|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
37-1124 |
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: 1228.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 37 LVKQHIDSFNYFINVEIKKIMKANEKITSDA-DPMWYLKYLNIYVGMPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 115
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 116 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNRIIVDqDRK 194
Cdd:cd00653 80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 195 GTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDAPIaiifkamgvesdqeivqmigteehvmaafapsleecqkaq 274
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 275 iftQTQALRYIGNKVrrqrmwggpkktkmeearellastilthvpvkefnfrakcIYLAVMVRRVI-LAQGDNKVDDRDY 353
Cdd:cd00653 199 ---QEEALKYIGKRF----------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDH 235
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 354 YGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGV 433
Cdd:cd00653 236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGL 313
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 434 TQVLSRLSFISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpiikla 512
Cdd:cd00653 314 SQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------ 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 513 fnlgvedvnllcgeelsyptvflvflngnilgvirdhqklvytfrlmrragfinefvsistnltdrcvyissdgGRLCRP 592
Cdd:cd00653 382 --------------------------------------------------------------------------GRIERP 387
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 593 YIIVKngkpavknkhieelsqgyrtfedflheslveyldvneendcnialyehmisKDTTHLEIEPFTLLGVCAGLIPYP 672
Cdd:cd00653 388 YRIVE---------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 673 HHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDAL 752
Cdd:cd00653 417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 753 VLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPmldaETRKPIWRHSILDADGICSPGEKVENKQVLVNKSMPTV 832
Cdd:cd00653 497 IINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGD----IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 833 TQTPLEGSAQPgQPQYREVPVSYKGATDSYIEKVMISS---NAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVP 909
Cdd:cd00653 573 ETESTPIFGEK-ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 910 QEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:cd00653 652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDG 731
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:cd00653 732 RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKS 811
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*
gi 125843259 1070 DAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLK 1124
Cdd:cd00653 812 DDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
24-1126 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1083.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 24 KWKLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITSDAdPMWYLKYLNIYVGMPDVEESFNVTRPVSPHECRLR 103
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 104 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLS 183
Cdd:PRK08565 80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 184 KNRIIVDQDRKG---TVGASVTSSTHEKKSRTNM-IVKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTEEHV 259
Cdd:PRK08565 160 PNRVLVDKGEAGssiTHTAKVISSRAGYRAQVTVeRRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 260 MAAFAPSLEECQKAQIfTQTQALRYIGNKVrrqrMWGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLAVMVRRV 339
Cdd:PRK08565 240 QQELLPSLEQASSIAA-TVEDALDYIGKRV----AIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 340 I-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRAAQFDVVkhMRQDQITNGMVNAIST 418
Cdd:PRK08565 315 LeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALAT 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 419 GNWSlkrfkMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 498
Cdd:PRK08565 393 GNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 499 ITTDMEDGPIIKLAFNLGVEDVNLLCGEElsYPTVFLVFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTD- 577
Cdd:PRK08565 468 ISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGe 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 578 -RCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGYRTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEI 656
Cdd:PRK08565 546 iNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEI 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 657 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNA 736
Cdd:PRK08565 626 WPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNA 705
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 737 TVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGE 816
Cdd:PRK08565 706 VVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEV 785
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 817 KVENKQVLVNKSMPTVTQTPLEGSAQPGQPQyREVPVSYKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSS 896
Cdd:PRK08565 786 EVKGGDVLIGKTSPPRFLEELEELSLGLQER-RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFAS 864
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 897 RHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRY 976
Cdd:PRK08565 865 RHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKL 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 977 GYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYG 1056
Cdd:PRK08565 945 GYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHG 1024
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 125843259 1057 ASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLA 1126
Cdd:PRK08565 1025 AAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
536-1126 |
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: 709.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGY 615
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 616 RTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 695
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 696 YNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 775
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 776 LRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGEKVENKQVLVNK-SMPTVTQTPLEGSAQPgqPQYREVPVS 854
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVT--ERRRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 855 YKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSR 934
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 935 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 1014
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1015 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1088
Cdd:TIGR03670 479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
|
570 580 590
....*....|....*....|....*....|....*...
gi 125843259 1089 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLA 1126
Cdd:TIGR03670 559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
29-1126 |
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: 603.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 29 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITsDADPMWYLKYLNIYVGMPdveesfnvtrPVSPHECRLRDMTYS 108
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE-DFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 109 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpmefsklnecpldpgGYFIVKGQEKVILIQEQLSKNRI 187
Cdd:COG0085 77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 188 IVDQDRKG---TVGASVTSSTH-----EKKSRTNMIVKQGRfylkhntlSEDAPIAIIFKAMGVESDQEIVQMIGtEEHV 259
Cdd:COG0085 133 FVEEEDKSgkdLYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFG-DDPI 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 260 MAAFAPSLEecqKAQIFTQTQALRYIGNKVRRqrmwGGPKKtkMEEARELLASTI-------LTHV-----------PVK 321
Cdd:COG0085 204 QEYILATLE---KDNTKTQEEALLEIYRKLRP----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVP 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 322 EFNFRAKCIYLAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELK-----KIADQIIPKQraa 395
Cdd:COG0085 275 PEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRermttQDVEAITPQS--- 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 396 qfdVVkhmRQDQITNGMVNAISTGNwsLKRFkMDRqgvTQVLSRLSF---ISALGM--MTRISSQFEktrkVsgpRSLQP 470
Cdd:COG0085 352 ---LI---NIRPVVAAIKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHP 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 471 SQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpiiklafnlgvedvnllcgeelsyptvflvflngnilgvirdhq 550
Cdd:COG0085 413 SHYGRMCPIETPEGPNIGLIGSLALYARV--------------------------------------------------- 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 551 klvytfrlmrragfiNEFvsistnltdrcvyissdgGRLCRPYIIVKNGKpaVKNKhieelsqgyrtfedflheslVEYL 630
Cdd:COG0085 442 ---------------NEY------------------GFIETPYRKVENGK--VTDE--------------------IEYL 466
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 631 DVNEENDCNIAL-----------------------YEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMG 687
Cdd:COG0085 467 TADEEENYYIAQanapldedgnfleervlvryrgeEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQ 546
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 688 KQAMG-----------TIGYNQRNRIDTlmyllAYPQRPMVKT----KTIELI------DFEKLPAGQNATVAVMSYSGY 746
Cdd:COG0085 547 RQAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGY 621
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 747 DIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYtnqtfdkvmgpMLDAE--TR-KP-----IWRHsiLDADGICSPGEKV 818
Cdd:COG0085 622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDT-----------KLGPEeiTRdIPnvseeALRN--LDEDGIIRIGAEV 688
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 819 ENKQVLVNKsmptVT------QTPLEG--SAQPGQPQyRE-------VPVSYKGatdsYIEKVMISSNAEDAFL------ 877
Cdd:COG0085 689 KGGDILVGK----VTpkgeteLTPEERllRAIFGEKA-REvrdtslrVPHGEKG----KVIDVKVFSREEGDELppgvnk 759
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 878 -VKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFH 956
Cdd:COG0085 760 lVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRV 839
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 957 YGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGR 1036
Cdd:COG0085 840 ATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGK 919
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1037 SRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQS 1116
Cdd:COG0085 920 AQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQS 989
|
1210
....*....|
gi 125843259 1117 MNIIPRLKLA 1126
Cdd:COG0085 990 LGLDVEVLSE 999
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
665-1038 |
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: 562.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 665 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYS 744
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 745 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLRRYTNQTFDKVMGPMldaeTRKPIWRHSILDADGICSPGEKVENKQVL 824
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 825 VNKSMPTVTQTPLEGSAQPGQPQYREVPVSYKGATDSYIEKVMI-SSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGV 903
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 904 CGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLIRYGYNYQ 981
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 125843259 982 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1038
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
536-597 |
1.00e-29 |
|
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pssm-ID: 428012 [Multi-domain] Cd Length: 62 Bit Score: 112.46 E-value: 1.00e-29
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 125843259 536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 597
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
618-658 |
3.86e-10 |
|
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: 56.39 E-value: 3.86e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 125843259 618 FEDFLHESLVEYLDVNEENDCNIALY------------EHMISKDTTHLEIEP 658
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTpedleessreerEGPYAHTYTHCEIHP 53
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
37-1124 |
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: 1228.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 37 LVKQHIDSFNYFINVEIKKIMKANEKITSDA-DPMWYLKYLNIYVGMPDVEESfNVTRPVSPHECRLRDMTYSAPITVDI 115
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG-GVTRKLTPNECRLRDLTYSAPLYVDI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 116 EYTRGSQRIIR-NALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNRIIVDqDRK 194
Cdd:cd00653 80 RLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 195 GTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDAPIaiifkamgvesdqeivqmigteehvmaafapsleecqkaq 274
Cdd:cd00653 159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 275 iftQTQALRYIGNKVrrqrmwggpkktkmeearellastilthvpvkefnfrakcIYLAVMVRRVI-LAQGDNKVDDRDY 353
Cdd:cd00653 199 ---QEEALKYIGKRF----------------------------------------EDLIYMIRKLIlLVLGKGKLDDIDH 235
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 354 YGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRaaQFDVVKHMRQDQITNGMVNAISTGNWSLKRFKMDRQGV 433
Cdd:cd00653 236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKK--DLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGL 313
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 434 TQVLSRLSFISALGMMTRISS-QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITtdmedgpiikla 512
Cdd:cd00653 314 SQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS------------ 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 513 fnlgvedvnllcgeelsyptvflvflngnilgvirdhqklvytfrlmrragfinefvsistnltdrcvyissdgGRLCRP 592
Cdd:cd00653 382 --------------------------------------------------------------------------GRIERP 387
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 593 YIIVKngkpavknkhieelsqgyrtfedflheslveyldvneendcnialyehmisKDTTHLEIEPFTLLGVCAGLIPYP 672
Cdd:cd00653 388 YRIVE---------------------------------------------------KEVTHIEISPSQILSVAASLIPFP 416
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 673 HHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDAL 752
Cdd:cd00653 417 EHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAI 496
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 753 VLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPmldaETRKPIWRHSILDADGICSPGEKVENKQVLVNKSMPTV 832
Cdd:cd00653 497 IINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGD----IPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKG 572
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 833 TQTPLEGSAQPgQPQYREVPVSYKGATDSYIEKVMISS---NAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVP 909
Cdd:cd00653 573 ETESTPIFGEK-ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILP 651
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 910 QEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:cd00653 652 QEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDG 731
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:cd00653 732 RTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKS 811
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*
gi 125843259 1070 DAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLK 1124
Cdd:cd00653 812 DDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
24-1126 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1083.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 24 KWKLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITSDAdPMWYLKYLNIYVGMPDVEESFNVTRPVSPHECRLR 103
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEPEIKEADGSERPITPMEARLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 104 DMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLS 183
Cdd:PRK08565 80 NLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 184 KNRIIVDQDRKG---TVGASVTSSTHEKKSRTNM-IVKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTEEHV 259
Cdd:PRK08565 160 PNRVLVDKGEAGssiTHTAKVISSRAGYRAQVTVeRRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPEI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 260 MAAFAPSLEECQKAQIfTQTQALRYIGNKVrrqrMWGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLAVMVRRV 339
Cdd:PRK08565 240 QQELLPSLEQASSIAA-TVEDALDYIGKRV----AIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 340 I-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRAAQFDVVkhMRQDQITNGMVNAIST 418
Cdd:PRK08565 315 LeLYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VRPDIITERIRHALAT 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 419 GNWSlkrfkMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 498
Cdd:PRK08565 393 GNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 499 ITTDMEDGPIIKLAFNLGVEDVNLLCGEElsYPTVFLVFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTD- 577
Cdd:PRK08565 468 ISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVAYIETGe 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 578 -RCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGYRTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEI 656
Cdd:PRK08565 546 iNEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPEHTHLEI 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 657 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNA 736
Cdd:PRK08565 626 WPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNA 705
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 737 TVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGE 816
Cdd:PRK08565 706 VVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEV 785
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 817 KVENKQVLVNKSMPTVTQTPLEGSAQPGQPQyREVPVSYKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSS 896
Cdd:PRK08565 786 EVKGGDVLIGKTSPPRFLEELEELSLGLQER-RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFAS 864
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 897 RHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRY 976
Cdd:PRK08565 865 RHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLKL 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 977 GYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYG 1056
Cdd:PRK08565 945 GYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHG 1024
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 125843259 1057 ASMLLLERLMISSDAFEVDVCGQCGLLGYSG------WCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLA 1126
Cdd:PRK08565 1025 AAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKLG 1100
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
536-1126 |
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: 709.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGY 615
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 616 RTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 695
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 696 YNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 775
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 776 LRRYTNQTFDKVMGPMLDAETRKPIWRHSILDADGICSPGEKVENKQVLVNK-SMPTVTQTPLEGSAQPgqPQYREVPVS 854
Cdd:TIGR03670 241 ERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtSPPRFLEELREFGLVT--ERRRDTSVT 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 855 YKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSR 934
Cdd:TIGR03670 319 VRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 935 MTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVL 1014
Cdd:TIGR03670 399 MTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1015 DKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY------SGW 1088
Cdd:TIGR03670 479 DKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrkgTAY 558
|
570 580 590
....*....|....*....|....*....|....*...
gi 125843259 1089 CHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLA 1126
Cdd:TIGR03670 559 CPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
536-1125 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 704.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVKNGKPAVKNKHIEELSQGY 615
Cdd:PRK07225 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 616 RTFEDFLHESLVEYLDVNEENDCNIALYEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIG 695
Cdd:PRK07225 87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 696 YNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCT 775
Cdd:PRK07225 167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 776 LRRYTNQTFDKVMGPmlDAETR----KPIWRHsiLDADGICSPGEKVENKQVLVNKSMPtvtqtP--LEGSAQPGQP--Q 847
Cdd:PRK07225 247 ERRYPGGQEDRFEIP--DKDVRgyrgEEAYRH--LDEDGLVNPETEVKEGDVLIGKTSP-----PrfLEEPDDFGISpeK 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 848 YREVPVSYKGATDSYIEKVMISSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMN 927
Cdd:PRK07225 318 RRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIIN 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 928 PHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQ 1007
Cdd:PRK07225 398 PHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQ 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1008 KLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGY-- 1085
Cdd:PRK07225 478 KLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIyd 557
|
570 580 590 600
....*....|....*....|....*....|....*....|....
gi 125843259 1086 ----SGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKL 1125
Cdd:PRK07225 558 kkrnRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
29-1126 |
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: 603.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 29 PAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITsDADPMWYLKYLNIYVGMPdveesfnvtrPVSPHECRLRDMTYS 108
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE-DFTGNLSLEFGDYRLGEP----------KYTPEECKERDLTYA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 109 APITVDIEYT-RGSQRIIRNALPIGRMPIMLRSsncvltgktpmefsklnecpldpgGYFIVKGQEKVILIQEQLSKNRI 187
Cdd:COG0085 77 APLYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVY 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 188 IVDQDRKG---TVGASVTSSTH-----EKKSRTNMIVKQGRfylkhntlSEDAPIAIIFKAMGVESDQEIVQMIGtEEHV 259
Cdd:COG0085 133 FVEEEDKSgkdLYSAKVIPSRGawlefETDKDGTIYVRIDR--------KRKIPVTVLLRALGLETDEEILEAFG-DDPI 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 260 MAAFAPSLEecqKAQIFTQTQALRYIGNKVRRqrmwGGPKKtkMEEARELLASTI-------LTHV-----------PVK 321
Cdd:COG0085 204 QEYILATLE---KDNTKTQEEALLEIYRKLRP----GEPPT--IERAEQLLDNLFfdpkrydLAHVgrykinkklglDVP 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 322 EFNFRAKCIYLAVMVRRVI-LAQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELK-----KIADQIIPKQraa 395
Cdd:COG0085 275 PEDRVLTAEDIVATIKYLLeLHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRermttQDVEAITPQS--- 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 396 qfdVVkhmRQDQITNGMVNAISTGNwsLKRFkMDRqgvTQVLSRLSF---ISALGM--MTRISSQFEktrkVsgpRSLQP 470
Cdd:COG0085 352 ---LI---NIRPVVAAIKEFFGSSQ--LSQF-MDQ---TNPLSELTHkrrLSALGPggLSRERAGFE----V---RDVHP 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 471 SQWGMLCPSDTPEGEACGLVKNLALMTHIttdmedgpiiklafnlgvedvnllcgeelsyptvflvflngnilgvirdhq 550
Cdd:COG0085 413 SHYGRMCPIETPEGPNIGLIGSLALYARV--------------------------------------------------- 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 551 klvytfrlmrragfiNEFvsistnltdrcvyissdgGRLCRPYIIVKNGKpaVKNKhieelsqgyrtfedflheslVEYL 630
Cdd:COG0085 442 ---------------NEY------------------GFIETPYRKVENGK--VTDE--------------------IEYL 466
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 631 DVNEENDCNIAL-----------------------YEHMISKDTTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMG 687
Cdd:COG0085 467 TADEEENYYIAQanapldedgnfleervlvryrgeEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQ 546
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 688 KQAMG-----------TIGYNQRNRIDTlmyllAYPQRPMVKT----KTIELI------DFEKLPAGQNATVAVMSYSGY 746
Cdd:COG0085 547 RQAVPllrpeapllhyPLQKFQRSNQGT-----CINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGY 621
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 747 DIEDALVLNKASLDRGFGRCLVYKNAKCTLRRYtnqtfdkvmgpMLDAE--TR-KP-----IWRHsiLDADGICSPGEKV 818
Cdd:COG0085 622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDT-----------KLGPEeiTRdIPnvseeALRN--LDEDGIIRIGAEV 688
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 819 ENKQVLVNKsmptVT------QTPLEG--SAQPGQPQyRE-------VPVSYKGatdsYIEKVMISSNAEDAFL------ 877
Cdd:COG0085 689 KGGDILVGK----VTpkgeteLTPEERllRAIFGEKA-REvrdtslrVPHGEKG----KVIDVKVFSREEGDELppgvnk 759
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 878 -VKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFH 956
Cdd:COG0085 760 lVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRV 839
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 957 YGTAFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGR 1036
Cdd:COG0085 840 ATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGK 919
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1037 SRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCgqcgllGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQS 1116
Cdd:COG0085 920 AQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQS 989
|
1210
....*....|
gi 125843259 1117 MNIIPRLKLA 1126
Cdd:COG0085 990 LGLDVEVLSE 999
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
665-1038 |
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: 562.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 665 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQRPMVKTKTIELIDFEKLPAGQNATVAVMSYS 744
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 745 GYDIEDALVLNKASLDRGFGRCLVYKnaKCTLRRYTNQTFDKVMGPMldaeTRKPIWRHSILDADGICSPGEKVENKQVL 824
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEITRDI----PNVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 825 VNKSMPTVTQTPLEGSAQPGQPQYREVPVSYKGATDSYIEKVMI-SSNAEDAFLVKILLRQTRRPEIGDKFSSRHGQKGV 903
Cdd:pfam00562 155 VGKVGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 904 CGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRFHYGTAFGGSK--VKDVCEDLIRYGYNYQ 981
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 125843259 982 GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1038
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
22-520 |
3.80e-113 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 360.80 E-value: 3.80e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 22 EEKWKLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMKANEKITSDADPMWYLKYLNIYVGMPDVEESFNVTRPVSPHECR 101
Cdd:PRK09606 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADGSEREIYPMEAR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 102 LRDMTYSAPITVDIEYTRGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQ 181
Cdd:PRK09606 83 LRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLED 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 182 LSKNRIIVDQDRKG---TVGASVTSSTHEKKSR-TNMIVKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTEE 257
Cdd:PRK09606 163 LAPNKILVEKDERYgdrIEVAKVFSQRRGYRALvTVERNRDGLLEVSFPSVPGSIPFVILMRALGLETDEEIVEAVSDDP 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 258 HVMAAFAPSLEEcqkAQIFTQTQALRYIGNKVRRqrmwGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLAVMVR 337
Cdd:PRK09606 243 EIVKFMLENLEE---AEVDTQEEALEYIGKRVAP----GQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAE 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 338 RVI-LAQGDNKVDDRDYYGNKRLELAGQLLsllfEDLFK-KFNSELKKIADQIipkQRAA----QFDVVKHMRQDQITNG 411
Cdd:PRK09606 316 ACFeLALGRREEDDKDHYANKRLKLAGDLM----EDLFRvAFNRLARDVKYQL---ERANmrnrELSIKTAVRSDVLTER 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 412 MVNAISTGNWslkrfKMDRQGVTQVLSRLSFISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVK 491
Cdd:PRK09606 389 LEHAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVK 463
|
490 500
....*....|....*....|....*....
gi 125843259 492 NLALMTHITTDMEDGPIIKLAFNLGVEDV 520
Cdd:PRK09606 464 NFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
36-410 |
1.56e-112 |
|
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: 355.53 E-value: 1.56e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 36 GLVKQHIDSFNYFINVEIKKIMKANEKITSDADP--------MWYLKYLNIYVGMPDVEESFNVTRPVSPHECRLRDMTY 107
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIqhpgengdKLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 108 SAPITVDIEYTR-GSQRIIRNALPIGRMPIMLRSSNCVLTGKTPMEFSKLNECPLDPGGYFIVKGQEKVILIQEQLSKNR 186
Cdd:pfam04563 81 SAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNH 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 187 IIVDQDR---KGTVGASVTSSTHE-----KKSRTNMI--VKQGRFYLKHNTLSEDAPIAIIFKAMGVESDQEIVQMIGTE 256
Cdd:pfam04563 161 PIVFKKAdpkKRGSVASVRSSAEIsvrpdSTSWVNVLeyLSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELICYD 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 257 EH---VMAAFAPSLEECQKAQIFTQTQALRYIGNKVRRQRMWGGPKKTKMEEARELLASTILTHVPVKEFNFRAKCIYLA 333
Cdd:pfam04563 241 VNdqqLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMGRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYFIG 320
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 125843259 334 VMVRRVIL-AQGDNKVDDRDYYGNKRLELAGQLLSLLFEDLFKKFNSELKKIADQIIPKQRAaqFDVVKHMRQDQITN 410
Cdd:pfam04563 321 YMIRRLLLlALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDD--LMLQLLVNAKPITS 396
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
29-1117 |
4.54e-68 |
|
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: 249.19 E-value: 4.54e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 29 PAFLKVKGLVKQHIDSFNYFINVE----------IKKIMKANEKITSDADPMwYLKYLNIYVGMPDVeesfnvtrpvSPH 98
Cdd:TIGR02013 12 PEVLEVPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPIEDYTGNI-ELEYLSYRLGEPKY----------SVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 99 ECRLRDMTYSAPITVDIEYT----RGSQRIIRNALPIGRMPIMlrssncvlTGKtpmefsklnecpldpgGYFIVKGQEK 174
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLM--------TDR----------------GTFIINGAER 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 175 VILIQEQLSKNrIIVDQDrkgtvgasVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEDA-----------PIAIIFKAMGV 243
Cdd:TIGR02013 137 VVVSQLHRSPG-VFFSSE--------KDTTKSGKVLFSARIIPYRGSWLEFETDKKDVlyvridrkrklPATVLLRALGY 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 244 ESDQEIVQMIGTEEHVMAAFapsleecQKAQIFTQTQALRYIGNKVRRqrmwGGPkkTKMEEARELLASTI-------LT 316
Cdd:TIGR02013 208 TIDTLILNRLGSGEYIRNTL-------RKDPTNSEEEALVEIYRKLRP----GEP--PTVEAARSLLENLFfdpkrydLG 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 317 HVPVKEFNFRAK-------CIY-----LAVMVRRVILAQGDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSELKKI 384
Cdd:TIGR02013 275 RVGRYKLNKKLGldvpesiGVLtkediIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQ-------NQFRVGLARM 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 385 ADQIipKQRAAQFDVVKHMRQDQITNGMVNAIST---GNWSLKRFkMDRqgvTQVLSRLSF---ISALGM--MTRISSQF 456
Cdd:TIGR02013 348 ERIV--RERMSTQDTDTLTPQDLINAKPISAAIKeffGSSQLSQF-MDQ---TNPLAELTHkrrLSALGPggLTRERAGF 421
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 457 EKtrkvsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLAlmthittdmedgpiiklafnlgvedvnllcgeelsyptvflv 536
Cdd:TIGR02013 422 EV-------RDVHPTHYGRICPIETPEGPNIGLINSLS------------------------------------------ 452
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 537 flngnilgvirdhqklVYTFrlmrragfINEFVSISTnltdrcvyissdggrlcrPYIIVKNGKPAVknkhieelsqgyr 616
Cdd:TIGR02013 453 ----------------TYAR--------VNEYGFIET------------------PYRKVKDGKVVV------------- 477
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 617 tfedflhESLVEYLDVNEENDCNIA-------------------LYEHMIS----KDTTHLEIEPFTLLGVCAGLIPYPH 673
Cdd:TIGR02013 478 -------TDEIDYLTADEEDNYVIAqanapldengrfvedlvvaRYRGEITlvspDQVDYMDVSPKQVVSVAASLIPFLE 550
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 674 HNQSPRNTYQCAMGKQAM-------------------------------GTIGYNQRNRI---------DTLMYLLAYP- 712
Cdd:TIGR02013 551 HDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVVEYVDAKRIvirydedeeEPDGGIDIYRl 630
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 713 -------------QRPMV----KTKTIELI------DFEKLPAGQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVY 769
Cdd:TIGR02013 631 lkyqrsnqdtcinQRPIVsvgdRVEAGDVLadgpstDLGELALGRNVLVAFMPWNGYNYEDAILISE---------RLVK 701
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 770 KNAKCT--LRRYTNQTFDKVMGPmlDAETR------KPIWRHsiLDADGICSPGEKVENKQVLVNKSMPT--VTQTPLEG 839
Cdd:TIGR02013 702 DDVFTSihIEEYEVEARDTKLGP--EEITRdipnvsEEALRN--LDENGIVRIGAEVKAGDILVGKVTPKgeTELTPEEK 777
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 840 --SAQPGQpQYREV-------PVSYKGAtdsyIEKVMISSNAEDAFL-------VKILLRQTRRPEIGDKFSSRHGQKGV 903
Cdd:TIGR02013 778 llRAIFGE-KARDVrdtslrvPPGVEGT----VIDVKVFSREQGDELppgvnklVKVYIAQKRKIQVGDKMAGRHGNKGV 852
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 904 CGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRF--HYGTA-FGGSKVKDVCEDLIRYGYNY 980
Cdd:TIGR02013 853 VSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKgvPIATPvFDGASEEEIKEYLEKAGLPR 932
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 981 QGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASML 1060
Cdd:TIGR02013 933 DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1012
|
1210 1220 1230 1240 1250 1260
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 125843259 1061 LLERLMISSD-------AFEVDVCGQcgllgysgwchycksscHVSSLRIPYACKLLFQELQSM 1117
Cdd:TIGR02013 1013 LQEMLTVKSDdvvgrtkAYEAIVKGE-----------------NVPEPGIPESFNVLIKELQSL 1059
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
33-1130 |
1.46e-59 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 223.04 E-value: 1.46e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 33 KVKGLVKQHIDSFNYFINVEIKKIMKANEKITsdaDPMWYLKYLNIYvgmpdveESFNVTRP-VSPHECRLRDMTYSAPI 111
Cdd:CHL00207 6 ALPDFLEIQRTSFCWFLNEGLNEELNIFSKIF---DYTGNLELLLFG-------KNYKLKYPkYNLLSAKSYDSNYSIQI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 112 TVDIEYTRGSQRIIRNA-LPIGRMPIMLRSSNCVLTGktpMEFSKLNECPLDPGGYFivkgqEKVIliqeqlsknriivd 190
Cdd:CHL00207 76 YLPLKFINLKTNKIKFInYLIGNLPKMTQRGTFIING---LERVIVSQIIRSPGIYF-----KKEI-------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 191 qDRKGTVGASVTSSTHEKKSRTNMIVKQGRFYLKHNTLSEdAPIAIIFKAMGVeSDQEIVQmigteeHVMAAFAPSLEEC 270
Cdd:CHL00207 134 -KKNSNKIYSATLIPNRGSWIKFELDKNKEIWIRIDKNRK-KPLIIFLKALGL-TDQDIYS------RLTKSEFLKKLKP 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 271 QKAQI--FTQTQALRYIGNKVRRQRMWGGPKKTKMEEAR----------ELLASTILTHVPVKEFNFRAKCIY---LAVM 335
Cdd:CHL00207 205 ILLNSnsYTNEEILLEIYKNLSPIEPATVNDANQNLFSRffdpknydlgKVGRYKINNKLNLNIPERVRNLTYediLSII 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 336 VRRVILAQGDNKVDDRDYYGNKRLELAGQLLsllfedlFKKFNSELKKIaDQIIPKQraaqfdVVKHmRQDQITNGMVNA 415
Cdd:CHL00207 285 DKLINLKINKGNFDDIDHLKNRRVRSVGELL-------QNQFRIGLKRL-ERILRNR------MTIC-DIDSLSKFNLIN 349
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 416 ISTGNWSLKRFKMDRQgVTQVLSRLSFISALGMMTRIS----SQFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLvk 491
Cdd:CHL00207 350 PKPLIALIREFFGSSQ-LSQYMDQTNPLSELTHKRRISilgpGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGL-- 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 492 nlalmthittdmedgpIIKLAFNLGVEDVNLLcgeelsyPTVFLVFLNGNILgvirDHQKLVYTfrlmrrAGFINEFVSI 571
Cdd:CHL00207 427 ----------------IGSLATNARINKFGFI-------ETPFYKVINGKVK----KFGNPIYL------TADSEDLYRI 473
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 572 STNltdrcvyissdggrlcrPYIIVKNGkpAVKNKHIEelsqgyrtfedflheslveyldVNEENDCNIALYEH--MISk 649
Cdd:CHL00207 474 APN-----------------DINLNKNN--YFKKNIIP----------------------VRYKQEFKTVNPSKvdFIA- 511
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 650 dtthleIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTI---------GYNQRNRIDTLM-------------- 706
Cdd:CHL00207 512 ------ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLypekpivgtGYEKQIALDSGMtiisltegivvsvs 585
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 707 ----------------YLLAYP---------QRPMV----KTKTIEL------IDFEKLPAGQNATVAVMSYSGYDIEDA 751
Cdd:CHL00207 586 aykiiiqddnnryihyYLQKYQrsnqntcinYRPIVwvgeKINIGQIladgsdIDNSELALGQNVLVAYMPWEGYNFEDA 665
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 752 LVLNKAsldrgfgrcLVYKNAkctlrrYTNQTFDKV-----MGPMLDAETRKPIWRHSI-----LDADGICSPGEKVENK 821
Cdd:CHL00207 666 ILINKR---------LVYEDL------FTSIHIEKYeielrQTKLGSEEITRNIPNVSEyslknLDENGIISIGSKVLAG 730
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 822 QVLVNK--SMPTVTQTPLE-------GSAQPGqpqYREVPVSYKGATDSYIEKVMI---SSNAEDAFLVKILLR----QT 885
Cdd:CHL00207 731 DILVGKitPKGESDQLPEGkllraifGEKAKD---VKDTSLRMPNGGYGRVIKVEIfsrSKGDELKFGYYLKIRvfiaQI 807
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 886 RRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAG-VLDGRF---HYGTAF 961
Cdd:CHL00207 808 RKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGdNLNKRFkilPFDEMY 887
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 962 GGSKVKDVCEDLIR-----------YGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTR 1030
Cdd:CHL00207 888 GSEYSRILINNKLNqasiknneywlFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQ 967
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1031 QPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCGQCGLLGYsgwchYCKSSCHVSSLrIPYACKLL 1110
Cdd:CHL00207 968 QPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD----DMQGRNETLNA-----IVKGQPIPKPG-TPESFKVL 1037
|
1210 1220
....*....|....*....|.
gi 125843259 1111 FQELQSMNI-IPRLKLARYNE 1130
Cdd:CHL00207 1038 MRELQSLGLdIEAYKIENFLE 1058
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1040-1126 |
3.42e-46 |
|
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: 160.06 E-value: 3.42e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 1040 GGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVCGQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNI 1119
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNKCPICKGETDISPGYIPESFKLLFQELQSLGI 80
|
....*..
gi 125843259 1120 IPRLKLA 1126
Cdd:pfam04560 81 DPRLLLE 87
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
733-1070 |
1.30e-43 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 172.78 E-value: 1.30e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 733 GQNATVAVMSYSGYDIEDALVLNKasldrgfgrCLVYKNAKCTL--RRY------TNQTFDKVMG--PMLDAEtrkpIWR 802
Cdd:CHL00001 652 GKNVLVAYMPWEGYNFEDAVLISE---------RLVYEDIYTSFhiRKYeiqthvTSQGPERITKeiPHLEAH----LLR 718
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 803 HsiLDADGICSPGEKVENKQVLVNKSMPtvtQTPLEGSAQP----------GQ-PQYRE----VPVSYKG-ATD-SYIEK 865
Cdd:CHL00001 719 N--LDKNGIVMLGSWVETGDILVGKLTP---QEAEESSYAPegrllraifgIQvSTSKEtclkLPIGGRGrVIDvRWIQK 793
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 866 VMISSNaeDAFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLA 945
Cdd:CHL00001 794 KGGSSY--NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL 871
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 946 GKAGVLDGRfHYgtafggsKVKDVCEdliRYG------------Y--------------NYQGKDYVTSGITGEPLEAYI 999
Cdd:CHL00001 872 GLAGDLLNR-HY-------RIAPFDE---RYEqeasrklvfselYeaskqtanpwvfepEYPGKSRLFDGRTGDPFEQPV 940
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 125843259 1000 YFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSD 1070
Cdd:CHL00001 941 TIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
877-1078 |
3.02e-40 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 162.19 E-value: 3.02e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 877 LVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAGKAGVLDGRfH 956
Cdd:PRK00405 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGI-K 947
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 957 YGT-AFGGSKVKDVCEDLIRYGYNYQGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEG 1035
Cdd:PRK00405 948 FATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 125843259 1036 RSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDafevDVCG 1078
Cdd:PRK00405 1028 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVVG 1066
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
344-1117 |
1.12e-30 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 131.97 E-value: 1.12e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 344 GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSELKKIADQIIPKQRAAQFDVVKHMRQDQITNGMVNAistgnwSL 423
Cdd:PRK09603 450 NQGKIDDRDHLGNRRIRAVGELLA-------NELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITS------TI 516
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 424 KRFKMDRQgVTQVLSRLSFISALGMMTRISSQFE----KTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTHI 499
Cdd:PRK09603 517 MEFFMGGQ-LSQFMDQTNPLSEVTHKRRLSALGEgglvKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV 595
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 500 ttdmedgpiiklafnlgvedvnllcgeelsyptvflvflngNILGVIRDHQKLVytfrlmrragfinefvsISTNLTDRC 579
Cdd:PRK09603 596 -----------------------------------------NDLGFIEAPYKKV-----------------VDGKVVGET 617
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 580 VYISS---DGgrlcrpYIIVKNGKPAVKNKHIEElsqgyrtfedflheSLVEyldvnEENDCNIALYEhmiSKDTTHLEI 656
Cdd:PRK09603 618 IYLTAiqeDS------HIIAPASTPIDEEGNILG--------------DLIE-----TRVEGEIVLNE---KSKVTLMDL 669
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 657 EPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM-----------------------GTIGYNQR---NRIDTL-MYLL 709
Cdd:PRK09603 670 SSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgtgiekiiardswGAIKANRAgvvEKIDSKnIYIL 749
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 710 ----------AYP--------------QRPMVKT-KTIEL---------IDFEKLPAGQNATVAVMSYSGYDIEDALVLN 755
Cdd:PRK09603 750 gegkeeayidAYSlqknlrtnqntsfnQVPIVKVgDKVEAgqiiadgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVS 829
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 756 KasldrgfgrCLVYKNAKCTLRRYTNQTFDKVMGPMLDAETRK-PIWRH---SILDADGICSPGEKVENKQVLVNKSMPT 831
Cdd:PRK09603 830 E---------RITKDDIFTSTHIYEKEVDARELKHGVEEFTADiPDVKEealAHLDESGIVKVGTYVSAGMILVGKTSPK 900
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 832 --VTQTP--------------------------LEGSA------------------------------------------ 841
Cdd:PRK09603 901 geIKSTPeerllraifgdkaghvvnkslycppsLEGTVidvkvftkkgyekdarvlsayeeekakldmehfdrltmlnre 980
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 842 -------------------------QPGQ--PQY------------------REVPVSYKGATDSYIE-KVMISSNAEDA 875
Cdd:PRK09603 981 ellrvssllsqaileepfshngkdyKEGDqiPKEeiasinrftlaslvkkysKEVQNHYEITKNNFLEqKKVLGEEHEEK 1060
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 876 F---------------LVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKL 940
Cdd:PRK09603 1061 LsilekddilpngvikKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQI 1140
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 941 IEL---LAGK------AGVLDGRFHYGTAFGGSKVKDVC-------------------EDLIRYGYNYQ----------- 981
Cdd:PRK09603 1141 LEMhlgLVGKefgkqiASMLEDKTKDFAKELRAKMLEIAnainekdpltihalencsdEELLEYAKDWSkgvkmaipvfe 1220
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 982 -------------------GKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGL 1042
Cdd:PRK09603 1221 gisqekfyklfelakiamdGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQ 1300
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 125843259 1043 RLGEMERDCLIGYGASMLLLERLMISSDafevDVCGQCGllGYSGwchyCKSSCHVSSLRIPYACKLLFQELQSM 1117
Cdd:PRK09603 1301 RFGEMEVWALEAYGAAHTLKEMLTIKSD----DIRGREN--AYRA----IAKGEQVGESEIPETFYVLTKELQSL 1365
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
536-597 |
1.00e-29 |
|
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pssm-ID: 428012 [Multi-domain] Cd Length: 62 Bit Score: 112.46 E-value: 1.00e-29
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 125843259 536 VFLNGNILGVIRDHQKLVYTFRLMRRAGFINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK 597
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
183-360 |
1.56e-25 |
|
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: 104.74 E-value: 1.56e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 183 SKNRIIVDQDRKGT-VGASVTSSTHEKKSRTNMIVKQGRFYLKHN-TLSEDAPIAIIFKAMGVESDQEIVQMI-GTEEHV 259
Cdd:pfam04561 1 RSNGIYVEKELDKNgIIATYTSSLISNRGSWLKLEIDGKTLIWSRpSKKRKIPIVIFLKALGLVSDREILDRLcYDFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 260 MAAFAPSLEECQKAQIFTQTQALRYIGNKVRRqrmwGGPKKTKMEEARELLAST-----ILTHVPVKE--FNFRAKCIYL 332
Cdd:pfam04561 81 QMLELLKPELEEAENIYTQEEALDYIGKGFAL----RRGEEPRLQRAREILYSRdpkynLNKHLGLNEpfENERLKAQDI 156
|
170 180
....*....|....*....|....*....
gi 125843259 333 AVMVRRVI-LAQGDNKVDDRDYYGNKRLE 360
Cdd:pfam04561 157 LYMIDRLLnLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
313-1070 |
2.76e-22 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 104.32 E-value: 2.76e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 313 TILTHVPVKEfnfrakciylavMVRRVILAQ-GDNKVDDRDYYGNKRLELAGQLLSllfedlfKKFNSELKKIADQIIPK 391
Cdd:PRK14844 439 TVLTHEDIIE------------IVRKIVLLRdGQGSVDDIDHLGNRRVRSVGEFIE-------NQFRTGLLKLERAVVDS 499
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 392 QRAAQFDVVK---HMRQDQITNGMVNAISTGNwsLKRFkMDRQGVTQVLSRLSFISALGM--MTRISSQFEKtrkvsgpR 466
Cdd:PRK14844 500 MSTSSLDKVSpsdFINPKVLTNVLRDFFNSSQ--LSQF-MDQTNPLSEITHKRRLSALGPggLTRERAGFEV-------R 569
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 467 SLQPSQWGMLCPSDTPEGEACGLVKNLALMTHITT-DMEDGPIIKLAFNLGVEDVNLLCG--EELSYPTVFLVFLNGNil 543
Cdd:PRK14844 570 DVHPTHYGRICPIETPEGQNIGLINSLAIYARINKyGFIESPYRKVVNRVVTDQIEYLSAidEGLYYIADTSAKLDEN-- 647
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 544 gvirdhQKLVYTFRLMRRAGfinEFVSISTnltDRCVYISsdggrlcrpyiivkngkpaVKNKHIEELSQgyrtfedflh 623
Cdd:PRK14844 648 ------NCFVDDMLYCRYAG---SFVMVSS---DQVSYID-------------------VSPKQVISVAA---------- 686
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 624 eSLVEYLdvnEENDCNIALYEHMISKDTTHL----------EIEPFTLLGVCA-------GLIpyphhNQSPRNTYQC-A 685
Cdd:PRK14844 687 -SLIPFL---ENDDANRALMGSNMQRQAVPLlkptaplvatGMESFVASGSGAvvlakrdGIV-----DSSDSNSIVIrA 757
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 686 MGKQAMGTIGYN-------QRNRIDTLMyllayPQRPMVKTKTI----------ELIDFEKLPAGQNATVAVMSYSGYDI 748
Cdd:PRK14844 758 FDKERVNYLDVDiyhlrkfQRSNHNTCI-----NQKPLVCVGDYvkegdviadgPAINSGELALGQNLLVAFMSWQGYNF 832
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 749 EDALVLNKASLDRGFGRCLVYKNAKCTLRRyTNQTFDKVMG--PMLDAETrkpiWRHsiLDADGICSPGEKVENKQVLVN 826
Cdd:PRK14844 833 EDSIIISSEVVKKDLFTSIHIEEFECVVHD-TPLGSEKITRaiPGVNEEN----LYH--LDDSGIVKIGTRVGPGYILVG 905
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 827 KSMPT----------------------------VTQTPLEGSAQPGQ--------PQYREVPVSYKGATD-----SYI-- 863
Cdd:PRK14844 906 KVTPKpslslppetkllmtifgeksfdcadsslYTSPDVEGTVIDVQvftrrgveENERALLIKQKEINDfekerDYIin 985
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 864 ----------EKVMISSNAED----------------------------------------------------------- 874
Cdd:PRK14844 986 vtseyfydelKKLLINSGSQDrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklhegydlpq 1065
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 875 --AFLVKILLRQTRRPEIGDKFSSRHGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGYPSRMTVGKLIELLAG------ 946
Cdd:PRK14844 1066 gvSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackkl 1145
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 947 ---------------------------------KAGVLDGR--------------------------------------- 954
Cdd:PRK14844 1146 gekvgnildeinkiksafckgirslnddnftkfAAAYLDNKkienidddeitasvlntpnknalndelnelvenylnsck 1225
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 955 -------------FHYGT--------------------------------AFGGSKVKDVCEDLIRYGYNYQGKDYVTSG 989
Cdd:PRK14844 1226 saysnlrnflievYSCGSnvsicnnirdisdnnliefarklrdgipvaapVFEGPKDEQIAKLFELAGLDNSGQAVLYDG 1305
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 125843259 990 ITGEPLEAYIYFGPVYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISS 1069
Cdd:PRK14844 1306 CSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKS 1385
|
.
gi 125843259 1070 D 1070
Cdd:PRK14844 1386 D 1386
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
435-498 |
3.99e-21 |
|
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: 87.97 E-value: 3.99e-21
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 125843259 435 QVLSRLSFISALGMMTRISS---QFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALMTH 498
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSprgGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
618-658 |
3.86e-10 |
|
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: 56.39 E-value: 3.86e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 125843259 618 FEDFLHESLVEYLDVNEENDCNIALY------------EHMISKDTTHLEIEP 658
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTpedleessreerEGPYAHTYTHCEIHP 53
|
|
| |
