|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
41-1148 |
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: 1135.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 41 LVKQHLVSFDHFVQEEIRSIMLSNQKITSDA-NPNFYLKYLDIRIGKPSSEEGlnMTHDKITPQECRLRDMTYSAPISVD 119
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 120 IEYTRGNQRVFK-KDLIIGRMPIMLRSSKCILRDLAEEELARVQECPYDPGGYFVVKGSEKVILIQEQLSKNRIMVgrns 198
Cdd:cd00653 79 IRLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIV---- 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 199 skelqcevlsstsERKSKTYVtmkkgkYSVRHNQLTDDVPVSIIFkamgVESDFDIvSTIGHEEKYvsafaqtleesina 278
Cdd:cd00653 155 -------------EDSKGKRI------YTKTSIPSYSPYRGSWLE----VKSDKKK-DRIYVRIDL-------------- 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 279 gvYTQQQALAYVTSKVkarkftpfgslpgtsvsvltppkeheavdflsnsmithiacpdgnfkmkaIYLGLMTRRLIQTE 358
Cdd:cd00653 197 --KRQEEALKYIGKRF--------------------------------------------------EDLIYMIRKLILLV 224
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 359 LGENGLDDRDFYGNKRLELAGSLLSLLFEDVFKRFNSELKRIADNALMKTMAapLDIVKHMRQDMITNTIVNAMSTGNWI 438
Cdd:cd00653 225 LGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKD--LTPQLLINSKPITSGIKEFLATGNWG 302
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 439 IKRFRMERLGVTQVLSRLSYISALGMMTRINST-FEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALISHITt 517
Cdd:cd00653 303 SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSLgLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 518 dsdekpvlrlllnsgvedlhnvhfshvnkpentliflngvligtavdpervvkavrdlrrsgllsefvsvsrsltnrsvf 597
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 598 issdgGRLCRPYIIVKNgtpmltqahvqelkegkmifedfvddgiveyldvnemndaliavygreigpETTHLEIEPFTL 677
Cdd:cd00653 382 -----GRIERPYRIVEK---------------------------------------------------EVTHIEISPSQI 405
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 678 LGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIAYNQQKRIDSIMYLLCYPQRPLVKSKTIELTNFEKLPAGANGIIAVM 757
Cdd:cd00653 406 LSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVM 485
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 758 SYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTAKKYPNQTFDRLLgpalDPNTRKPIFKHKNLDQEGIVFAGARIMPK 837
Cdd:cd00653 486 SYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITR----GDIPNVSEEKLKNLDEDGIIRPGARVEPG 561
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 838 QTIINKHMPVVSGESGPGASASAntigiagrqVDYKDVSITYKTPTPSYAERVLLTY---NEDEAHLFKVLLRQTRRPEL 914
Cdd:cd00653 562 DILVGKITPKGETESTPIFGEKA---------RDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQI 632
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 915 GDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKAGVVNGTYHYGTAFGGDQVKDVC 994
Cdd:cd00653 633 GDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDIS 712
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 995 EELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEMERD 1074
Cdd:cd00653 713 ELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERD 792
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 25144348 1075 CLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIGSKGWCQKCRSSKSMANIKIPYACKLLFQELQSMNIVPRLD 1148
Cdd:cd00653 793 ALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
28-1150 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1046.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 28 KWLLVPAFLKVRGLVKQHLVSFDHFVQEEIRSImLSNQKITSDANPNFYLKYLDIRIGKPSSEEGLNMTHDkITPQECRL 107
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEI-VDEFGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERP-ITPMEARL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 108 RDMTYSAPISVDIEYTRGNQRVFKKDLIIGRMPIMLRSSKCILRDLAEEELARVQECPYDPGGYFVVKGSEKVILIQEQL 187
Cdd:PRK08565 79 RNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 188 SKNRIMVGR---NSSKELQCEVLSSTSERKSKTYVTMKK-GKYSVRHNQLTDDVPVSIIFKAMGVESDFDIVSTIGHEEK 263
Cdd:PRK08565 159 APNRVLVDKgeaGSSITHTAKVISSRAGYRAQVTVERRKdGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPE 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 264 YVSAFAQTLEESINAGVyTQQQALAYVTSKVkarkftpfgsLPGTsvsvltpPKE---HEAVDFLSNSMITHIACPDGNF 340
Cdd:PRK08565 239 IQQELLPSLEQASSIAA-TVEDALDYIGKRV----------AIGQ-------PREyriERAEQILDKYLLPHLGTSPEDR 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 341 KMKAIYLGLMTRRLIQTELGENGLDDRDFYGNKRLELAGSLLSLLFEDVFKRFNSELKRIADNALMKTMAAPLDIVkhMR 420
Cdd:PRK08565 301 IKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VR 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 421 QDMITNTIVNAMSTGNWIikrfrMERLGVTQVLSRLSYISALGMMTRINSTFEKTRKVSGPRSLQPSQWGMLCPSDTPEG 500
Cdd:PRK08565 379 PDIITERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEG 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 501 EACGLVKNLALISHITTDSDEKPVLRLLLNSGVEDLHNVHFShvNKPENTLIFLNGVLIGTAVDPERVVKAVRDLRRSGL 580
Cdd:PRK08565 454 PNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE--EYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGK 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 581 LSEFVSVS--RSLTNRSVFISSDGGRLCRPYIIVKNGTPMLTQAHVQELKEGKMIFEDFVDDGIVEYLDVNEMNDALIAV 658
Cdd:PRK08565 532 ISDEVNVAyiETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVAL 611
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 659 YGREIGPETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIAYNQQKRIDSIMYLLCYPQRPLVKSKTI 738
Cdd:PRK08565 612 DPEDLTPEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRAL 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 739 ELTNFEKLPAGANGIIAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTAKKYPNQTFDRLLGPalDPNTR--KPI 816
Cdd:PRK08565 692 EIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRgyRGE 769
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 817 FKHKNLDQEGIVFAGARIMPKQTIINKhmpvvsgESGPGASASANTIGIAGrqVDYKDVSITYKTPTPSYAERVLLTYNE 896
Cdd:PRK08565 770 EYYRKLDEDGIVSPEVEVKGGDVLIGK-------TSPPRFLEELEELSLGL--QERRDTSVTVRHGEKGIVDTVLITESP 840
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 897 DEAHLFKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKAGVVN 976
Cdd:PRK08565 841 EGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALE 920
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 977 GTYHYGTAFGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQP 1056
Cdd:PRK08565 921 GRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQP 1000
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1057 TEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIG------SKGWCQKCRSSKSMANIKIPYA 1130
Cdd:PRK08565 1001 TEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAwydrrkNKYVCPIHGDKGNISPVEVSYA 1080
|
1130 1140
....*....|....*....|
gi 25144348 1131 CKLLFQELQSMNIVPRLDLA 1150
Cdd:PRK08565 1081 FKLLLQELMSMGISPRLKLG 1100
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
552-1150 |
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: 677.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 552 IFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSLTNRSVFISSDGGRLCRPYIIVKNGTPMLTQAHVQELKEGK 631
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 632 MIFEDFVDDGIVEYLDVNEMNDALIAVYGREIGPETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIA 711
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 712 YNQQKRIDSIMYLLCYPQRPLVKSKTIELTNFEKLPAGANGIIAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGT 791
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 792 AKKYPNQTFDRLLGPalDPNTR--KPIFKHKNLDQEGIVFAGARIMPKQTIINKHMPvvsgesgPGASASANTIGIAGRQ 869
Cdd:TIGR03670 241 ERRYPGGQEDRFEIP--EPDVRgyRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PRFLEELREFGLVTER 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 870 vdYKDVSITYKTPTPSYAERVLLTYNEDEAHLFKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMI 949
Cdd:TIGR03670 312 --RRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLI 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 950 MNPHGYPSRMTVGKLMELLSGKAGVVNGTYHYGTAFGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIY 1029
Cdd:TIGR03670 390 INPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIY 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1030 YQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIG- 1108
Cdd:TIGR03670 470 YQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAw 549
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 25144348 1109 -----SKGWCQKCRSSKSMANIKIPYACKLLFQELQSMNIVPRLDLA 1150
Cdd:TIGR03670 550 edkrkGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
32-1147 |
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: 580.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 32 VPAFLKVRGLVKQHLVSFDHFVQEEIRSImLSNQKITSDANPNFYLKYLDIRIGKPsseeglnmthdKITPQECRLRDMT 111
Cdd:COG0085 7 IKEPLELPNLLEIQLDSFNWFLEEGLQEI-FDEISPIEDFTGNLSLEFGDYRLGEP-----------KYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 112 YSAPISVDIEYTRGN------QRVFkkdliIGRMPIMLRSskcilrdlaeeelarvqecpydpgGYFVVKGSEKVILIQE 185
Cdd:COG0085 75 YAAPLYVKVRLVNKEtgeikeQEVF-----MGDFPLMTDS------------------------GTFIINGTERVIVSQL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 186 QLSKNRIMVGRN--SSKEL-QCEVLSStseRKSKTYV-TMKKGKYSVRHNQLTDdVPVSIIFKAMGVESDFDIVSTIGHE 261
Cdd:COG0085 126 VRSPGVYFVEEEdkSGKDLySAKVIPS---RGAWLEFeTDKDGTIYVRIDRKRK-IPVTVLLRALGLETDEEILEAFGDD 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 262 EKYVSaFAQTLEESinaGVYTQQQALAYVTSKVKarkftpfgslPGTsvsvltPPKEHEAVDFLSNSMIT---------- 331
Cdd:COG0085 202 PIQEY-ILATLEKD---NTKTQEEALLEIYRKLR----------PGE------PPTIERAEQLLDNLFFDpkrydlahvg 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 332 --------HIACPDGNFKMKAIYLGLMTRRLIQTELGENGLDDRDFYGNKRLELAGSLLSLLFEDVFKRfnseLKRIADN 403
Cdd:COG0085 262 rykinkklGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSR----MERVVRE 337
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 404 ALMKTMAAPLDIvkhmrQDMITNTIVNAmstgnwIIKRFrMERLGVTQV------LSRLSY---ISALGM--MTRINSTF 472
Cdd:COG0085 338 RMTTQDVEAITP-----QSLINIRPVVA------AIKEF-FGSSQLSQFmdqtnpLSELTHkrrLSALGPggLSRERAGF 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 473 EktrkVsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLALISHIttdsdekpvlrlllnsgvedlhnvhfshvnkpentli 552
Cdd:COG0085 406 E----V---RDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV------------------------------------- 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 553 flngvligtavdpervvkavrdlrrsgllSEFvsvsrsltnrsvfissdgGRLCRPYIIVKNGtpmltqahvqelkegkm 632
Cdd:COG0085 442 -----------------------------NEY------------------GFIETPYRKVENG----------------- 457
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 633 ifedFVDDGIvEYLDVNEMNDALIAVYGREIG-----------------------PETTHLEIEPFTLLGVCAGLIPYPH 689
Cdd:COG0085 458 ----KVTDEI-EYLTADEEENYYIAQANAPLDedgnfleervlvryrgeevlvppEEVDYMDVSPKQIVSVATSLIPFLE 532
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 690 HNQSPRNTYQCAMGKQAMGTIA-------YNQQKRIDSIMYLlCYPQRPLVKS-KTIEL---------TNFEKLPAGANG 752
Cdd:COG0085 533 HDDANRALMGANMQRQAVPLLRpeapllhYPLQKFQRSNQGT-CINQRPIVRVgDRVEKgdvladgpaTDNGELALGQNL 611
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 753 IIAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTAKKYPnqtfdrlLGP---ALD-PNTRKPIFKhkNLDQEGIV 828
Cdd:COG0085 612 LVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTK-------LGPeeiTRDiPNVSEEALR--NLDEDGII 682
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 829 FAGARIMPKQTIINKhmpvVS--GESGPGAS-ASANTI-GIAGRQVdyKDVSItyKTPtpsYAER-----VLLTYNEDEA 899
Cdd:COG0085 683 RIGAEVKGGDILVGK----VTpkGETELTPEeRLLRAIfGEKAREV--RDTSL--RVP---HGEKgkvidVKVFSREEGD 751
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 900 HLF-------KVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKA 972
Cdd:COG0085 752 ELPpgvnklvRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWA 831
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 973 GVVNGTYHYGTAFGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAAL 1052
Cdd:COG0085 832 AALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLI 911
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1053 TRQPTEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDefkvDVCtgcgviGSKGWCQKCRSSKSMANIKIPYACK 1132
Cdd:COG0085 912 TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFK 981
|
1210
....*....|....*
gi 25144348 1133 LLFQELQSMNIVPRL 1147
Cdd:COG0085 982 VLLKELQSLGLDVEV 996
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
681-1062 |
3.20e-174 |
|
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: 516.70 E-value: 3.20e-174
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 681 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIAYNQQKRIDSIMYLLCYPQRPLVKSKTIELTNFEKLPAGANGIIAVMSYS 760
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 761 GYDIEDALVLNKASLDRGYGRCLVYKHVKgtAKKYPNQTFDRLLGpalDPNtRKPIFKHKNLDQEGIVFAGARIMPKQTI 840
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPIEEITR---DIP-NVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 841 INKHMPvvsgesgPGASASANTIGIAGRQvDYKDVSITYKTPTPSYAERVLL-TYNEDEAHLFKVLLRQTRRPELGDKFS 919
Cdd:pfam00562 155 VGKVGP-------TELTKLLRAIFGEKAR-DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFA 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 920 SRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKAGVVNGTYHYGTAFGG--DQVKDVCEEL 997
Cdd:pfam00562 227 SRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGasTEVEDIGELL 306
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 25144348 998 AACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSR 1062
Cdd:pfam00562 307 EKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
552-613 |
4.60e-26 |
|
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: 101.67 E-value: 4.60e-26
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 25144348 552 IFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSLTNRSVFISSDGGRLCRPYIIVK 613
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
634-674 |
2.90e-09 |
|
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: 53.70 E-value: 2.90e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 25144348 634 FEDFVDDGIVEYLDVNEMNDALIAVY-------GREIG-----PETTHLEIEP 674
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. ... |
41-1148 |
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: 1135.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 41 LVKQHLVSFDHFVQEEIRSIMLSNQKITSDA-NPNFYLKYLDIRIGKPSSEEGlnMTHDKITPQECRLRDMTYSAPISVD 119
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 120 IEYTRGNQRVFK-KDLIIGRMPIMLRSSKCILRDLAEEELARVQECPYDPGGYFVVKGSEKVILIQEQLSKNRIMVgrns 198
Cdd:cd00653 79 IRLTVNDKGKIKeQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIV---- 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 199 skelqcevlsstsERKSKTYVtmkkgkYSVRHNQLTDDVPVSIIFkamgVESDFDIvSTIGHEEKYvsafaqtleesina 278
Cdd:cd00653 155 -------------EDSKGKRI------YTKTSIPSYSPYRGSWLE----VKSDKKK-DRIYVRIDL-------------- 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 279 gvYTQQQALAYVTSKVkarkftpfgslpgtsvsvltppkeheavdflsnsmithiacpdgnfkmkaIYLGLMTRRLIQTE 358
Cdd:cd00653 197 --KRQEEALKYIGKRF--------------------------------------------------EDLIYMIRKLILLV 224
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 359 LGENGLDDRDFYGNKRLELAGSLLSLLFEDVFKRFNSELKRIADNALMKTMAapLDIVKHMRQDMITNTIVNAMSTGNWI 438
Cdd:cd00653 225 LGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKD--LTPQLLINSKPITSGIKEFLATGNWG 302
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 439 IKRFRMERLGVTQVLSRLSYISALGMMTRINST-FEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALISHITt 517
Cdd:cd00653 303 SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSLgLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 518 dsdekpvlrlllnsgvedlhnvhfshvnkpentliflngvligtavdpervvkavrdlrrsgllsefvsvsrsltnrsvf 597
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 598 issdgGRLCRPYIIVKNgtpmltqahvqelkegkmifedfvddgiveyldvnemndaliavygreigpETTHLEIEPFTL 677
Cdd:cd00653 382 -----GRIERPYRIVEK---------------------------------------------------EVTHIEISPSQI 405
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 678 LGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIAYNQQKRIDSIMYLLCYPQRPLVKSKTIELTNFEKLPAGANGIIAVM 757
Cdd:cd00653 406 LSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVM 485
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 758 SYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTAKKYPNQTFDRLLgpalDPNTRKPIFKHKNLDQEGIVFAGARIMPK 837
Cdd:cd00653 486 SYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITR----GDIPNVSEEKLKNLDEDGIIRPGARVEPG 561
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 838 QTIINKHMPVVSGESGPGASASAntigiagrqVDYKDVSITYKTPTPSYAERVLLTY---NEDEAHLFKVLLRQTRRPEL 914
Cdd:cd00653 562 DILVGKITPKGETESTPIFGEKA---------RDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQI 632
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 915 GDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKAGVVNGTYHYGTAFGGDQVKDVC 994
Cdd:cd00653 633 GDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDIS 712
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 995 EELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEMERD 1074
Cdd:cd00653 713 ELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERD 792
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 25144348 1075 CLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIGSKGWCQKCRSSKSMANIKIPYACKLLFQELQSMNIVPRLD 1148
Cdd:cd00653 793 ALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
28-1150 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1046.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 28 KWLLVPAFLKVRGLVKQHLVSFDHFVQEEIRSImLSNQKITSDANPNFYLKYLDIRIGKPSSEEGLNMTHDkITPQECRL 107
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEI-VDEFGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERP-ITPMEARL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 108 RDMTYSAPISVDIEYTRGNQRVFKKDLIIGRMPIMLRSSKCILRDLAEEELARVQECPYDPGGYFVVKGSEKVILIQEQL 187
Cdd:PRK08565 79 RNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 188 SKNRIMVGR---NSSKELQCEVLSSTSERKSKTYVTMKK-GKYSVRHNQLTDDVPVSIIFKAMGVESDFDIVSTIGHEEK 263
Cdd:PRK08565 159 APNRVLVDKgeaGSSITHTAKVISSRAGYRAQVTVERRKdGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPE 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 264 YVSAFAQTLEESINAGVyTQQQALAYVTSKVkarkftpfgsLPGTsvsvltpPKE---HEAVDFLSNSMITHIACPDGNF 340
Cdd:PRK08565 239 IQQELLPSLEQASSIAA-TVEDALDYIGKRV----------AIGQ-------PREyriERAEQILDKYLLPHLGTSPEDR 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 341 KMKAIYLGLMTRRLIQTELGENGLDDRDFYGNKRLELAGSLLSLLFEDVFKRFNSELKRIADNALMKTMAAPLDIVkhMR 420
Cdd:PRK08565 301 IKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAI--VR 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 421 QDMITNTIVNAMSTGNWIikrfrMERLGVTQVLSRLSYISALGMMTRINSTFEKTRKVSGPRSLQPSQWGMLCPSDTPEG 500
Cdd:PRK08565 379 PDIITERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEG 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 501 EACGLVKNLALISHITTDSDEKPVLRLLLNSGVEDLHNVHFShvNKPENTLIFLNGVLIGTAVDPERVVKAVRDLRRSGL 580
Cdd:PRK08565 454 PNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE--EYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGK 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 581 LSEFVSVS--RSLTNRSVFISSDGGRLCRPYIIVKNGTPMLTQAHVQELKEGKMIFEDFVDDGIVEYLDVNEMNDALIAV 658
Cdd:PRK08565 532 ISDEVNVAyiETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVAL 611
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 659 YGREIGPETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIAYNQQKRIDSIMYLLCYPQRPLVKSKTI 738
Cdd:PRK08565 612 DPEDLTPEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRAL 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 739 ELTNFEKLPAGANGIIAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTAKKYPNQTFDRLLGPalDPNTR--KPI 816
Cdd:PRK08565 692 EIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRgyRGE 769
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 817 FKHKNLDQEGIVFAGARIMPKQTIINKhmpvvsgESGPGASASANTIGIAGrqVDYKDVSITYKTPTPSYAERVLLTYNE 896
Cdd:PRK08565 770 EYYRKLDEDGIVSPEVEVKGGDVLIGK-------TSPPRFLEELEELSLGL--QERRDTSVTVRHGEKGIVDTVLITESP 840
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 897 DEAHLFKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKAGVVN 976
Cdd:PRK08565 841 EGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALE 920
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 977 GTYHYGTAFGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQP 1056
Cdd:PRK08565 921 GRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQP 1000
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1057 TEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIG------SKGWCQKCRSSKSMANIKIPYA 1130
Cdd:PRK08565 1001 TEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAwydrrkNKYVCPIHGDKGNISPVEVSYA 1080
|
1130 1140
....*....|....*....|
gi 25144348 1131 CKLLFQELQSMNIVPRLDLA 1150
Cdd:PRK08565 1081 FKLLLQELMSMGISPRLKLG 1100
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
552-1149 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 678.99 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 552 IFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSLTNRSVFISSDGGRLCRPYIIVKNGTPMLTQAHVQELKEGK 631
Cdd:PRK07225 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 632 MIFEDFVDDGIVEYLDVNEMNDALIAVYGREIGPETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIA 711
Cdd:PRK07225 87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 712 YNQQKRIDSIMYLLCYPQRPLVKSKTIELTNFEKLPAGANGIIAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGT 791
Cdd:PRK07225 167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 792 AKKYPNQTFDRLLGPALDPNTRKPIFKHKNLDQEGIVFAGARIMPKQTIINKHMP--VVSGESGPGASASANtigiagrq 869
Cdd:PRK07225 247 ERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPprFLEEPDDFGISPEKR-------- 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 870 vdyKDVSITYKTPTPSYAERVLLTYNEDEAHLFKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMI 949
Cdd:PRK07225 319 ---RETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLI 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 950 MNPHGYPSRMTVGKLMELLSGKAGVVNGTYHYGTAFGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIY 1029
Cdd:PRK07225 396 INPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIY 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1030 YQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIG- 1108
Cdd:PRK07225 476 YQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAi 555
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 25144348 1109 -----SKGWCQKCRSSKSMANIKIPYACKLLFQELQSMNIVPRLDL 1149
Cdd:PRK07225 556 ydkkrNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
552-1150 |
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: 677.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 552 IFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSLTNRSVFISSDGGRLCRPYIIVKNGTPMLTQAHVQELKEGK 631
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 632 MIFEDFVDDGIVEYLDVNEMNDALIAVYGREIGPETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIA 711
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 712 YNQQKRIDSIMYLLCYPQRPLVKSKTIELTNFEKLPAGANGIIAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGT 791
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 792 AKKYPNQTFDRLLGPalDPNTR--KPIFKHKNLDQEGIVFAGARIMPKQTIINKHMPvvsgesgPGASASANTIGIAGRQ 869
Cdd:TIGR03670 241 ERRYPGGQEDRFEIP--EPDVRgyRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PRFLEELREFGLVTER 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 870 vdYKDVSITYKTPTPSYAERVLLTYNEDEAHLFKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMI 949
Cdd:TIGR03670 312 --RRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLI 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 950 MNPHGYPSRMTVGKLMELLSGKAGVVNGTYHYGTAFGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIY 1029
Cdd:TIGR03670 390 INPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIY 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1030 YQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIG- 1108
Cdd:TIGR03670 470 YQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAw 549
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 25144348 1109 -----SKGWCQKCRSSKSMANIKIPYACKLLFQELQSMNIVPRLDLA 1150
Cdd:TIGR03670 550 edkrkGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELG 596
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
32-1147 |
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: 580.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 32 VPAFLKVRGLVKQHLVSFDHFVQEEIRSImLSNQKITSDANPNFYLKYLDIRIGKPsseeglnmthdKITPQECRLRDMT 111
Cdd:COG0085 7 IKEPLELPNLLEIQLDSFNWFLEEGLQEI-FDEISPIEDFTGNLSLEFGDYRLGEP-----------KYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 112 YSAPISVDIEYTRGN------QRVFkkdliIGRMPIMLRSskcilrdlaeeelarvqecpydpgGYFVVKGSEKVILIQE 185
Cdd:COG0085 75 YAAPLYVKVRLVNKEtgeikeQEVF-----MGDFPLMTDS------------------------GTFIINGTERVIVSQL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 186 QLSKNRIMVGRN--SSKEL-QCEVLSStseRKSKTYV-TMKKGKYSVRHNQLTDdVPVSIIFKAMGVESDFDIVSTIGHE 261
Cdd:COG0085 126 VRSPGVYFVEEEdkSGKDLySAKVIPS---RGAWLEFeTDKDGTIYVRIDRKRK-IPVTVLLRALGLETDEEILEAFGDD 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 262 EKYVSaFAQTLEESinaGVYTQQQALAYVTSKVKarkftpfgslPGTsvsvltPPKEHEAVDFLSNSMIT---------- 331
Cdd:COG0085 202 PIQEY-ILATLEKD---NTKTQEEALLEIYRKLR----------PGE------PPTIERAEQLLDNLFFDpkrydlahvg 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 332 --------HIACPDGNFKMKAIYLGLMTRRLIQTELGENGLDDRDFYGNKRLELAGSLLSLLFEDVFKRfnseLKRIADN 403
Cdd:COG0085 262 rykinkklGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSR----MERVVRE 337
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 404 ALMKTMAAPLDIvkhmrQDMITNTIVNAmstgnwIIKRFrMERLGVTQV------LSRLSY---ISALGM--MTRINSTF 472
Cdd:COG0085 338 RMTTQDVEAITP-----QSLINIRPVVA------AIKEF-FGSSQLSQFmdqtnpLSELTHkrrLSALGPggLSRERAGF 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 473 EktrkVsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLALISHIttdsdekpvlrlllnsgvedlhnvhfshvnkpentli 552
Cdd:COG0085 406 E----V---RDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV------------------------------------- 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 553 flngvligtavdpervvkavrdlrrsgllSEFvsvsrsltnrsvfissdgGRLCRPYIIVKNGtpmltqahvqelkegkm 632
Cdd:COG0085 442 -----------------------------NEY------------------GFIETPYRKVENG----------------- 457
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 633 ifedFVDDGIvEYLDVNEMNDALIAVYGREIG-----------------------PETTHLEIEPFTLLGVCAGLIPYPH 689
Cdd:COG0085 458 ----KVTDEI-EYLTADEEENYYIAQANAPLDedgnfleervlvryrgeevlvppEEVDYMDVSPKQIVSVATSLIPFLE 532
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 690 HNQSPRNTYQCAMGKQAMGTIA-------YNQQKRIDSIMYLlCYPQRPLVKS-KTIEL---------TNFEKLPAGANG 752
Cdd:COG0085 533 HDDANRALMGANMQRQAVPLLRpeapllhYPLQKFQRSNQGT-CINQRPIVRVgDRVEKgdvladgpaTDNGELALGQNL 611
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 753 IIAVMSYSGYDIEDALVLNKASLDRGYGRCLVYKHVKGTAKKYPnqtfdrlLGP---ALD-PNTRKPIFKhkNLDQEGIV 828
Cdd:COG0085 612 LVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTK-------LGPeeiTRDiPNVSEEALR--NLDEDGII 682
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 829 FAGARIMPKQTIINKhmpvVS--GESGPGAS-ASANTI-GIAGRQVdyKDVSItyKTPtpsYAER-----VLLTYNEDEA 899
Cdd:COG0085 683 RIGAEVKGGDILVGK----VTpkGETELTPEeRLLRAIfGEKAREV--RDTSL--RVP---HGEKgkvidVKVFSREEGD 751
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 900 HLF-------KVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKA 972
Cdd:COG0085 752 ELPpgvnklvRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWA 831
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 973 GVVNGTYHYGTAFGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAAL 1052
Cdd:COG0085 832 AALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLI 911
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1053 TRQPTEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDefkvDVCtgcgviGSKGWCQKCRSSKSMANIKIPYACK 1132
Cdd:COG0085 912 TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFK 981
|
1210
....*....|....*
gi 25144348 1133 LLFQELQSMNIVPRL 1147
Cdd:COG0085 982 VLLKELQSLGLDVEV 996
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
681-1062 |
3.20e-174 |
|
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: 516.70 E-value: 3.20e-174
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 681 CAGLIPYPHHNQSPRNTYQCAMGKQAMGTIAYNQQKRIDSIMYLLCYPQRPLVKSKTIELTNFEKLPAGANGIIAVMSYS 760
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 761 GYDIEDALVLNKASLDRGYGRCLVYKHVKgtAKKYPNQTFDRLLGpalDPNtRKPIFKHKNLDQEGIVFAGARIMPKQTI 840
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPIEEITR---DIP-NVSEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 841 INKHMPvvsgesgPGASASANTIGIAGRQvDYKDVSITYKTPTPSYAERVLL-TYNEDEAHLFKVLLRQTRRPELGDKFS 919
Cdd:pfam00562 155 VGKVGP-------TELTKLLRAIFGEKAR-DVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFA 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 920 SRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKAGVVNGTYHYGTAFGG--DQVKDVCEEL 997
Cdd:pfam00562 227 SRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGasTEVEDIGELL 306
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 25144348 998 AACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSR 1062
Cdd:pfam00562 307 EKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
26-534 |
3.34e-108 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 348.09 E-value: 3.34e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 26 EDKWLLVPAFLKVRGLVKQHLVSFDHFVQEEIRSIMLSNQKITSDANPNFYLKYLDIRIGKPSSEEGlNMTHDKITPQEC 105
Cdd:PRK09606 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEA-DGSEREIYPMEA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 106 RLRDMTYSAPISVDIEYTRGNQRVFKKDLIIGRMPIMLRSSKCILRDLAEEELARVQECPYDPGGYFVVKGSEKVILIQE 185
Cdd:PRK09606 82 RLRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 186 QLSKNRIMVGRNSSKELQCEVLSSTSERKS-KTYVTM---KKGKYSVRHNQLTDDVPVSIIFKAMGVESDFDIVSTIGHE 261
Cdd:PRK09606 162 DLAPNKILVEKDERYGDRIEVAKVFSQRRGyRALVTVernRDGLLEVSFPSVPGSIPFVILMRALGLETDEEIVEAVSDD 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 262 EKYVSAFAQTLEEsinAGVYTQQQALAYVTSKVkarkftpfgsLPGTsvsvltpPKEHE---AVDFLSNSMITHIACPDG 338
Cdd:PRK09606 242 PEIVKFMLENLEE---AEVDTQEEALEYIGKRV----------APGQ-------TKEYRikrAEYVIDRYLLPHLGVEPE 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 339 NFKMKAIYLGLMTRRLIQTELGENGLDDRDFYGNKRLELAGSLLSLLFEDVFKRFNSELKRIADNALMKTmaAPLDIVKH 418
Cdd:PRK09606 302 VRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRN--RELSIKTA 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 419 MRQDMITNTIVNAMSTGNWIikrfrMERLGVTQVLSRLSYISALGMMTRINSTFEKTRKVSGPRSLQPSQWGMLCPSDTP 498
Cdd:PRK09606 380 VRSDVLTERLEHAMATGNWV-----GGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETP 454
|
490 500 510
....*....|....*....|....*....|....*.
gi 25144348 499 EGEACGLVKNLALISHITTDSDEKPVLRLLLNSGVE 534
Cdd:PRK09606 455 EGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
40-426 |
4.77e-97 |
|
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: 314.70 E-value: 4.77e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 40 GLVKQHLVSFDHFVQEEIRSIMLSNQKITSDANP--------NFYLKYLDIRIGKPSSEEGLNMTHdKITPQECRLRDMT 111
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIqhpgengdKLSLKFGQIRLGKPMFDETDGSTR-EIYPQECRLRNLT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 112 YSAPISVDIEYTRGNQRVFKKDLI-IGRMPIMLRSSKCILRDLAEEELARVQECPYDPGGYFVVKGSEKVILIQEQLSKN 190
Cdd:pfam04563 80 YSAPLYVDLELSVYNGEDIKPIEVfIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRN 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 191 RIMVGRNSSKE---LQCEVLSSTSE--RKSKTYVT-----MKKGKYSVRHNQLTDDVPVSIIFKAMGVESDFDIVSTIGH 260
Cdd:pfam04563 160 HPIVFKKADPKkrgSVASVRSSAEIsvRPDSTSWVnvleyLSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELICY 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 261 EEK---YVSAFAQTLEESINAGVYTQQQALAYVTSKVKARKftpfgslpgtSVSVLTPPKEHEAVDFLSNSMITHIACPD 337
Cdd:pfam04563 240 DVNdqqLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIF----------RMGRPREPRIKYAEEILQKEVLPHLGTYE 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 338 GNFKMKAIYLGLMTRRLIQTELGENGLDDRDFYGNKRLELAGSLLSLLFEDVFKRFNSELKRIADNALMKTMAAPLDIVk 417
Cdd:pfam04563 310 LDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLL- 388
|
....*....
gi 25144348 418 hMRQDMITN 426
Cdd:pfam04563 389 -VNAKPITS 396
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
32-1141 |
1.28e-66 |
|
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: 244.96 E-value: 1.28e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 32 VPAFLKVRGLVKQHLVSFDHFVQ----------EEIRSIMLSNQKITsDANPNFYLKYLDIRIGKPsseeglnmthdKIT 101
Cdd:TIGR02013 11 IPEVLEVPNLLEIQLDSYDWFLQqdtppekrkeEGLEEVFKSIFPIE-DYTGNIELEYLSYRLGEP-----------KYS 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 102 PQECRLRDMTYSAPISVDIEYT----RGNQRVFKKDLIIGRMPIMLRSskcilrdlaeeelarvqecpydpgGYFVVKGS 177
Cdd:TIGR02013 79 VEECKERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLMTDR------------------------GTFIINGA 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 178 EKVILIQEQLSKNRIMVGRNSSKELQCEVLSST--SERKS-KTYVTMKKGKYSVRHNQlTDDVPVSIIFKAMGVESDFDI 254
Cdd:TIGR02013 135 ERVVVSQLHRSPGVFFSSEKDTTKSGKVLFSARiiPYRGSwLEFETDKKDVLYVRIDR-KRKLPATVLLRALGYTIDTLI 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 255 VSTIGHEEKYVSafaqTLEesiNAGVYTQQQALAYVTSKVKarkftpfgslPGTsvsvltPPKEHEAVDFLSNSMIThia 334
Cdd:TIGR02013 214 LNRLGSGEYIRN----TLR---KDPTNSEEEALVEIYRKLR----------PGE------PPTVEAARSLLENLFFD--- 267
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 335 cPD-------GNFKMK-------AIYLGLMT--------RRLIQTELGENGLDDRDFYGNKRLELAGSLLSllfedvfKR 392
Cdd:TIGR02013 268 -PKrydlgrvGRYKLNkklgldvPESIGVLTkediiatiKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQ-------NQ 339
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 393 FNSELKRIADNA--LMKTMaaplDIVKHMRQDMITNTIVNAmstgnwIIKRFrmerLGVTQV---------LSRLSY--- 458
Cdd:TIGR02013 340 FRVGLARMERIVreRMSTQ----DTDTLTPQDLINAKPISA------AIKEF----FGSSQLsqfmdqtnpLAELTHkrr 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 459 ISALGM--MTRINSTFEKtrkvsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLALISHIttdsdekpvlrlllnsgvedl 536
Cdd:TIGR02013 406 LSALGPggLTRERAGFEV-------RDVHPTHYGRICPIETPEGPNIGLINSLSTYARV--------------------- 457
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 537 hnvhfshvnkpentliflngvligtavdpervvkavrdlrrsgllsefvsvsrsltNRSVFISSdggrlcrPYIIVKNGt 616
Cdd:TIGR02013 458 --------------------------------------------------------NEYGFIET-------PYRKVKDG- 473
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 617 pmltqahvqelkegkmifeDFVDDGIVEYLDVNEMNDALIA----------------VYGR------EIGPET-THLEIE 673
Cdd:TIGR02013 474 -------------------KVVVTDEIDYLTADEEDNYVIAqanapldengrfvedlVVARyrgeitLVSPDQvDYMDVS 534
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 674 PFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM-------------------------------GTIAYNQQKRI---- 718
Cdd:TIGR02013 535 PKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVVEYVDAKRIviry 614
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 719 ---------DSIMYLL----------CYPQRPLVK--SKTIE--------LTNFEKLPAGANGIIAVMSYSGYDIEDALV 769
Cdd:TIGR02013 615 dedeeepdgGIDIYRLlkyqrsnqdtCINQRPIVSvgDRVEAgdvladgpSTDLGELALGRNVLVAFMPWNGYNYEDAIL 694
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 770 LNKasldrgygrCLVYKHVKGTA--KKYPNQTFDRLLGP----ALDPNTRKPIFKhkNLDQEGIVFAGARIMPKQTIINK 843
Cdd:TIGR02013 695 ISE---------RLVKDDVFTSIhiEEYEVEARDTKLGPeeitRDIPNVSEEALR--NLDENGIVRIGAEVKAGDILVGK 763
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 844 HMPvvSGESGP-----------GASASantigiagrqvDYKDVSITyktpTPSYAE------RVLLTYNEDE-----AHL 901
Cdd:TIGR02013 764 VTP--KGETELtpeekllraifGEKAR-----------DVRDTSLR----VPPGVEgtvidvKVFSREQGDElppgvNKL 826
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 902 FKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKAGVVNGTY-- 979
Cdd:TIGR02013 827 VKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKgv 906
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 980 HYGTA-FGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTE 1058
Cdd:TIGR02013 907 PIATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLG 986
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1059 GRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDEfkvdvctgcgVIGskgwcqkcRSSKSMANIK--------IPYA 1130
Cdd:TIGR02013 987 GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD----------VVG--------RTKAYEAIVKgenvpepgIPES 1048
|
1290
....*....|.
gi 25144348 1131 CKLLFQELQSM 1141
Cdd:TIGR02013 1049 FNVLIKELQSL 1059
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
47-1152 |
2.25e-52 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 200.70 E-value: 2.25e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 47 VSFDHFVQEEIRSIMLSNQKITsdaNPNFYLKYLDIRigkpsseEGLNMTHDKITPQECRLRDMTYSAPISVDIEYTRGN 126
Cdd:CHL00207 16 TSFCWFLNEGLNEELNIFSKIF---DYTGNLELLLFG-------KNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFINLK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 127 QR-VFKKDLIIGRMPIMLRSskcilrdlaeeelarvqecpydpgGYFVVKGSEKVILIQE--------QLSKNRIMVGRN 197
Cdd:CHL00207 86 TNkIKFINYLIGNLPKMTQR------------------------GTFIINGLERVIVSQIirspgiyfKKEIKKNSNKIY 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 198 SSKELqcevlsstSERKS-KTYVTMKKGKYSVRHNQLTDdVPVSIIFKAMGVeSDFDIVS-TIGHEEKYVSAFAQTLEES 275
Cdd:CHL00207 142 SATLI--------PNRGSwIKFELDKNKEIWIRIDKNRK-KPLIIFLKALGL-TDQDIYSrLTKSEFLKKLKPILLNSNS 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 276 inagvYTQQQALAYVTSKVKARKFTPFGSLPGTSVSVLTPPKEHEAVDFLSNSMITHIACPDGNFKMKAIYLGLM--TRR 353
Cdd:CHL00207 212 -----YTNEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILsiIDK 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 354 LIQTELGENGLDDRDFYGNKRLELAGSLLSLLFEDVFKRFNSELKRiadnalmktmaapldivKHMRQDmITNTIVNAMS 433
Cdd:CHL00207 287 LINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRN-----------------RMTICD-IDSLSKFNLI 348
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 434 TGNWIIKRFRmERLGVTQVLSRLSYISALGMMT---RIN----STFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLV 506
Cdd:CHL00207 349 NPKPLIALIR-EFFGSSQLSQYMDQTNPLSELThkrRISilgpGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLI 427
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 507 KNLAliSHITTDSD---EKPVLRLL------------LNSGVEDLHNVHFSHVNKPENTLIFLNGVLIG-----TAVDPE 566
Cdd:CHL00207 428 GSLA--TNARINKFgfiETPFYKVIngkvkkfgnpiyLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRykqefKTVNPS 505
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 567 RVvkavrdlrRSGLLS--EFVSVSRSLTNrsvFISSDGGrlCRPYIivknGTPMLTQA----------------HVQELK 628
Cdd:CHL00207 506 KV--------DFIAISpiQVFSIAESLIP---FLEHNDA--NRALM----GSNMQRQAvpllypekpivgtgyeKQIALD 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 629 EGKMIFEdfVDDGIVEYLDVNE---MNDaliavYGREIgpeTTHLEiepftllgvcagliPYPHHNQsprNTyqcamgkq 705
Cdd:CHL00207 569 SGMTIIS--LTEGIVVSVSAYKiiiQDD-----NNRYI---HYYLQ--------------KYQRSNQ---NT-------- 613
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 706 amgtiaynqqkridsimyllCYPQRPLV----KSKTIEL------TNFEKLPAGANGIIAVMSYSGYDIEDALVLNKAsl 775
Cdd:CHL00207 614 --------------------CINYRPIVwvgeKINIGQIladgsdIDNSELALGQNVLVAYMPWEGYNFEDAILINKR-- 671
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 776 drgygrcLVYKHVKGTA--KKYP---NQTFDRLLGPALD-PNTRKPIFKhkNLDQEGIVFAGARIMPKQTIINKHMPVVS 849
Cdd:CHL00207 672 -------LVYEDLFTSIhiEKYEielRQTKLGSEEITRNiPNVSEYSLK--NLDENGIISIGSKVLAGDILVGKITPKGE 742
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 850 GESGPgasASANTIGIAGRQV-DYKDVSItyKTPTPSYA---ERVLLTYNEDEAH------LFKVLLRQTRRPELGDKFS 919
Cdd:CHL00207 743 SDQLP---EGKLLRAIFGEKAkDVKDTSL--RMPNGGYGrviKVEIFSRSKGDELkfgyylKIRVFIAQIRKIQVGDKLA 817
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 920 SRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSGKAG--------VVNGTYHYGTAFGGDQVK 991
Cdd:CHL00207 818 GRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGdnlnkrfkILPFDEMYGSEYSRILIN 897
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 992 DVCEELAACGYNYM-------GKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREG 1064
Cdd:CHL00207 898 NKLNQASIKNNEYWlfnsyhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHG 977
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1065 GLRLGEMERDCLIAYGASMLLIERLMVSSDEfkvdvctgcgVIGSKGWCQKCRSSKSMANIKIPYACKLLFQELQSMNiv 1144
Cdd:CHL00207 978 GQRFGEMEVWALEAFGAAYTLKELLTIKSDD----------MQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLG-- 1045
|
....*...
gi 25144348 1145 prLDLARY 1152
Cdd:CHL00207 1046 --LDIEAY 1051
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1064-1150 |
1.59e-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: 149.66 E-value: 1.59e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1064 GGLRLGEMERDCLIAYGASMLLIERLMVSSDEFKVDVCTGCGVIGSKGWCQKCRSSKSMANIKIPYACKLLFQELQSMNI 1143
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNKCPICKGETDISPGYIPESFKLLFQELQSLGI 80
|
....*..
gi 25144348 1144 VPRLDLA 1150
Cdd:pfam04560 81 DPRLLLE 87
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
354-1094 |
3.72e-39 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 158.53 E-value: 3.72e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 354 LIQTELGENGLDDRDFYGNKRLELAGSLLSllfedvfKRFNSELKRIaDNALMKTMAaplDIVKHMR----QDMITNTIV 429
Cdd:CHL00001 293 LIGMKFGMGTLDDIDHLKNKRIRSVADLLQ-------DQFGLALNRL-ENAVRGTIC---GAIRRKLiptpQNLVTSTPL 361
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 430 NAMstgnwiIKRFrmerLGVTQvLSRLsyisalgmMTRINSTFEKT--RKVS--GP------------RSLQPSQWGMLC 493
Cdd:CHL00001 362 TTT------YESF----FGSHP-LSQF--------LDQTNPLTEIVhgRKLSslGPggltgrtasfrvRDIHPSHYGRIC 422
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 494 PSDTPEGEACGLVKNLALISHITtdsdekpvlrlllNSGvedlhnvhfshvnkpentliflngvligtavdpervvkavr 573
Cdd:CHL00001 423 PIDTSEGINAGLIGSLAIHARIG-------------HWG----------------------------------------- 448
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 574 dlrrsGLLSEFVSVS-RSLTNRSVFISSDGGRlcrpYIIVKNGTPMltqAHVQELKEGKMIfedfvddgiveyldvnemn 652
Cdd:CHL00001 449 -----SLESPFYEISeRSKEERMVYLSPSEDE----YYMIAAGNSL---ALNQGIQEEQVV------------------- 497
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 653 dalIAVYGRE---IGPETTHLE-IEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM--------------------- 707
Cdd:CHL00001 498 ---PARYRQEfltIAWEQIHLRsIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVplsrsekcivgtglerqvald 574
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 708 ----------GTIAYNQQKRIDS-----------IMYL-----LCYPQRPLVK--------------SKTI--ELTnfek 745
Cdd:CHL00001 575 sgvvaiaeheGKIIYTDTDKIILsgngdtlsiplVMYQrsnknTCMHQKPQVRrgkcvkkgqiladgAATVggELA---- 650
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 746 lpAGANGIIAVMSYSGYDIEDALVLNKasldrgygrCLVYK------HVKgtakKYPNQTFDRLLGPalDPNTRK-P-IF 817
Cdd:CHL00001 651 --LGKNVLVAYMPWEGYNFEDAVLISE---------RLVYEdiytsfHIR----KYEIQTHVTSQGP--ERITKEiPhLE 713
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 818 KH--KNLDQEGIVFAGARIMPKQTIINKHMPVVSGES-------------GPGASASANT-----IGIAGRQVDYKdvSI 877
Cdd:CHL00001 714 AHllRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESsyapegrllraifGIQVSTSKETclklpIGGRGRVIDVR--WI 791
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 878 TYKTPTPSYAERVlltynedeahlfKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPS 957
Cdd:CHL00001 792 QKKGGSSYNPETI------------HVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPS 859
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 958 RMTVGKLMELLSGKAGVVNGTyHYG-TAFG---GDQV--KDVCEEL----AACGY------NYMGKDMLTSGITGQPLSA 1021
Cdd:CHL00001 860 RMNVGQIFECLLGLAGDLLNR-HYRiAPFDeryEQEAsrKLVFSELyeasKQTANpwvfepEYPGKSRLFDGRTGDPFEQ 938
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 25144348 1022 YIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSD 1094
Cdd:CHL00001 939 PVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
48-1094 |
5.41e-37 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 151.79 E-value: 5.41e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 48 SFDHFVQEE-------IRSIMLSNQKITsDANPNFYLKYLDIRIGKPsseeglnmthdKITPQECRLRDMTYSAPISVDI 120
Cdd:PRK00405 34 SFDWFLQLDvppedegLEEVFRSIFPIE-DFNGNLSLEFVSYELGEP-----------KYDVEECKERGLTYSAPLRVKL 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 121 EYTRGN------QRVFkkdliIGRMPIMlrsskcilrdlaeeelarvqecpyDPGGYFVVKGSEKVILIQeqlsknriMV 194
Cdd:PRK00405 102 RLINKEtgeikeQEVY-----MGDIPLM------------------------TENGTFIINGTERVIVSQ--------LH 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 195 -----------GRNSSKELQ--CEVLSStseRKSKTYVTM-KKGKYSVRhnqltDD----VPVSIIFKAMGVeSDFDIVS 256
Cdd:PRK00405 145 rspgvyfdhdkDKTSSGKLLysARIIPY---RGSWLEFEFdPKDILYVR-----IDrrrkLPVTVLLRALGY-SDEEILD 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 257 TIGHEEKYVSAFAQTLEESInaGVYTQQQALAYVTSKVKARKFTPFGSLPGTSVSVLT---------------------- 314
Cdd:PRK00405 216 LFYEKEEFGKEIEVPVEYLL--GKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTlekdptssreealveiyrrlrp 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 315 --PPKEHEAVDFLSNsmitHIACPD-------GNFKM--KaiyLGLMT----------------RRLIQTELGENGLDDR 367
Cdd:PRK00405 294 gePPTVEAARSLLEN----LFFDPKrydlskvGRYKLnkK---LGLDEdedvrvltkediiatiKYLINLRNGKGEVDDI 366
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 368 DFYGNKRLELAGSLLSllfedvfKRFNSELKRIAdNALMKTMAApLDIVKHMRQDMITNTIVNAmstgnwIIKRFrmerL 447
Cdd:PRK00405 367 DHLGNRRVRSVGELLQ-------NQFRIGLSRME-RAVRERMSL-QDLDTLTPQDLINAKPVVA------AIKEF----F 427
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 448 GVTQV---------LSRLSY---ISALGM--MTRINSTFEktrkVsgpRSLQPSQWGMLCPSDTPEGEACGLVKNLALis 513
Cdd:PRK00405 428 GSSQLsqfmdqtnpLSELTHkrrLSALGPggLTRERAGFE----V---RDVHPTHYGRICPIETPEGPNIGLINSLAT-- 498
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 514 hittdsdekpvlrlllnsgvedlhnvhFSHVNKpentliflNGVLIgTavdPERVVKAVRdlrrsgllsefvsvsrsLTN 593
Cdd:PRK00405 499 ---------------------------YARVNE--------YGFIE-T---PYRKVVDGK-----------------VTD 522
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 594 RSVFISSD--GGrlcrpYIIVkngtpmltQAHVqELKEGKMIFEDFV------DDGIVEYLDVNEMndaliavygreigp 665
Cdd:PRK00405 523 EIVYLTADeeDN-----YVIA--------QANA-PLDEDGRFVDELVtarykgEFVLVPPEEVDYM-------------- 574
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 666 etthlEIEPFTLLGVCAGLIPYPHHNQSPRntyqcA-MG----KQA--------------M-----------------GT 709
Cdd:PRK00405 575 -----DVSPKQVVSVAASLIPFLEHDDANR-----AlMGsnmqRQAvpllrpeaplvgtgMerrvardsgavvvakrdGV 644
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 710 IAYNQQKRI------------DSIMYLL----------CYPQRPLVK---------------SktielTNFEKLPAGANG 752
Cdd:PRK00405 645 VEYVDASRIvvrveeldpgedGVDIYNLikfqrsnqntCINQRPIVKvgdrvekgdvladgpS-----TDNGELALGQNV 719
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 753 IIAVMSYSGYDIEDALVLNkaslDRgygrcLVYK------HVKgtakKYPNQTFDRLLGP-------------ALdpntr 813
Cdd:PRK00405 720 LVAFMPWNGYNFEDAILIS----ER-----LVKEdvftsiHIE----EYEIEARDTKLGPeeitrdipnvseeAL----- 781
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 814 kpifkhKNLDQEGIVFAGA----------RIMPKqtiinkhmpvvsGESGP-----------GASASantigiagrqvDY 872
Cdd:PRK00405 782 ------RNLDESGIVRIGAevkpgdilvgKVTPK------------GETELtpeekllraifGEKAR-----------DV 832
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 873 KDVSItyKTPtPSYAERV----LLTYNE--DEA-----HLFKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFND 941
Cdd:PRK00405 833 KDTSL--RVP-HGEEGTVidvkVFTRIEqgDELppgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLE 909
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 942 LGMVPDMIMNPHGYPSRMTVGKLMELLSGKAGVVNGTyHYGT-AFGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLS 1020
Cdd:PRK00405 910 DGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGI-KFATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFD 988
|
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 25144348 1021 AYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPTEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSD 1094
Cdd:PRK00405 989 RPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1062
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
354-1141 |
3.68e-30 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 130.43 E-value: 3.68e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 354 LIQTELGENGLDDRDFYGNKRLELAGSLLSllfEDVFKRFNSELKRIADNalMKTMAAPLD-IVKH--MRQDMITNTIVN 430
Cdd:PRK09603 444 LMKIKNNQGKIDDRDHLGNRRIRAVGELLA---NELHSGLVKMQKTIKDK--LTTMSGAFDsLMPHdlVNSKMITSTIME 518
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 431 AMSTGNwiIKRFrMERlgvTQVLSRLSY---ISALGmmtriNSTFEKTRKVSGPRSLQPSQWGMLCPSDTPEGEacglvk 507
Cdd:PRK09603 519 FFMGGQ--LSQF-MDQ---TNPLSEVTHkrrLSALG-----EGGLVKDRVGFEARDVHPTHYGRICPIETPEGQ------ 581
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 508 NLALISHITTdsdekpvlrlllnsgvedlhnvhFSHVNKpentliflngvlIGTAVDPERVVkavrdlrrsgllsefvsV 587
Cdd:PRK09603 582 NIGLINTLST-----------------------FTRVND------------LGFIEAPYKKV-----------------V 609
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 588 SRSLTNRSVFISS---DGgrlcrpYIIVKNGTPMLTQAHvqelkegkmIFEDFVDDGIVEYLDVNEMNdaliavygreig 664
Cdd:PRK09603 610 DGKVVGETIYLTAiqeDS------HIIAPASTPIDEEGN---------ILGDLIETRVEGEIVLNEKS------------ 662
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 665 pETTHLEIEPFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAM----------GT-----IAYNQQ-----------KRI 718
Cdd:PRK09603 663 -KVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivGTgiekiIARDSWgaikanragvvEKI 741
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 719 DSI-MYLL------------------------CYPQRPLVK-SKTIE----------LTNFEkLPAGANGIIAVMSYSGY 762
Cdd:PRK09603 742 DSKnIYILgegkeeayidayslqknlrtnqntSFNQVPIVKvGDKVEagqiiadgpsMDRGE-LALGKNVRVAFMPWNGY 820
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 763 DIEDALVLNKASL-DRGYGRCLVY-KHVKGTAKKYPNQTFDRLLgpaldPNTRKPIFKHknLDQEGIVFAG--------- 831
Cdd:PRK09603 821 NFEDAIVVSERITkDDIFTSTHIYeKEVDARELKHGVEEFTADI-----PDVKEEALAH--LDESGIVKVGtyvsagmil 893
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 832 -ARIMPKQTI--------------------INKHM---PVVSGE-------SGPGASASANTIGI--------------- 865
Cdd:PRK09603 894 vGKTSPKGEIkstpeerllraifgdkaghvVNKSLycpPSLEGTvidvkvfTKKGYEKDARVLSAyeeekakldmehfdr 973
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 866 ---------------------------------AGRQVDYKDVS----ITYKTPTPSYAERVLLTYNE------------ 896
Cdd:PRK09603 974 ltmlnreellrvssllsqaileepfshngkdykEGDQIPKEEIAsinrFTLASLVKKYSKEVQNHYEItknnfleqkkvl 1053
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 897 DEAH-------------------LFKVLLRQTRRPELGDKFSSRHGQKGVCGLIAQQEDMPFNDLGMVPDMIMNPHGYPS 957
Cdd:PRK09603 1054 GEEHeeklsilekddilpngvikKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPS 1133
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 958 RMTVGKLMEL---LSGK----------------------------AGVVNGT----------------------YHYGTA 984
Cdd:PRK09603 1134 RMNIGQILEMhlgLVGKefgkqiasmledktkdfakelrakmleiANAINEKdpltihalencsdeelleyakdWSKGVK 1213
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 985 FGGDQVKDVCEE-------LAACGYNymGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRAALTRQPT 1057
Cdd:PRK09603 1214 MAIPVFEGISQEkfyklfeLAKIAMD--GKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPV 1291
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 1058 EGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDEFKvdvctgcgviGSKGWCQKCRSSKSMANIKIPYACKLLFQE 1137
Cdd:PRK09603 1292 GGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIR----------GRENAYRAIAKGEQVGESEIPETFYVLTKE 1361
|
....
gi 25144348 1138 LQSM 1141
Cdd:PRK09603 1362 LQSL 1365
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
552-613 |
4.60e-26 |
|
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: 101.67 E-value: 4.60e-26
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 25144348 552 IFLNGVLIGTAVDPERVVKAVRDLRRSGLLSEFVSVSRSLTNRSVFISSDGGRLCRPYIIVK 613
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
451-514 |
1.20e-20 |
|
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: 86.81 E-value: 1.20e-20
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 25144348 451 QVLSRLSYISALGMMTRINST---FEKTRKVSGPRSLQPSQWGMLCPSDTPEGEACGLVKNLALISH 514
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPrggLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
188-376 |
1.74e-20 |
|
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: 90.10 E-value: 1.74e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 188 SKNRIMVGRNSSKE--LQCEVLSSTSERKSKTYVTMKKGKYSVRHNQLTDDVPVSIIFKAMGVESDFDIVSTIGH-EEKY 264
Cdd:pfam04561 1 RSNGIYVEKELDKNgiIATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLCYdFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 265 VSAFAQTLEESINAGVYTQQQALAYVTSKVKARKFTPFGSLPGTSVSVLTPPKEHeavdflsnsMITHIAC--PDGNFKM 342
Cdd:pfam04561 81 QMLELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREILYSRDPKYN---------LNKHLGLnePFENERL 151
|
170 180 190
....*....|....*....|....*....|....
gi 25144348 343 KAIYLGLMTRRLIQTELGENGLDDRDFYGNKRLE 376
Cdd:pfam04561 152 KAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
350-1095 |
2.71e-19 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 94.69 E-value: 2.71e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 350 MTRRLIQTELGENGLDDRDFYGNKRLELAGSLLsllfEDVFKRFNSELKRiadnALMKTMA-APLDIVK---HMRQDMIT 425
Cdd:PRK14844 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFI----ENQFRTGLLKLER----AVVDSMStSSLDKVSpsdFINPKVLT 520
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 426 NTIVNAMSTGNwiIKRFrMERlgvTQVLSRLSY---ISALGM--MTRINSTFEKtrkvsgpRSLQPSQWGMLCPSDTPEG 500
Cdd:PRK14844 521 NVLRDFFNSSQ--LSQF-MDQ---TNPLSEITHkrrLSALGPggLTRERAGFEV-------RDVHPTHYGRICPIETPEG 587
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 501 EACGLVKNLALISHITTDSDEKPVLRLLLNSGVED-----------LHNVHFSHVNKPENTLiFLNGVL----IGTAVDP 565
Cdd:PRK14844 588 QNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDqieylsaidegLYYIADTSAKLDENNC-FVDDMLycryAGSFVMV 666
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 566 ERVVKAVRDLRRSGLLSEFVSVSRSLTNRSVFISSDGGRLCRPYI-IVKNGTPMLTQAHVQELKEGKMIFEDFVDDGIVe 644
Cdd:PRK14844 667 SSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVpLLKPTAPLVATGMESFVASGSGAVVLAKRDGIV- 745
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 645 ylDVNEMNDALIAVYGREigpETTHLEIEPFTLlgvcaglipyPHHNQSPRNTyqcamgkqamgtiaynqqkridsimyl 724
Cdd:PRK14844 746 --DSSDSNSIVIRAFDKE---RVNYLDVDIYHL----------RKFQRSNHNT--------------------------- 783
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 725 lCYPQRPLV-------KSKTIE---LTNFEKLPAGANGIIAVMSYSGYDIEDALVLNK--------ASLDRGYGRCLVYK 786
Cdd:PRK14844 784 -CINQKPLVcvgdyvkEGDVIAdgpAINSGELALGQNLLVAFMSWQGYNFEDSIIISSevvkkdlfTSIHIEEFECVVHD 862
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 787 HVKGTAK---KYPNQTFDRL--------------LGP--------------ALDPNTR--KPIFKHKNLD---------- 823
Cdd:PRK14844 863 TPLGSEKitrAIPGVNEENLyhlddsgivkigtrVGPgyilvgkvtpkpslSLPPETKllMTIFGEKSFDcadsslytsp 942
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 824 -QEGIVF-------AGAR-----IMPKQTIINK------HMPVVSGE------------SGPGASASANTI---GIAGRQ 869
Cdd:PRK14844 943 dVEGTVIdvqvftrRGVEeneraLLIKQKEINDfekerdYIINVTSEyfydelkkllinSGSQDREKFDSIereQWWGIG 1022
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 870 VDYKDVSITYKTPTPSYAERVLLTYNE--------DEAHLF--------KVLLRQTRRPELGDKFSSRHGQKGVCGLIAQ 933
Cdd:PRK14844 1023 LKNQSISEQVKSLKKDFDEKVSHAIAQfkrkveklHEGYDLpqgvsmsvKVFIAVKHSLQPGDKMAGRHGNKGVISRVVP 1102
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 934 QEDMPFNDLGMVPDMIMNPHGYPSRMTVGKLMELLSG------------------------------------------- 970
Cdd:PRK14844 1103 VEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgekvgnildeinkiksafckgirslnddnftkfaaay 1182
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 971 --------------KAGVVN----------------------------------GTYHYGT------------------- 983
Cdd:PRK14844 1183 ldnkkienidddeiTASVLNtpnknalndelnelvenylnscksaysnlrnfliEVYSCGSnvsicnnirdisdnnlief 1262
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144348 984 -------------AFGGDQVKDVCEELAACGYNYMGKDMLTSGITGQPLSAYIYFGPIYYQKLKHMVLDKMHARARGPRA 1050
Cdd:PRK14844 1263 arklrdgipvaapVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYS 1342
|
970 980 990 1000
....*....|....*....|....*....|....*....|....*
gi 25144348 1051 ALTRQPTEGRSREGGLRLGEMERDCLIAYGASMLLIERLMVSSDE 1095
Cdd:PRK14844 1343 LVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDD 1387
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
634-674 |
2.90e-09 |
|
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: 53.70 E-value: 2.90e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 25144348 634 FEDFVDDGIVEYLDVNEMNDALIAVY-------GREIG-----PETTHLEIEP 674
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTpedleesSREERegpyaHTYTHCEIHP 53
|
|
| |
