------EG------ELTWDDLVKQGVIEYLDAEEEENAYIALDPEELTP-------------------EH-----T 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 740 HCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPA 819
Cdd:TIGR03670 118 HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPA 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 820 GQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPqrTNTLRMKHG--TYDKLDDDG 897
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGeeAYKHLDEDG 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 898 LIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIG 977
Cdd:TIGR03670 276 IVYPEVEVKGGDVLIGKTSPPRFLEELREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELG 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 978 DKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISK 1057
Cdd:TIGR03670 356 DKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRK 435
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1058 LLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDC 1137
Cdd:TIGR03670 436 ELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDV 515
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 343781198 1138 MIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKlNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRL 1216
Cdd:TIGR03670 516 LIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDK-RKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
30-1217 |
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: 725.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 30 SWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDStlileqlaqhttESDNISRKYEISFGKIYVTKPMVnesdgvt 109
Cdd:COG0085 3 SFAKIKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEIS------------PIEDFTGNLSLEFGDYRLGEPKY------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 110 halYPQEARLRNLTYSSGLFVDVkkrtyeaidvpgrelkyELIAEESEDdSESGKVFIGRLPIMLRSkncylseatesdl 189
Cdd:COG0085 64 ---TPEECKERDLTYAAPLYVKV-----------------RLVNKETGE-IKEQEVFMGDFPLMTDS------------- 109
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 190 yklkecpfdmgGYFIINGSEKVLIAQE-RSAGNIVqVFKKAAPSPISHVAEIRSA------LEKGSRfiSTLQVKLYGre 262
Cdd:COG0085 110 -----------GTFIINGTERVIVSQLvRSPGVYF-VEEEDKSGKDLYSAKVIPSrgawleFETDKD--GTIYVRIDR-- 173
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 263 gssartikatlpyiKQDIPIVIIFRALGIIPDGEILEHIcydvNDWQMLEMLKPCVEDGfVIQDRETALDFIGRRgtaLG 342
Cdd:COG0085 174 --------------KRKIPVTVLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRK---LR 231
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 343 IKKEKRIQYAKDILQKEF-------LPHI---------TQLEGFESR--KAFFLGYMINRLLLCALDRKDQDDRDHFGKK 404
Cdd:COG0085 232 PGEPPTIERAEQLLDNLFfdpkrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNR 311
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 405 RLDLAGPLLAQLFKTLFKKLTKDIfRYmQRTVEEAHDFNMKLAINAKTITSGLKYALATGnwgeqkkamssraGVSQVLN 484
Cdd:COG0085 312 RVRLVGELLQNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMD 376
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 485 RYTYSSTLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMscisvgtdpmpiit 556
Cdd:COG0085 377 QTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALY-------------- 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 557 flsewgmepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkGDINPEvsmirdirekelkiftdaGRVYRP 636
Cdd:COG0085 439 --------------------------------------------------ARVNEY------------------GFIETP 450
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 637 LFIVEDdeslGhkelKVRKGhiaklmateyqdieggfedveeytwssllneglVEYIDAEEEESILIAMQPEDLePAEAN 716
Cdd:COG0085 451 YRKVEN----G----KVTDE---------------------------------IEYLTADEEENYYIAQANAPL-DEDGN 488
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 717 EENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNynvrmdtmANIL 796
Cdd:COG0085 489 FLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLL 560
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 797 YYP--------------QKPLgtTRAMEYLK------------FRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGL 850
Cdd:COG0085 561 HYPlqkfqrsnqgtcinQRPI--VRVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 851 FRSLFFRSYMDQEKKY--GMSITeTFEKPqrtntlrmKHG--TYDKLDDDGLIAPGVRVSGEDVIIGKTTP-----ISPD 921
Cdd:COG0085 639 LTSIHIEEYEIEARDTklGPEEI-TRDIP--------NVSeeALRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteLTPE 709
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 922 EEELgqRTAYHSK----RDASTPLRSTENGIVDQVLVTTNQDG-------LKFVKVRVRTTKIPQIGDKFASRHGQKGTI 990
Cdd:COG0085 710 ERLL--RAIFGEKarevRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVI 787
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 991 GITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFE 1070
Cdd:COG0085 788 SRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1071 VMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKER 1150
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1151 LMEASDafrvhicGICGLMTV---IAKlnhnqfeckgcdnKIDIYQIHIPYAAKLLFQELMAMNITPRLY 1217
Cdd:COG0085 948 LTIKSD-------DVCGRVKVyeaIVK-------------GENIPEPGIPESFKVLLKELQSLGLDVEVL 997
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
42-455 |
0e+00 |
|
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: 555.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 42 GLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNisrKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRN 121
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGD---KLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 122 LTYSSGLFVDVKKRTYeaidvpgrelkyeliaeeSEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGG 201
Cdd:pfam04563 78 LTYSAPLYVDLELSVY------------------NGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGG 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 202 YFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYgrEGSSARTIKATLPYIKQDIP 281
Cdd:pfam04563 140 YFIINGSEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVL--EYLSNGTIYFKFPYIKKEIP 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 282 IVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVI--QDRETALDFIGRRGTA---LGIKKEKRIQYAKDIL 356
Cdd:pfam04563 218 IVIILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEIL 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 357 QKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTV 436
Cdd:pfam04563 298 QKEVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVL 377
|
410
....*....|....*....
gi 343781198 437 EEAHDFNMKLAINAKTITS 455
Cdd:pfam04563 378 GSPDDLMLQLLVNAKPITS 396
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
31-1216 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1273.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 31 WAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEdstlileqlaqhTTESDNISRKYEISFGKIYVTKPMVNESDGVTH 110
Cdd:PRK08565 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE------------FGEIKTEIPGLKIVLGKIRVGEPEIKEADGSER 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 111 ALYPQEARLRNLTYSSGLFVDVKkrtyeaIDVPGRELKYEliaeeseddsesgKVFIGRLPIMLRSKNCYLSEATESDLY 190
Cdd:PRK08565 70 PITPMEARLRNLTYAAPLYLTMI------PVENGIEYEPE-------------EVKIGDLPIMVKSKICPLSGLSPDELI 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 191 KLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSAlEKGSRfiSTLQVKlYGREGssarTIK 270
Cdd:PRK08565 131 EIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISS-RAGYR--AQVTVE-RRKDG----TIY 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 271 ATLPYIKQDIPIVIIFRALGIIPDGEILEHIcydVNDWQMLEMLKPCVEDGF-VIQDRETALDFIGRRgTALGIKKEKRI 349
Cdd:PRK08565 203 VSFPAVPGKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKR-VAIGQPREYRI 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 350 QYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIF 429
Cdd:PRK08565 279 ERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLK 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 430 RYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGeqkkamSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLA 509
Cdd:PRK08565 359 YQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHF 432
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 510 KPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGV 589
Cdd:PRK08565 433 EARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGY 512
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 590 HRNPARLMETLRTLRRKGDINPEVSM--IRDIREKELKIFTDAGRVYRPLFIVEDDEslghkeLKVRKGHIAKLmateyq 667
Cdd:PRK08565 513 HPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGK------PKLTREHVEKL------ 580
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 668 dieggfeDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPaeaneendldvdpakrirvSHhattfTHCEIHPSM 747
Cdd:PRK08565 581 -------KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTP-------------------EH-----THLEIWPPA 629
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 748 ILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAI 827
Cdd:PRK08565 630 ILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAV 709
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 828 ACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPqrTNTLRMKHG--TYDKLDDDGLIAPGVRV 905
Cdd:PRK08565 710 LSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRKLDEDGIVSPEVEV 787
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 906 SGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHG 985
Cdd:PRK08565 788 KGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHG 867
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 986 QKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQ 1065
Cdd:PRK08565 868 QKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKLGYK 947
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1066 SRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAS 1145
Cdd:PRK08565 948 PDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAM 1027
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 343781198 1146 FLKERLMEASDAFRVHICGICGLMTVIAKlNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRL 1216
Cdd:PRK08565 1028 LLKERLLDSSDKTTIYVCELCGHIAWYDR-RKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRL 1097
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
43-1217 |
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: 1173.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 43 LVSQQLDSFNQFVDYTLQDIICEDSTLileqlaqhttESDNISRKYEISFGKIYVTKPMVNEsDGVTHALYPQEARLRNL 122
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPI----------TDTDDDGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 123 TYSSGLFVDVKKRTYEaidvpgrelkyeliaeesEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGY 202
Cdd:cd00653 70 TYSAPLYVDIRLTVND------------------KGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGY 131
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 203 FIINGSEKVLIAQERSAGNIVQVFkkaaPSPISHVAEIRSALEKGSRFISTLQVKLYGREGssarTIKATLPYIKQdipi 282
Cdd:cd00653 132 FIINGTEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKKD----RIYVRIDLKRQ---- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 283 viifralgiipdgeilehicydvndwqmlemlkpcvedgfviqdrETALDFIGRRGtalgikkekriqyakdilqkeflp 362
Cdd:cd00653 200 ---------------------------------------------EEALKYIGKRF------------------------ 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 363 hitqlegfesrkaFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDF 442
Cdd:cd00653 211 -------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL 277
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 443 NMKLAINAKTITSGLKYALATGNWGeQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGL 521
Cdd:cd00653 278 TPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGR 356
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 522 VCPAETPEGQACGLVKNLSLMSCISvgtdpmpiitflsewgmepledyvphqspdatrvfvngvwhgvhrnparlmetlr 601
Cdd:cd00653 357 ICPIETPEGENCGLVKNLALMARIS------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 602 tlrrkgdinpevsmirdirekelkiftdaGRVYRPLFIVEDDeslghkelkvrkghiaklmateyqdieggfedveeytw 681
Cdd:cd00653 382 -----------------------------GRIERPYRIVEKE-------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 682 ssllneglveyidaeeeesiliamqpedlepaeaneendldvdpakrirvshhattFTHCEIHPSMILGVAASIIPFPDH 761
Cdd:cd00653 395 --------------------------------------------------------VTHIEISPSQILSVAASLIPFPEH 418
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 762 NQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIM 841
Cdd:cd00653 419 NQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIII 498
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 842 NQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFekpqRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPD 921
Cdd:cd00653 499 NKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGET 574
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 922 EEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTT---NQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRRED 998
Cdd:cd00653 575 ESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQED 654
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 999 MPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTG 1078
Cdd:cd00653 655 MPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTG 734
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1079 KKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAF 1158
Cdd:cd00653 735 EPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDV 814
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*....
gi 343781198 1159 RVHICGICGLMTVIaklnhnqFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLY 1217
Cdd:cd00653 815 VARVCVKCGIILSA-------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
580-1216 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 774.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 580 VFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDEslghkeLKVRKGHIA 659
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGK------PKLTREHVE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 660 KLMateyqdiEGgfedveEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPaeaneendldvdpakrirvSHhattfT 739
Cdd:TIGR03670 75 KLK-------EG------ELTWDDLVKQGVIEYLDAEEEENAYIALDPEELTP-------------------EH-----T 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 740 HCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPA 819
Cdd:TIGR03670 118 HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPA 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 820 GQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPqrTNTLRMKHG--TYDKLDDDG 897
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGeeAYKHLDEDG 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 898 LIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIG 977
Cdd:TIGR03670 276 IVYPEVEVKGGDVLIGKTSPPRFLEELREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELG 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 978 DKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISK 1057
Cdd:TIGR03670 356 DKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRK 435
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1058 LLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDC 1137
Cdd:TIGR03670 436 ELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDV 515
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 343781198 1138 MIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKlNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRL 1216
Cdd:TIGR03670 516 LIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWEDK-RKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
578-1216 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 742.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 578 TRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESlghkelKVRKGH 657
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEP------LLTEEH 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 658 IAKLmateyqdiEGGfedveEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAeaneendldvdpakrirvshHatt 737
Cdd:PRK07225 79 IEKL--------KNG-----ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE--------------------H--- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 738 fTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFREL 817
Cdd:PRK07225 123 -THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDER 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 818 PAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTntLRMKHG--TYDKLDD 895
Cdd:PRK07225 202 PAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKD--VRGYRGeeAYRHLDE 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 896 DGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQ 975
Cdd:PRK07225 280 DGLVNPETEVKEGDVLIGKTSPPRFLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPE 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 976 IGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGI 1055
Cdd:PRK07225 360 LGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDL 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1056 SKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMER 1135
Cdd:PRK07225 440 REALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMER 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1136 DCMIAHGAASFLKERLMEASDAFRVHICGICGlMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPR 1215
Cdd:PRK07225 520 DVLIGHGAAMLLKERLLDESDKVEIYVCAKCG-MIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPR 598
|
.
gi 343781198 1216 L 1216
Cdd:PRK07225 599 L 599
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
30-1217 |
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: 725.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 30 SWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDStlileqlaqhttESDNISRKYEISFGKIYVTKPMVnesdgvt 109
Cdd:COG0085 3 SFAKIKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEIS------------PIEDFTGNLSLEFGDYRLGEPKY------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 110 halYPQEARLRNLTYSSGLFVDVkkrtyeaidvpgrelkyELIAEESEDdSESGKVFIGRLPIMLRSkncylseatesdl 189
Cdd:COG0085 64 ---TPEECKERDLTYAAPLYVKV-----------------RLVNKETGE-IKEQEVFMGDFPLMTDS------------- 109
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 190 yklkecpfdmgGYFIINGSEKVLIAQE-RSAGNIVqVFKKAAPSPISHVAEIRSA------LEKGSRfiSTLQVKLYGre 262
Cdd:COG0085 110 -----------GTFIINGTERVIVSQLvRSPGVYF-VEEEDKSGKDLYSAKVIPSrgawleFETDKD--GTIYVRIDR-- 173
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 263 gssartikatlpyiKQDIPIVIIFRALGIIPDGEILEHIcydvNDWQMLEMLKPCVEDGfVIQDRETALDFIGRRgtaLG 342
Cdd:COG0085 174 --------------KRKIPVTVLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRK---LR 231
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 343 IKKEKRIQYAKDILQKEF-------LPHI---------TQLEGFESR--KAFFLGYMINRLLLCALDRKDQDDRDHFGKK 404
Cdd:COG0085 232 PGEPPTIERAEQLLDNLFfdpkrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNR 311
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 405 RLDLAGPLLAQLFKTLFKKLTKDIfRYmQRTVEEAHDFNMKLAINAKTITSGLKYALATGnwgeqkkamssraGVSQVLN 484
Cdd:COG0085 312 RVRLVGELLQNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMD 376
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 485 RYTYSSTLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMscisvgtdpmpiit 556
Cdd:COG0085 377 QTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALY-------------- 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 557 flsewgmepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkGDINPEvsmirdirekelkiftdaGRVYRP 636
Cdd:COG0085 439 --------------------------------------------------ARVNEY------------------GFIETP 450
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 637 LFIVEDdeslGhkelKVRKGhiaklmateyqdieggfedveeytwssllneglVEYIDAEEEESILIAMQPEDLePAEAN 716
Cdd:COG0085 451 YRKVEN----G----KVTDE---------------------------------IEYLTADEEENYYIAQANAPL-DEDGN 488
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 717 EENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNynvrmdtmANIL 796
Cdd:COG0085 489 FLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLL 560
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 797 YYP--------------QKPLgtTRAMEYLK------------FRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGL 850
Cdd:COG0085 561 HYPlqkfqrsnqgtcinQRPI--VRVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 851 FRSLFFRSYMDQEKKY--GMSITeTFEKPqrtntlrmKHG--TYDKLDDDGLIAPGVRVSGEDVIIGKTTP-----ISPD 921
Cdd:COG0085 639 LTSIHIEEYEIEARDTklGPEEI-TRDIP--------NVSeeALRNLDEDGIIRIGAEVKGGDILVGKVTPkgeteLTPE 709
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 922 EEELgqRTAYHSK----RDASTPLRSTENGIVDQVLVTTNQDG-------LKFVKVRVRTTKIPQIGDKFASRHGQKGTI 990
Cdd:COG0085 710 ERLL--RAIFGEKarevRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVI 787
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 991 GITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFE 1070
Cdd:COG0085 788 SRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1071 VMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKER 1150
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1151 LMEASDafrvhicGICGLMTV---IAKlnhnqfeckgcdnKIDIYQIHIPYAAKLLFQELMAMNITPRLY 1217
Cdd:COG0085 948 LTIKSD-------DVCGRVKVyeaIVK-------------GENIPEPGIPESFKVLLKELQSLGLDVEVL 997
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
42-455 |
0e+00 |
|
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: 555.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 42 GLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNisrKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRN 121
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGD---KLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 122 LTYSSGLFVDVKKRTYeaidvpgrelkyeliaeeSEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGG 201
Cdd:pfam04563 78 LTYSAPLYVDLELSVY------------------NGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGG 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 202 YFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYgrEGSSARTIKATLPYIKQDIP 281
Cdd:pfam04563 140 YFIINGSEKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVL--EYLSNGTIYFKFPYIKKEIP 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 282 IVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVI--QDRETALDFIGRRGTA---LGIKKEKRIQYAKDIL 356
Cdd:pfam04563 218 IVIILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEIL 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 357 QKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTV 436
Cdd:pfam04563 298 QKEVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVL 377
|
410
....*....|....*....
gi 343781198 437 EEAHDFNMKLAINAKTITS 455
Cdd:pfam04563 378 GSPDDLMLQLLVNAKPITS 396
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
753-1124 |
0e+00 |
|
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: 541.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 753 ASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSG 832
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYTG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 833 YNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMsITETFEKPqrtntLRMKHGTYDKLDDDGLIAPGVRVSGEDVII 912
Cdd:pfam00562 82 YNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGP-IEEITRDI-----PNVSEEALKKLDEDGIVRVGAEVKPGDILV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 913 GKTTPISPDEE--ELGQRTAYHsKRDASTPLRSTENGIVDQVLV-TTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGT 989
Cdd:pfam00562 156 GKVGPTELTKLlrAIFGEKARD-VKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 990 IGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFT--DITVEGISKLLREHGYQSR 1067
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 343781198 1068 GFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSR 1124
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
28-566 |
2.89e-128 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 402.79 E-value: 2.89e-128
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 28 EDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEdstlileqlaQHTTESDnISRKYEISFGKIYVTKPMVNESDG 107
Cdd:PRK09606 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDE----------QGPIETE-IEDGVYVELGKIRVGKPVVKEADG 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 108 VTHALYPQEARLRNLTYSSGLFVdvkkrtyeaidvpgrelkyELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATES 187
Cdd:PRK09606 72 SEREIYPMEARLRNLTYSAPLYL-------------------EMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEE 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 188 DLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSAlEKGSRFISTLQVKlygREGssar 267
Cdd:PRK09606 133 ELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKILVEKDERYGDRIEVAKVFSQ-RRGYRALVTVERN---RDG---- 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 268 TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNdwQMLEMLKPCVEDGfvIQDRETALDFIGRRGtALGIKKEK 347
Cdd:PRK09606 205 LLEVSFPSVPGSIPFVILMRALGLETDEEIVEAVSDDPE--IVKFMLENLEEAE--VDTQEEALEYIGKRV-APGQTKEY 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 348 RIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKD 427
Cdd:PRK09606 280 RIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARD 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 428 IFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWgeqkkaMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGK 507
Cdd:PRK09606 360 VKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQP 433
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*....
gi 343781198 508 LAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPL 566
Cdd:PRK09606 434 HFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
30-1156 |
1.42e-74 |
|
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: 269.61 E-value: 1.42e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 30 SWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL--ILEQLAQHTTESDNISRKY-EISFGKIYVTkpmvnesd 106
Cdd:TIGR02013 7 DFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLeeVFKSIFPIEDYTGNIELEYlSYRLGEPKYS-------- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 107 gvthalyPQEARLRNLTYSSGLFVDVKKRTYEAIDVpgrelkYELIAEEseddsesgkVFIGRLPIMlrskncylseaTE 186
Cdd:TIGR02013 79 -------VEECKERGLTYSAPLKVKLRLINKEEDGT------KEIKEQD---------VYMGDIPLM-----------TD 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 187 SdlyklkecpfdmgGYFIINGSEKVLIAQ-ERSAGnivQVFKKAAPSPIShvaeirsalekgsrfistlqvklyGREGSS 265
Cdd:TIGR02013 126 R-------------GTFIINGAERVVVSQlHRSPG---VFFSSEKDTTKS------------------------GKVLFS 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 266 ARTI------------KATLPYIKQD----IPIVIIFRALGIIPDGEILEHIcyDVNDWQMLEMLK-PCvedgfviQDRE 328
Cdd:TIGR02013 166 ARIIpyrgswlefetdKKDVLYVRIDrkrkLPATVLLRALGYTIDTLILNRL--GSGEYIRNTLRKdPT-------NSEE 236
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 329 TALDFIGRRgtaLGIKKEKRIQYAKDILQKEFLphitqlegfeSRKAFFLG----YMINRLLL-------CALDRKD--- 394
Cdd:TIGR02013 237 EALVEIYRK---LRPGEPPTVEAARSLLENLFF----------DPKRYDLGrvgrYKLNKKLGldvpesiGVLTKEDiia 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 395 --------------QDDRDHFGKKRLDLAGPLLAQLFKTLFKKltkdifryMQRTVEE---AHDFNmKLA----INAKTI 453
Cdd:TIGR02013 304 tikyliklrngkgeIDDIDHLGNRRIRSVGELLQNQFRVGLAR--------MERIVRErmsTQDTD-TLTpqdlINAKPI 374
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 454 TSGLKYALATGNwgeqkkamssragVSQVLNRYTYSSTLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGLVCPAETPE 529
Cdd:TIGR02013 375 SAAIKEFFGSSQ-------------LSQFMDQTNPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPE 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 530 GQACGLVKNLSlmscisvgtdpmpiiTFlsewgmepledyvphqspdaTRVfvngvwhgvhrNPARLMETlrtlrrkgdi 609
Cdd:TIGR02013 442 GPNIGLINSLS---------------TY--------------------ARV-----------NEYGFIET---------- 465
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 610 nPevsmirdirekelkiftdagrvYRplfiveddeslghkelKVRKGhiaklmateyqdiEGGFEDVeeytwssllnegl 689
Cdd:TIGR02013 466 -P----------------------YR----------------KVKDG-------------KVVVTDE------------- 480
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 690 VEYIDAEEEESILIAmqpedlePAEAN-EENDLDVDPAKRIRVSHHATTF-----THCEIHPSMILGVAASIIPFPDHNQ 763
Cdd:TIGR02013 481 IDYLTADEEDNYVIA-------QANAPlDENGRFVEDLVVARYRGEITLVspdqvDYMDVSPKQVVSVAASLIPFLEHDD 553
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 764 SPRNTYQSAMGKQAM-------------------------------GV---------FLTNYNVRMDTMANILYYP---- 799
Cdd:TIGR02013 554 ANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVveyvdakriVIRYDEDEEEPDGGIDIYRllky 633
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 800 ----------QKPL---------GTTRAMEYLKFR-ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSY 859
Cdd:TIGR02013 634 qrsnqdtcinQRPIvsvgdrveaGDVLADGPSTDLgELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEY 713
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 860 --MDQEKKYGMS-ITEtfEKPQrtntlrMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPIS----PDEEELgQRTAYH 932
Cdd:TIGR02013 714 evEARDTKLGPEeITR--DIPN------VSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGetelTPEEKL-LRAIFG 784
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 933 SK----RDASTPLRSTENGIVDQVLVTTNQDG-------LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPF 1001
Cdd:TIGR02013 785 EKardvRDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPF 864
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1002 TAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGD--ASP-FTDITVEGISKLLREHGYQSRGFEVMYNGHTG 1078
Cdd:TIGR02013 865 LEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTG 944
|
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 343781198 1079 KKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASD 1156
Cdd:TIGR02013 945 EQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
219-407 |
1.38e-55 |
|
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: 191.02 E-value: 1.38e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 219 AGNIVQVFKKAAPSPIShvaeirsaleKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEIL 298
Cdd:pfam04561 1 RSNGIYVEKELDKNGII----------ATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREIL 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 299 EHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGrRGTALGIKKEKRIQYAKDILQK-----EFLPHITQLEGFESR 373
Cdd:pfam04561 71 DRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIG-KGFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEPFENE 149
|
170 180 190
....*....|....*....|....*....|....*.
gi 343781198 374 --KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLD 407
Cdd:pfam04561 150 rlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
43-1156 |
9.72e-54 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 205.72 E-value: 9.72e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 43 LVSQQLDSFNQFVDytlQDIICEDSTLileqlaQHTTES----DNISRKYEISFGKIYVTKPMVNEsdgvthalypQEAR 118
Cdd:PRK00405 27 LLEIQLDSFDWFLQ---LDVPPEDEGL------EEVFRSifpiEDFNGNLSLEFVSYELGEPKYDV----------EECK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 119 LRNLTYSSGLFVDVkkrtyeaidvpgrelkyELIAEESEDDSESgKVFIGRLPIMlrskncylseaTESdlyklkecpfd 198
Cdd:PRK00405 88 ERGLTYSAPLRVKL-----------------RLINKETGEIKEQ-EVYMGDIPLM-----------TEN----------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 199 mgGYFIINGSEKVLIAQ-ERSAGnivqVFkkaapspishvaeirsalekgsrFISTLQVKLYGREGSSARTI-------- 269
Cdd:PRK00405 128 --GTFIINGTERVIVSQlHRSPG----VY-----------------------FDHDKDKTSSGKLLYSARIIpyrgswle 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 270 -----KATLpYIKQD----IPIVIIFRALGIiPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTA 340
Cdd:PRK00405 179 fefdpKDIL-YVRIDrrrkLPVTVLLRALGY-SDEEILDLFYEKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEAN 256
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 341 LGIKKEKRIQYAKDILQKEflPHITQLEGF---------------ESRKAFF-----------LG----YMINRLL---- 386
Cdd:PRK00405 257 DEITEELDGPYIRNTLEKD--PTSSREEALveiyrrlrpgepptvEAARSLLenlffdpkrydLSkvgrYKLNKKLglde 334
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 387 ------------------LCAL--DRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKltkdifryMQRTVEEahdfNMKL 446
Cdd:PRK00405 335 dedvrvltkediiatikyLINLrnGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSR--------MERAVRE----RMSL 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 447 A----------INAKTITSGLKYALATGnwgeQkkamssragVSQV------LnrytysSTLSHLRRTNT--PIG----- 503
Cdd:PRK00405 403 QdldtltpqdlINAKPVVAAIKEFFGSS----Q---------LSQFmdqtnpL------SELTHKRRLSAlgPGGltrer 463
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 504 -----RDgklakprqLHNTHWGLVCPAETPEGQACGLVKNLSlmscisvgtdpmpiiTFlsewgmepledyvphqspdaT 578
Cdd:PRK00405 464 agfevRD--------VHPTHYGRICPIETPEGPNIGLINSLA---------------TY--------------------A 500
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 579 RVfvngvwhgvhrNPARLMETlrtlrrkgdinPevsmirdirekelkiftdagrvYRplfiveddeslghkelKVRKGHI 658
Cdd:PRK00405 501 RV-----------NEYGFIET-----------P----------------------YR----------------KVVDGKV 520
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 659 aklmateyqdieggfedveeytwsslLNEglVEYIDAEEEESILIAmqpedlepaEANEEndldVDPAKRI-------RV 731
Cdd:PRK00405 521 --------------------------TDE--IVYLTADEEDNYVIA---------QANAP----LDEDGRFvdelvtaRY 559
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 732 SHHATTFTHCEIH-----PSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAmgVFLtnynVRmdtmanilyyPQKPL-GT 805
Cdd:PRK00405 560 KGEFVLVPPEEVDymdvsPKQVVSVAASLIPFLEHDDANRALMGSNMQRQA--VPL----LR----------PEAPLvGT 623
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 806 trAMEY---------------------------------------------LKFR------------------------- 815
Cdd:PRK00405 624 --GMERrvardsgavvvakrdgvveyvdasrivvrveeldpgedgvdiynlIKFQrsnqntcinqrpivkvgdrvekgdv 701
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 816 ----------ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLffrsymdqekkygmSITEtFEKPQRtNTlrm 885
Cdd:PRK00405 702 ladgpstdngELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSI--------------HIEE-YEIEAR-DT--- 762
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 886 KHG----TYD----------KLDDDGLIAPGVRVSGEDVIIGKTTP-----ISPdEEEL-----GQRTAYHskRDAStpL 941
Cdd:PRK00405 763 KLGpeeiTRDipnvseealrNLDESGIVRIGAEVKPGDILVGKVTPkgeteLTP-EEKLlraifGEKARDV--KDTS--L 837
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 942 R--STENGIVDQVLV-TTNQDG-------LKFVKVRV---RttKIpQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVP 1008
Cdd:PRK00405 838 RvpHGEEGTVIDVKVfTRIEQGdelppgvNKLVKVYIaqkR--KI-QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPV 914
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1009 DLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGdASP-FTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFF 1087
Cdd:PRK00405 915 DIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKF-ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTV 993
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 343781198 1088 GPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASD 1156
Cdd:PRK00405 994 GYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1062
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
201-1212 |
5.89e-53 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 203.01 E-value: 5.89e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 201 GYFIINGSEKVLIAQE-RSAGNIVQVFKKaapspishvaeirsalEKGSRFISTLQVKLYGR----EGSSARTIKATLPY 275
Cdd:CHL00207 106 GTFIINGLERVIVSQIiRSPGIYFKKEIK----------------KNSNKIYSATLIPNRGSwikfELDKNKEIWIRIDK 169
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 276 IKQdIPIVIIFRALGIiPDGEILEHICYDVN-------------------DWQMLEMLKPCVEDGFVIQDRETALDFIGR 336
Cdd:CHL00207 170 NRK-KPLIIFLKALGL-TDQDIYSRLTKSEFlkklkpillnsnsytneeiLLEIYKNLSPIEPATVNDANQNLFSRFFDP 247
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 337 RGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESrkafflgymINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQL 416
Cdd:CHL00207 248 KNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSI---------IDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQ 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 417 F----KTLFKKLTKDIFRYMQRTVEeahDFNMklaINAKTITSGLKYALAtgnwgeqkkamSSRagVSQVLNRYTYSSTL 492
Cdd:CHL00207 319 FriglKRLERILRNRMTICDIDSLS---KFNL---INPKPLIALIREFFG-----------SSQ--LSQYMDQTNPLSEL 379
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 493 SHLRRTNT--PIGRDgKLAKP---RQLHNTHWGLVCPAETPEGQACGLVKnlSLMSCISVGTDPMPIITFLsewgmeple 567
Cdd:CHL00207 380 THKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIG--SLATNARINKFGFIETPFY--------- 447
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 568 dyvphqspdatRVFVNGVWhgVHRNPARLMETLRTLRRkgdINPEvsmirDIREKELKIFTDagrvyrplfiveddeslg 647
Cdd:CHL00207 448 -----------KVINGKVK--KFGNPIYLTADSEDLYR---IAPN-----DINLNKNNYFKK------------------ 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 648 hKELKVRKGHIAKLmateyqdieggfedveeytwssllneglveyIDAEEEESILIAmqpedlepaeaneendldvdpak 727
Cdd:CHL00207 489 -NIIPVRYKQEFKT-------------------------------VNPSKVDFIAIS----------------------- 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 728 rirvshhattfthceihPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMG---------------------------- 779
Cdd:CHL00207 514 -----------------PIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPllypekpivgtgyekqialdsgmtiisl 576
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 780 -----VFLTNYNVRMDTMAN--ILYYPQK-------------PL---------GTTRAM-EYLKFRELPAGQNAIVAIAC 829
Cdd:CHL00207 577 tegivVSVSAYKIIIQDDNNryIHYYLQKyqrsnqntcinyrPIvwvgekiniGQILADgSDIDNSELALGQNVLVAYMP 656
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 830 YSGYNQEDSMIMNQSSIDRGLFRSLFFrsymdqeKKYGMSITETFEKPQRTNTLRMKHGTYD--KLDDDGLIAPGVRVSG 907
Cdd:CHL00207 657 WEGYNFEDAILINKRLVYEDLFTSIHI-------EKYEIELRQTKLGSEEITRNIPNVSEYSlkNLDENGIISIGSKVLA 729
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 908 EDVIIGKTTPIS----PDEEELGQRTAYHSKRDA-STPLRSTENG---IVDQVLVTTNQ-DGLKF---VKVRVRTTKIP- 974
Cdd:CHL00207 730 GDILVGKITPKGesdqLPEGKLLRAIFGEKAKDVkDTSLRMPNGGygrVIKVEIFSRSKgDELKFgyyLKIRVFIAQIRk 809
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 975 -QIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVE 1053
Cdd:CHL00207 810 iQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGS 889
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1054 GISKLLREHGYQSRGFE---------------VMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQP 1118
Cdd:CHL00207 890 EYSRILINNKLNQASIKnneywlfnsyhpgkmVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQP 969
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1119 VEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVhicgicglmtviaklnhNQFECKGCDNKIDIYQIHIPY 1198
Cdd:CHL00207 970 LGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQG-----------------RNETLNAIVKGQPIPKPGTPE 1032
|
1130
....*....|....
gi 343781198 1199 AAKLLFQELMAMNI 1212
Cdd:CHL00207 1033 SFKVLMRELQSLGL 1046
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1126-1219 |
1.01e-42 |
|
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: 150.43 E-value: 1.01e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1126 GGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKlnhnqfeCKGCDNKIDIYQIHIPYAAKLLFQ 1205
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNK-------CPICKGETDISPGYIPESFKLLFQ 73
|
90
....*....|....
gi 343781198 1206 ELMAMNITPRLYTD 1219
Cdd:pfam04560 74 ELQSLGIDPRLLLE 87
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
42-1162 |
1.52e-37 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 153.52 E-value: 1.52e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 42 GLVSQQLDSFNQFVDytlqdiicedsTLILEQLAQHTTESDnISRKYEIS-FGKIY-VTKPMVNEsdgvthalypQEARL 119
Cdd:CHL00001 14 GFNQIQFEGFCRFID-----------QGLTEELSKFPKIED-TDQEIEFQlFVETYqLVEPLIKE----------RDAVY 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 120 RNLTYSSGLFVDVkkrtyeaidvpgrelkyELIAEESEDDSESgKVFIGRLPIMlrskncylseatesdlyklkecpfDM 199
Cdd:CHL00001 72 ESLTYSSELYVPA-----------------GLIWKKSRDMQEQ-TVFIGNIPLM------------------------NS 109
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 200 GGYFIINGSEKVLIAQersagnIVQvfkkaapSP-ISHVAEIRSaleKGSR-----FIST----LQVKLYGREGSSARTI 269
Cdd:CHL00001 110 LGTFIINGIYRVVINQ------ILR-------SPgIYYRSELDH---NGISvytgtIISDwggrLELEIDRKARIWARVS 173
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 270 KatlpyiKQDIPIVIIFRALGIIPDgEILEHICYdvndwqmLEMLKPCVEDgfviqdretaldfigrrgtalgiKKEKRI 349
Cdd:CHL00001 174 R------KQKISILVLLSAMGLNLR-EILDNVCY-------PEIFLSFLND-----------------------KEKKKI 216
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 350 QYAKD-ILqkEFLPHITQLEGF---------ESRKAFF-----LGYM----INRLL----------------LCALDRKD 394
Cdd:CHL00001 217 GSKENaIL--EFYQQFACVGGDpvfseslckELQKKFFqqrceLGRIgrrnMNRKLnldipenntfllpqdvLAAADYLI 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 395 Q--------DDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLK-----YAL 461
Cdd:CHL00001 295 GmkfgmgtlDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYEsffgsHPL 374
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 462 atgnwgeqkkamssragvSQVLNRYTYSSTLSHLRRTNT--PIGRDGKLA--KPRQLHNTHWGLVCPAETPEGQACGLVK 537
Cdd:CHL00001 375 ------------------SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG 436
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 538 nlSLMSCISVGTdpmpiitflseWGMepLEdyvphqSPdatrvfvngvwhgvhrnparlmetlrtlrrkgdinpevsmir 617
Cdd:CHL00001 437 --SLAIHARIGH-----------WGS--LE------SP------------------------------------------ 453
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 618 direkelkiftdagrvyrplfiveddeslghkelkvrkghiaklmateyqdieggFedveeYTWSSLLNEGLVEYIDAEE 697
Cdd:CHL00001 454 -------------------------------------------------------F-----YEISERSKEERMVYLSPSE 473
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 698 EESILIAMQpEDLepAEANEENDLDVDPAkRIRVSHHATTFTHCE---IHPSMILGVAASIIPFPDHNQSPRNTYQSAMG 774
Cdd:CHL00001 474 DEYYMIAAG-NSL--ALNQGIQEEQVVPA-RYRQEFLTIAWEQIHlrsIFPFQYFSIGASLIPFLEHNDANRALMGSNMQ 549
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 775 KQAM-----------------------GVFLTNYNVRMD----------TMANILYYP--------------QKPlgTTR 807
Cdd:CHL00001 550 RQAVplsrsekcivgtglerqvaldsgVVAIAEHEGKIIytdtdkiilsGNGDTLSIPlvmyqrsnkntcmhQKP--QVR 627
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 808 AMEYLKFRELPA------------GQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRsymdqekKYGMSITETFE 875
Cdd:CHL00001 628 RGKCVKKGQILAdgaatvggelalGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIR-------KYEIQTHVTSQ 700
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 876 KPQR-TN--------TLRmkhgtydKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEE-----------LGQRTAyhSKR 935
Cdd:CHL00001 701 GPERiTKeiphleahLLR-------NLDKNGIVMLGSWVETGDILVGKLTPQEAEESSyapegrllraiFGIQVS--TSK 771
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 936 DasTPLRSTENG---IVDQVLVTTNQDGLKFVK-VRV---RTTKIpQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVP 1008
Cdd:CHL00001 772 E--TCLKLPIGGrgrVIDVRWIQKKGGSSYNPEtIHVyilQKREI-QVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPV 848
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1009 DLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGIS-KLLREHGYQSRG-------FEVMY------- 1073
Cdd:CHL00001 849 DMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASrKLVFSELYEASKqtanpwvFEPEYpgksrlf 928
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1074 NGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLME 1153
Cdd:CHL00001 929 DGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTY 1008
|
....*....
gi 343781198 1154 ASDafrvHI 1162
Cdd:CHL00001 1009 KSD----HI 1013
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
396-1156 |
5.05e-37 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 152.77 E-value: 5.05e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 396 DDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIfRYMQRTVEEAHDFNMKL-AINAKTITSGLKYALATGNwgeqkkams 474
Cdd:PRK09603 455 DDRDHLGNRRIRAVGELLANELHSGLVKMQKTI-KDKLTTMSGAFDSLMPHdLVNSKMITSTIMEFFMGGQ--------- 524
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 475 sragVSQVLNRYTYSSTLSHLRRTNTpIGrDGKLAK------PRQLHNTHWGLVCPAETPEGQACGLVKNLSlmscisvg 548
Cdd:PRK09603 525 ----LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS-------- 590
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 549 tdpmpiiTFlsewgmepledyvphqspdaTRVfvngvwhgvhrnparlmetlrtlrrkgdinpevsmirdirekelkifT 628
Cdd:PRK09603 591 -------TF--------------------TRV-----------------------------------------------N 596
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 629 DAGRVYRPLfiveddeslghkeLKVRKGHIAklmateyqdieggfedveeytwssllneGLVEYIDAEEEESILIAMQPE 708
Cdd:PRK09603 597 DLGFIEAPY-------------KKVVDGKVV----------------------------GETIYLTAIQEDSHIIAPAST 635
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 709 DLEPAEANEENDLDVDPAKRIRVSHHATTfTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNV- 787
Cdd:PRK09603 636 PIDEEGNILGDLIETRVEGEIVLNEKSKV-TLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIv 714
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 788 -------------------------RMDTM-----------ANILYYP-QKPLGTTRAMEY------------------- 811
Cdd:PRK09603 715 gtgiekiiardswgaikanragvveKIDSKniyilgegkeeAYIDAYSlQKNLRTNQNTSFnqvpivkvgdkveagqiia 794
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 812 ----LKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRS--LFFRSYMDQEKKYGmsITETFEKPQRTNTLRM 885
Cdd:PRK09603 795 dgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSthIYEKEVDARELKHG--VEEFTADIPDVKEEAL 872
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 886 KHgtydkLDDDGLIAPGVRVSGEDVIIGKTTP---ISPDEEELGQRTAYHSK---------------------------- 934
Cdd:PRK09603 873 AH-----LDESGIVKVGTYVSAGMILVGKTSPkgeIKSTPEERLLRAIFGDKaghvvnkslycppslegtvidvkvftkk 947
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 935 ---RDAST-------------------------------------PLRS------------------------------- 943
Cdd:PRK09603 948 gyeKDARVlsayeeekakldmehfdrltmlnreellrvssllsqaILEEpfshngkdykegdqipkeeiasinrftlasl 1027
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 944 --------------TENGIVDQ--VLVTTNQDGL--------------KFVKVRVRTTKIPQIGDKFASRHGQKGTIGIT 993
Cdd:PRK09603 1028 vkkyskevqnhyeiTKNNFLEQkkVLGEEHEEKLsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNI 1107
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 994 YRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSG-----------------------------NEGD- 1043
Cdd:PRK09603 1108 VPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGkqiasmledktkdfakelrakmleianaiNEKDp 1187
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1044 ---------------------------ASP-FTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRL 1095
Cdd:PRK09603 1188 ltihalencsdeelleyakdwskgvkmAIPvFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKL 1267
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 343781198 1096 RHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASD 1156
Cdd:PRK09603 1268 HHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
580-641 |
7.05e-32 |
|
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pssm-ID: 428012 [Multi-domain] Cd Length: 62 Bit Score: 118.62 E-value: 7.05e-32
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 343781198 580 VFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVE 641
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
481-543 |
2.18e-29 |
|
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: 111.46 E-value: 2.18e-29
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 343781198 481 QVLNRYTYSSTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMS 543
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
381-1182 |
7.09e-26 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 116.65 E-value: 7.09e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 381 MINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEE---AHDFnmklaINAKTITSGL 457
Cdd:PRK14844 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDkvsPSDF-----INPKVLTNVL 523
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 458 KyalatgnwgeqkkAMSSRAGVSQVLNRYTYSSTLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGLVCPAETPEGQAC 533
Cdd:PRK14844 524 R-------------DFFNSSQLSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 534 GLVKNLSLMSCISvgtdpmpiitflsEWGM--EPLEDYVPHQSPDATRvFVNGVWHGVHR---------NPARLMETLRT 602
Cdd:PRK14844 591 GLINSLAIYARIN-------------KYGFieSPYRKVVNRVVTDQIE-YLSAIDEGLYYiadtsakldENNCFVDDMLY 656
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 603 LRRKGDI----NPEVSMIrDIREKELkIFTDAGRVyrPlFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEE 678
Cdd:PRK14844 657 CRYAGSFvmvsSDQVSYI-DVSPKQV-ISVAASLI--P-FLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVAS 731
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 679 YTWSSLL--NEGLVeyiDAEEEESILI-AMQPEDLepaeaneeNDLDVD--PAKRIRVSHHATTFthceihpsmilgvaa 753
Cdd:PRK14844 732 GSGAVVLakRDGIV---DSSDSNSIVIrAFDKERV--------NYLDVDiyHLRKFQRSNHNTCI--------------- 785
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 754 siipfpdhNQSPRntyqsamgkqamgVFLTNYNVRMDTMANilyYPQKPLGttrameylkfrELPAGQNAIVAIACYSGY 833
Cdd:PRK14844 786 --------NQKPL-------------VCVGDYVKEGDVIAD---GPAINSG-----------ELALGQNLLVAFMSWQGY 830
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 834 NQEDSMIMNQSSIDRGLFRSLFFRSY--------MDQEKkygmsITETFEKPQRTNtlrMKHgtydkLDDDGLIAPGVRV 905
Cdd:PRK14844 831 NFEDSIIISSEVVKKDLFTSIHIEEFecvvhdtpLGSEK-----ITRAIPGVNEEN---LYH-----LDDSGIVKIGTRV 897
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 906 SGEDVIIGKTTP------------------------------ISPDEE--------------ELGQRtAYHSKRDASTPL 941
Cdd:PRK14844 898 GPGYILVGKVTPkpslslppetkllmtifgeksfdcadsslyTSPDVEgtvidvqvftrrgvEENER-ALLIKQKEINDF 976
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 942 RSTENGIVD-----------QVLVTT-NQDGLKF---------------------------------------------- 963
Cdd:PRK14844 977 EKERDYIINvtseyfydelkKLLINSgSQDREKFdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkvek 1056
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 964 --------------VKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIEC 1029
Cdd:PRK14844 1057 lhegydlpqgvsmsVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILET 1136
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1030 LL-------------------------------------SKVAAL---------------------SGNEG--------- 1042
Cdd:PRK14844 1137 HVgwackklgekvgnildeinkiksafckgirslnddnfTKFAAAyldnkkienidddeitasvlnTPNKNalndelnel 1216
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1043 ---------------------------------------------------DASPFTDITVEG-----ISKLLREHGYQS 1066
Cdd:PRK14844 1217 venylnscksaysnlrnflievyscgsnvsicnnirdisdnnliefarklrDGIPVAAPVFEGpkdeqIAKLFELAGLDN 1296
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 343781198 1067 RGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASF 1146
Cdd:PRK14844 1297 SGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYT 1376
|
1050 1060 1070
....*....|....*....|....*....|....*.
gi 343781198 1147 LKERLMEASDafrvHICGICGLMTVIAKLNHNqFEC 1182
Cdd:PRK14844 1377 LQEMLTVKSD----DINGRVKIYESIIKGDSN-FEC 1407
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
681-745 |
7.62e-22 |
|
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.
Pssm-ID: 428013 [Multi-domain] Cd Length: 53 Bit Score: 89.52 E-value: 7.62e-22
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 343781198 681 WSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEaneendldvdpaKRIRVSHHATTFTHCEIHP 745
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESS------------REEREGPYAHTYTHCEIHP 53
|
|
| |
