|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
45-1157 |
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: 1105.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 45 LVKQHLDSFNYFINVGIHKIVKANSRITSTV-DPSIYLRFKKVRVGEPSIINVNTVENINPHMCRLADMTYAAPIFVNIE 123
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 124 YVHGshgNKAKSAKDNVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRIIIDsD 203
Cdd:cd00653 81 LTVN---DKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-D 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 204 KKGNINASVTSSTEMTkSKTVIQMEKeKIYLFLHRFVKKIPIIIvlkamgmesdqeivqmvgrdprfsasllpsieecvs 283
Cdd:cd00653 157 SKGKRIYTKTSIPSYS-PYRGSWLEV-KSDKKKDRIYVRIDLKR------------------------------------ 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 284 egvntQKQALDYLEAKVkkisygtppekdgralsilrdlflahvpvpdnnfrqkcFYVGVMLRRMIEAMLNKDAMDDKDY 363
Cdd:cd00653 199 -----QEEALKYIGKRF--------------------------------------EDLIYMIRKLILLVLGKGKLDDIDH 235
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 364 VGNKRLELSGQLISLLFEDLFKTMLSEAIKNVDHILNKpirasRFDFSQCLNKDSRYsISLGLERTLSTGNFDIKRFRMH 443
Cdd:cd00653 236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSK-----KKDLTPQLLINSKP-ITSGIKEFLATGNWGSKRFLMQ 309
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 444 RKGMTQVLTRLSFIGSMGFITKIS-PQFEKSRKVSGPRSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVTtdeeegpl 522
Cdd:cd00653 310 RSGLSQVLDRLNPLSELSHKRRISsLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 523 vamcyklgvtdlevlsaeelhtpdsflvilnglilgkhsrpqyfanslrrlrragkigefvsvftnekqhcvyvasdvGR 602
Cdd:cd00653 382 ------------------------------------------------------------------------------GR 383
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 603 VCRPLVIADKgisrvkqhhmkelqdgvrtfddfirdglieyldvneennalialyesdgtteldegaeaakaDTTHIEIE 682
Cdd:cd00653 384 IERPYRIVEK--------------------------------------------------------------EVTHIEIS 401
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 683 PFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAYNQLNRMDTLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNAT 762
Cdd:cd00653 402 PSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAI 481
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 763 VAVMSFSGYDIEDAIVMNKSSLDRGFGRCIVMKKIVAMSQKYDNCTADRILiPQRTGPDAEKMQILDDDGLATPGEIIRP 842
Cdd:cd00653 482 VAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITR-GDIPNVSEEKLKNLDEDGIIRPGARVEP 560
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 843 NDIYINKQVPV-DTVTKFTSALSDSQYRPAREYFKGpeGETQVVDRVALCS---DKKGQLCIKYIIRHTRRPELGDKFSS 918
Cdd:cd00653 561 GDILVGKITPKgETESTPIFGEKARDVRDTSLKYPG--GEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFAS 638
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 919 RHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIELLGSKAGVSCGRFHYGSAFGErsghaDKVETISA 998
Cdd:cd00653 639 RHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDG-----AEEEDISE 713
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 999 TLVEKGFSYSGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDC 1078
Cdd:cd00653 714 LLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDA 793
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 79529842 1079 LIAYGASMLIYERLMISSDPFEVQVCRACGLLGYYNYklkkavCTTCKNGDNIATMKLPYACKLLFQELQSMNVVPRLK 1157
Cdd:cd00653 794 LIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANL------CRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
35-1160 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1032.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 35 LVPEFLKVRGLVKQHLDSFNYFINVGIHKIVKANSRItSTVDPSIYLRFKKVRVGEPSIINVNTVEN-INPHMCRLADMT 113
Cdd:PRK08565 4 VVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEI-KTEIPGLKIVLGKIRVGEPEIKEADGSERpITPMEARLRNLT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 114 YAAPIFVNIEYVHgshgNKAKSAKDNVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFIIKGTEKVLLIQEQL 193
Cdd:PRK08565 83 YAAPLYLTMIPVE----NGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 194 SKNRIIIDSDKKGNIN---ASVTSSTEMTKSKTVIQMEKEK-IYLFLHRFVKKIPIIIVLKAMGMESDQEIVQMVGRDPR 269
Cdd:PRK08565 159 APNRVLVDKGEAGSSIthtAKVISSRAGYRAQVTVERRKDGtIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPE 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 270 FSASLLPSIEEcVSEGVNTQKQALDYLEakvKKISYGTP-PEKDGRALSILRDLFLAHVPVPDNNFRQKCFYVGVMLRRM 348
Cdd:PRK08565 239 IQQELLPSLEQ-ASSIAATVEDALDYIG---KRVAIGQPrEYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 349 IEAMLNKDAMDDKDYVGNKRLELSGQLISLLFEDLFKTMLSEAIKNVDHILNkpiRASRFDFSQCLNKDSrysISLGLER 428
Cdd:PRK08565 315 LELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYA---RGRKLDLRAIVRPDI---ITERIRH 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 429 TLSTGNFDikrfrMHRKGMTQVLTRLSFIGSMGFITKI-------SPQFEKsrkvsgpRSLQPSQWGMLCPCDTPEGESC 501
Cdd:PRK08565 389 ALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVvsplsrgQPHFEA-------RDLHGTQWGRICPFETPEGPNC 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 502 GLVKNLALMTHVTTDEEEGPLVAMCYKLGVTDLEVLSAEElhTPDSFLVILNGLILGKHSRPQYFANSLRRLRRAGKIGE 581
Cdd:PRK08565 457 GLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISD 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 582 FVSV------FTNEkqhcVYVASDVGRVCRPLVIADKGISRVKQHHMKELQDGVRTFDDFIRDGLIEYLDVNEENNALIA 655
Cdd:PRK08565 535 EVNVayietgEINE----VYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVA 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 656 LYESDGTTEldegaeaakadTTHIEIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAYNQLNRMDTLLYLLV 735
Cdd:PRK08565 611 LDPEDLTPE-----------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLH 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 736 YPQRPLLTTRTIELVGYDKLGAGQNATVAVMSFSGYDIEDAIVMNKSSLDRGFGRCIVMKKIVAMSQKYDNCTADRILIP 815
Cdd:PRK08565 680 YPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP 759
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 816 QRT-----GPDAEKMqiLDDDGLATPGEIIRPNDIYINKQVPVDTVTKFTSALSDSQYR-----PAREyfkgpeGETQVV 885
Cdd:PRK08565 760 EPNvrgyrGEEYYRK--LDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERrdtsvTVRH------GEKGIV 831
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 886 DRVALCSDKKGQLCIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIEL 965
Cdd:PRK08565 832 DTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLES 911
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 966 LGSKAGVSCGRFHYGSAFgersgHADKVETISATLVEKGFSYSGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMH 1045
Cdd:PRK08565 912 IAGKVAALEGRFVDATPF-----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIH 986
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1046 ARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLMISSDPFEVQVCRACGLLGYYNYKLKKAVCTTC 1125
Cdd:PRK08565 987 ARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIH 1066
|
1130 1140 1150
....*....|....*....|....*....|....*
gi 79529842 1126 KNGDNIATMKLPYACKLLFQELQSMNVVPRLKLTE 1160
Cdd:PRK08565 1067 GDKGNISPVEVSYAFKLLLQELMSMGISPRLKLGD 1101
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
550-1161 |
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: 664.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 550 VILNGLILGKHSRPQYFANSLRRLRRAGKIGEFVSVFTNEKQHCVYVASDVGRVCRPLVIADKGISRVKQHHMKELQDGV 629
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 630 RTFDDFIRDGLIEYLDVNEENNALIALYESDGTTEldegaeaakadTTHIEIEPFTILGVVAGLIPYPHHNQSPRNTYQC 709
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-----------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 710 AMGKQAMGNIAYNQLNRMDTLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSFSGYDIEDAIVMNKSSLDRGFG 789
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 790 RCIVMKKIVAMSQKYDNCTADRILIPQRT-----GPDAEKMqiLDDDGLATPGEIIRPNDIYINKQVPVDTVTKFTSALS 864
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDvrgyrGEEAYKH--LDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELREFGL 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 865 DSQYR-----PAREyfkgpeGETQVVDRVALCSDKKGQLCIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSE 939
Cdd:TIGR03670 308 VTERRrdtsvTVRH------GEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTE 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 940 LGICPDLIMNPHGFPSRMTVGKMIELLGSKAGVSCGRFHYGSAFGErsghaDKVETISATLVEKGFSYSGKDLLYSGISG 1019
Cdd:TIGR03670 382 DGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEG-----EPEEELRKELLKLGFKPDGKEVMYDGITG 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1020 EPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLMISSDPF 1099
Cdd:TIGR03670 457 EKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKY 536
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 79529842 1100 EVQVCRACGLLGYYNYKLKKAVCTTCKNGDNIATMKLPYACKLLFQELQSMNVVPRLKLTEA 1161
Cdd:TIGR03670 537 VVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGDK 598
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
33-1160 |
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: 622.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 33 FQLVPEFLKVRGLVKQHLDSFNYFINVGIHKIVKANSRITsTVDPSIYLRFKKVRVGEPSIinvnTVENinphmCRLADM 112
Cdd:COG0085 4 FAKIKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE-DFTGNLSLEFGDYRLGEPKY----TPEE-----CKERDL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 113 TYAAPIFVNIEYVHGSHGnKAKSakDNVIIGRMPIMLRScrcvlhgkdeeelarlgecpldpgGYFIIKGTEKVLLIQEQ 192
Cdd:COG0085 74 TYAAPLYVKVRLVNKETG-EIKE--QEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLV 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 193 LSKNRIIIDSDKKGN---INASVTSS----TEMTKSKtviqmeKEKIYLFLHRfVKKIPIIIVLKAMGMESDQEIVQMVG 265
Cdd:COG0085 127 RSPGVYFVEEEDKSGkdlYSAKVIPSrgawLEFETDK------DGTIYVRIDR-KRKIPVTVLLRALGLETDEEILEAFG 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 266 RDPRFSaSLLPSIEEcvsEGVNTQKQALDYLEakvKKISYGTPPEKDgRALSILRDLF-------LAHV----------- 327
Cdd:COG0085 200 DDPIQE-YILATLEK---DNTKTQEEALLEIY---RKLRPGEPPTIE-RAEQLLDNLFfdpkrydLAHVgrykinkklgl 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 328 PVPDNNFRQKCFYVGVMLRRMIEAMLNKDAMDDKDYVGNKRLELSGQLIsllfEDLFKTMLSEAIKNVdhilnkpirasr 407
Cdd:COG0085 272 DVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELL----QNQFRVGLSRMERVV------------ 335
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 408 fdfsqclnkdsRYSISLGLERTLSTG---NFD-----IKRFrMHRKGMTQV---------LT---RLSFIGSMGfITKIS 467
Cdd:COG0085 336 -----------RERMTTQDVEAITPQsliNIRpvvaaIKEF-FGSSQLSQFmdqtnplseLThkrRLSALGPGG-LSRER 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 468 PQFEksrkVsgpRSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVttdeeegplvamcyklgvtdlevlsaeelhtpds 547
Cdd:COG0085 403 AGFE----V---RDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV---------------------------------- 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 548 flvilnglilgkhsrpqyfanslrrlrragkigefvsvftnekqhcvyvaSDVGRVCRPLViadkgisRVKqhhmkelqD 627
Cdd:COG0085 442 --------------------------------------------------NEYGFIETPYR-------KVE--------N 456
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 628 GVRTFDdfirdglIEYLDVNEENNALIALYESDGTTE------------LDEGAEAAKADTTHIEIEPFTILGVVAGLIP 695
Cdd:COG0085 457 GKVTDE-------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryRGEEVLVPPEEVDYMDVSPKQIVSVATSLIP 529
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 696 YPHHNQSPRNTYQCAMGKQAMGNIAYNqlnrMDTLLYLLV----------YPQRPLltTRTIELVG------------YD 753
Cdd:COG0085 530 FLEHDDANRALMGANMQRQAVPLLRPE----APLLHYPLQkfqrsnqgtcINQRPI--VRVGDRVEkgdvladgpatdNG 603
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 754 KLGAGQNATVAVMSFSGYDIEDAIVMNKSSLDRGFGRCIVMKKIVAMSQKY-----DNcTADrilIPQrTGPDAEKMqiL 828
Cdd:COG0085 604 ELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTklgpeEI-TRD---IPN-VSEEALRN--L 676
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 829 DDDGLATPGEIIRPNDIYINKqvpvdtVT--KFTSaLSdSQYRPAREYF--KGPE----------GETQVVDRVALCSDK 894
Cdd:COG0085 677 DEDGIIRIGAEVKGGDILVGK------VTpkGETE-LT-PEERLLRAIFgeKAREvrdtslrvphGEKGKVIDVKVFSRE 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 895 KG--------QLcIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIELL 966
Cdd:COG0085 749 EGdelppgvnKL-VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETH 827
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 967 GSKAGVSCGRFHYGSAF-GErsghadKVETISATLVEKGFSYSGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMH 1045
Cdd:COG0085 828 LGWAAALLGRRVATPVFdGA------PEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIH 901
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1046 ARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLMISSDpfevqvcRACGLLGYYNYKLKkavcttc 1125
Cdd:COG0085 902 ARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD-------DVCGRVKVYEAIVK------- 967
|
1210 1220 1230
....*....|....*....|....*....|....*
gi 79529842 1126 knGDNIATMKLPYACKLLFQELQSMNVVPRLKLTE 1160
Cdd:COG0085 968 --GENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
690-1065 |
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: 535.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 690 VAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAYNQLNRMDTLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSFS 769
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 770 GYDIEDAIVMNKSSLDRGFGRCIVMKKIVAmsQKYDNCTADRILIPQRTGPDaEKMQILDDDGLATPGEIIRPNDIYINK 849
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA--RKTKLGPIEEITRDIPNVSE-EALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 850 QVPVDTVTKFTSALSDSQYRPAREYFKGPEGETQVVDRVALCS-DKKGQLCIKYIIRHTRRPELGDKFSSRHGQKGVCGI 928
Cdd:pfam00562 158 VGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFElPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSR 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 929 IIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIELLGSKAGVSCGRFHYGSAFGERSghaDKVETISATLVEKGFSYS 1008
Cdd:pfam00562 238 ILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAS---TEVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 79529842 1009 GKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSK 1065
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
550-611 |
5.92e-25 |
|
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: 98.59 E-value: 5.92e-25
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 79529842 550 VILNGLILGKHSRPQYFANSLRRLRRAGKIGEFVSVFTNEKQHCVYVASDVGRVCRPLVIAD 611
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
632-683 |
1.12e-13 |
|
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: 66.41 E-value: 1.12e-13
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 79529842 632 FDDFIRDGLIEYLDVNEENNALIALYESDGTTELDEGAEAAKADT-THIEIEP 683
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. ... |
45-1157 |
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: 1105.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 45 LVKQHLDSFNYFINVGIHKIVKANSRITSTV-DPSIYLRFKKVRVGEPSIINVNTVENINPHMCRLADMTYAAPIFVNIE 123
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDdDGRLKLKFGDIYLGKPKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 124 YVHGshgNKAKSAKDNVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRIIIDsD 203
Cdd:cd00653 81 LTVN---DKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE-D 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 204 KKGNINASVTSSTEMTkSKTVIQMEKeKIYLFLHRFVKKIPIIIvlkamgmesdqeivqmvgrdprfsasllpsieecvs 283
Cdd:cd00653 157 SKGKRIYTKTSIPSYS-PYRGSWLEV-KSDKKKDRIYVRIDLKR------------------------------------ 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 284 egvntQKQALDYLEAKVkkisygtppekdgralsilrdlflahvpvpdnnfrqkcFYVGVMLRRMIEAMLNKDAMDDKDY 363
Cdd:cd00653 199 -----QEEALKYIGKRF--------------------------------------EDLIYMIRKLILLVLGKGKLDDIDH 235
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 364 VGNKRLELSGQLISLLFEDLFKTMLSEAIKNVDHILNKpirasRFDFSQCLNKDSRYsISLGLERTLSTGNFDIKRFRMH 443
Cdd:cd00653 236 LGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSK-----KKDLTPQLLINSKP-ITSGIKEFLATGNWGSKRFLMQ 309
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 444 RKGMTQVLTRLSFIGSMGFITKIS-PQFEKSRKVSGPRSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVTtdeeegpl 522
Cdd:cd00653 310 RSGLSQVLDRLNPLSELSHKRRISsLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 523 vamcyklgvtdlevlsaeelhtpdsflvilnglilgkhsrpqyfanslrrlrragkigefvsvftnekqhcvyvasdvGR 602
Cdd:cd00653 382 ------------------------------------------------------------------------------GR 383
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 603 VCRPLVIADKgisrvkqhhmkelqdgvrtfddfirdglieyldvneennalialyesdgtteldegaeaakaDTTHIEIE 682
Cdd:cd00653 384 IERPYRIVEK--------------------------------------------------------------EVTHIEIS 401
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 683 PFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAYNQLNRMDTLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNAT 762
Cdd:cd00653 402 PSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAI 481
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 763 VAVMSFSGYDIEDAIVMNKSSLDRGFGRCIVMKKIVAMSQKYDNCTADRILiPQRTGPDAEKMQILDDDGLATPGEIIRP 842
Cdd:cd00653 482 VAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITR-GDIPNVSEEKLKNLDEDGIIRPGARVEP 560
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 843 NDIYINKQVPV-DTVTKFTSALSDSQYRPAREYFKGpeGETQVVDRVALCS---DKKGQLCIKYIIRHTRRPELGDKFSS 918
Cdd:cd00653 561 GDILVGKITPKgETESTPIFGEKARDVRDTSLKYPG--GEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFAS 638
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 919 RHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIELLGSKAGVSCGRFHYGSAFGErsghaDKVETISA 998
Cdd:cd00653 639 RHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDG-----AEEEDISE 713
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 999 TLVEKGFSYSGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDC 1078
Cdd:cd00653 714 LLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDA 793
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 79529842 1079 LIAYGASMLIYERLMISSDPFEVQVCRACGLLGYYNYklkkavCTTCKNGDNIATMKLPYACKLLFQELQSMNVVPRLK 1157
Cdd:cd00653 794 LIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANL------CRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
35-1160 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1032.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 35 LVPEFLKVRGLVKQHLDSFNYFINVGIHKIVKANSRItSTVDPSIYLRFKKVRVGEPSIINVNTVEN-INPHMCRLADMT 113
Cdd:PRK08565 4 VVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEI-KTEIPGLKIVLGKIRVGEPEIKEADGSERpITPMEARLRNLT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 114 YAAPIFVNIEYVHgshgNKAKSAKDNVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFIIKGTEKVLLIQEQL 193
Cdd:PRK08565 83 YAAPLYLTMIPVE----NGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 194 SKNRIIIDSDKKGNIN---ASVTSSTEMTKSKTVIQMEKEK-IYLFLHRFVKKIPIIIVLKAMGMESDQEIVQMVGRDPR 269
Cdd:PRK08565 159 APNRVLVDKGEAGSSIthtAKVISSRAGYRAQVTVERRKDGtIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLDPE 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 270 FSASLLPSIEEcVSEGVNTQKQALDYLEakvKKISYGTP-PEKDGRALSILRDLFLAHVPVPDNNFRQKCFYVGVMLRRM 348
Cdd:PRK08565 239 IQQELLPSLEQ-ASSIAATVEDALDYIG---KRVAIGQPrEYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKL 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 349 IEAMLNKDAMDDKDYVGNKRLELSGQLISLLFEDLFKTMLSEAIKNVDHILNkpiRASRFDFSQCLNKDSrysISLGLER 428
Cdd:PRK08565 315 LELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYA---RGRKLDLRAIVRPDI---ITERIRH 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 429 TLSTGNFDikrfrMHRKGMTQVLTRLSFIGSMGFITKI-------SPQFEKsrkvsgpRSLQPSQWGMLCPCDTPEGESC 501
Cdd:PRK08565 389 ALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVvsplsrgQPHFEA-------RDLHGTQWGRICPFETPEGPNC 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 502 GLVKNLALMTHVTTDEEEGPLVAMCYKLGVTDLEVLSAEElhTPDSFLVILNGLILGKHSRPQYFANSLRRLRRAGKIGE 581
Cdd:PRK08565 457 GLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEE--YISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISD 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 582 FVSV------FTNEkqhcVYVASDVGRVCRPLVIADKGISRVKQHHMKELQDGVRTFDDFIRDGLIEYLDVNEENNALIA 655
Cdd:PRK08565 535 EVNVayietgEINE----VYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVA 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 656 LYESDGTTEldegaeaakadTTHIEIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAYNQLNRMDTLLYLLV 735
Cdd:PRK08565 611 LDPEDLTPE-----------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLH 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 736 YPQRPLLTTRTIELVGYDKLGAGQNATVAVMSFSGYDIEDAIVMNKSSLDRGFGRCIVMKKIVAMSQKYDNCTADRILIP 815
Cdd:PRK08565 680 YPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP 759
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 816 QRT-----GPDAEKMqiLDDDGLATPGEIIRPNDIYINKQVPVDTVTKFTSALSDSQYR-----PAREyfkgpeGETQVV 885
Cdd:PRK08565 760 EPNvrgyrGEEYYRK--LDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERrdtsvTVRH------GEKGIV 831
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 886 DRVALCSDKKGQLCIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIEL 965
Cdd:PRK08565 832 DTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLES 911
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 966 LGSKAGVSCGRFHYGSAFgersgHADKVETISATLVEKGFSYSGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMH 1045
Cdd:PRK08565 912 IAGKVAALEGRFVDATPF-----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIH 986
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1046 ARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLMISSDPFEVQVCRACGLLGYYNYKLKKAVCTTC 1125
Cdd:PRK08565 987 ARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIH 1066
|
1130 1140 1150
....*....|....*....|....*....|....*
gi 79529842 1126 KNGDNIATMKLPYACKLLFQELQSMNVVPRLKLTE 1160
Cdd:PRK08565 1067 GDKGNISPVEVSYAFKLLLQELMSMGISPRLKLGD 1101
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
550-1161 |
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: 664.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 550 VILNGLILGKHSRPQYFANSLRRLRRAGKIGEFVSVFTNEKQHCVYVASDVGRVCRPLVIADKGISRVKQHHMKELQDGV 629
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 630 RTFDDFIRDGLIEYLDVNEENNALIALYESDGTTEldegaeaakadTTHIEIEPFTILGVVAGLIPYPHHNQSPRNTYQC 709
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-----------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 710 AMGKQAMGNIAYNQLNRMDTLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSFSGYDIEDAIVMNKSSLDRGFG 789
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 790 RCIVMKKIVAMSQKYDNCTADRILIPQRT-----GPDAEKMqiLDDDGLATPGEIIRPNDIYINKQVPVDTVTKFTSALS 864
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDvrgyrGEEAYKH--LDEDGIVYPEVEVKGGDVLIGKTSPPRFLEELREFGL 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 865 DSQYR-----PAREyfkgpeGETQVVDRVALCSDKKGQLCIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSE 939
Cdd:TIGR03670 308 VTERRrdtsvTVRH------GEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTE 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 940 LGICPDLIMNPHGFPSRMTVGKMIELLGSKAGVSCGRFHYGSAFGErsghaDKVETISATLVEKGFSYSGKDLLYSGISG 1019
Cdd:TIGR03670 382 DGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEG-----EPEEELRKELLKLGFKPDGKEVMYDGITG 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1020 EPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLMISSDPF 1099
Cdd:TIGR03670 457 EKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKY 536
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 79529842 1100 EVQVCRACGLLGYYNYKLKKAVCTTCKNGDNIATMKLPYACKLLFQELQSMNVVPRLKLTEA 1161
Cdd:TIGR03670 537 VVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGDK 598
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
550-1161 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 654.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 550 VILNGLILGKHSRPQYFANSLRRLRRAGKIGEFVSVFTNEKQHCVYVASDVGRVCRPLVIADKGISRVKQHHMKELQDGV 629
Cdd:PRK07225 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 630 RTFDDFIRDGLIEYLDVNEENNALIALYESDGTTEldegaeaakadTTHIEIEPFTILGVVAGLIPYPHHNQSPRNTYQC 709
Cdd:PRK07225 87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE-----------HTHLEIDPSLILGIGAGMIPYPEHNASPRITMGA 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 710 AMGKQAMGNIAYNQLNRMDTLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSFSGYDIEDAIVMNKSSLDRGFG 789
Cdd:PRK07225 156 GMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLG 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 790 RCIVMKKIVAMSQKYDNCTADRILIPQ---RTGPDAEKMQILDDDGLATPGEIIRPNDIYINKQVPVDTVTKFTSALSDS 866
Cdd:PRK07225 236 RSHFFRTYEGEERRYPGGQEDRFEIPDkdvRGYRGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPRFLEEPDDFGISP 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 867 QYRpaREY-FKGPEGETQVVDRVALCSDKKGQLCIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPD 945
Cdd:PRK07225 316 EKR--RETsVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPD 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 946 LIMNPHGFPSRMTVGKMIELLGSKAGVSCGRFHYGSAFgersgHADKVETISATLVEKGFSYSGKDLLYSGISGEPVEAY 1025
Cdd:PRK07225 394 LIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAF-----SGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAE 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1026 IFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLMISSDPFEVQVCR 1105
Cdd:PRK07225 469 IFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCA 548
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*.
gi 79529842 1106 ACGLLGYYNYKLKKAVCTTCKNGDNIATMKLPYACKLLFQELQSMNVVPRLKLTEA 1161
Cdd:PRK07225 549 KCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELEDK 604
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
33-1160 |
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: 622.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 33 FQLVPEFLKVRGLVKQHLDSFNYFINVGIHKIVKANSRITsTVDPSIYLRFKKVRVGEPSIinvnTVENinphmCRLADM 112
Cdd:COG0085 4 FAKIKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIE-DFTGNLSLEFGDYRLGEPKY----TPEE-----CKERDL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 113 TYAAPIFVNIEYVHGSHGnKAKSakDNVIIGRMPIMLRScrcvlhgkdeeelarlgecpldpgGYFIIKGTEKVLLIQEQ 192
Cdd:COG0085 74 TYAAPLYVKVRLVNKETG-EIKE--QEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLV 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 193 LSKNRIIIDSDKKGN---INASVTSS----TEMTKSKtviqmeKEKIYLFLHRfVKKIPIIIVLKAMGMESDQEIVQMVG 265
Cdd:COG0085 127 RSPGVYFVEEEDKSGkdlYSAKVIPSrgawLEFETDK------DGTIYVRIDR-KRKIPVTVLLRALGLETDEEILEAFG 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 266 RDPRFSaSLLPSIEEcvsEGVNTQKQALDYLEakvKKISYGTPPEKDgRALSILRDLF-------LAHV----------- 327
Cdd:COG0085 200 DDPIQE-YILATLEK---DNTKTQEEALLEIY---RKLRPGEPPTIE-RAEQLLDNLFfdpkrydLAHVgrykinkklgl 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 328 PVPDNNFRQKCFYVGVMLRRMIEAMLNKDAMDDKDYVGNKRLELSGQLIsllfEDLFKTMLSEAIKNVdhilnkpirasr 407
Cdd:COG0085 272 DVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELL----QNQFRVGLSRMERVV------------ 335
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 408 fdfsqclnkdsRYSISLGLERTLSTG---NFD-----IKRFrMHRKGMTQV---------LT---RLSFIGSMGfITKIS 467
Cdd:COG0085 336 -----------RERMTTQDVEAITPQsliNIRpvvaaIKEF-FGSSQLSQFmdqtnplseLThkrRLSALGPGG-LSRER 402
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 468 PQFEksrkVsgpRSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVttdeeegplvamcyklgvtdlevlsaeelhtpds 547
Cdd:COG0085 403 AGFE----V---RDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV---------------------------------- 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 548 flvilnglilgkhsrpqyfanslrrlrragkigefvsvftnekqhcvyvaSDVGRVCRPLViadkgisRVKqhhmkelqD 627
Cdd:COG0085 442 --------------------------------------------------NEYGFIETPYR-------KVE--------N 456
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 628 GVRTFDdfirdglIEYLDVNEENNALIALYESDGTTE------------LDEGAEAAKADTTHIEIEPFTILGVVAGLIP 695
Cdd:COG0085 457 GKVTDE-------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryRGEEVLVPPEEVDYMDVSPKQIVSVATSLIP 529
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 696 YPHHNQSPRNTYQCAMGKQAMGNIAYNqlnrMDTLLYLLV----------YPQRPLltTRTIELVG------------YD 753
Cdd:COG0085 530 FLEHDDANRALMGANMQRQAVPLLRPE----APLLHYPLQkfqrsnqgtcINQRPI--VRVGDRVEkgdvladgpatdNG 603
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 754 KLGAGQNATVAVMSFSGYDIEDAIVMNKSSLDRGFGRCIVMKKIVAMSQKY-----DNcTADrilIPQrTGPDAEKMqiL 828
Cdd:COG0085 604 ELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTklgpeEI-TRD---IPN-VSEEALRN--L 676
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 829 DDDGLATPGEIIRPNDIYINKqvpvdtVT--KFTSaLSdSQYRPAREYF--KGPE----------GETQVVDRVALCSDK 894
Cdd:COG0085 677 DEDGIIRIGAEVKGGDILVGK------VTpkGETE-LT-PEERLLRAIFgeKAREvrdtslrvphGEKGKVIDVKVFSRE 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 895 KG--------QLcIKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIELL 966
Cdd:COG0085 749 EGdelppgvnKL-VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETH 827
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 967 GSKAGVSCGRFHYGSAF-GErsghadKVETISATLVEKGFSYSGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMH 1045
Cdd:COG0085 828 LGWAAALLGRRVATPVFdGA------PEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIH 901
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1046 ARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLMISSDpfevqvcRACGLLGYYNYKLKkavcttc 1125
Cdd:COG0085 902 ARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD-------DVCGRVKVYEAIVK------- 967
|
1210 1220 1230
....*....|....*....|....*....|....*
gi 79529842 1126 knGDNIATMKLPYACKLLFQELQSMNVVPRLKLTE 1160
Cdd:COG0085 968 --GENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
690-1065 |
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: 535.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 690 VAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAYNQLNRMDTLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSFS 769
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 770 GYDIEDAIVMNKSSLDRGFGRCIVMKKIVAmsQKYDNCTADRILIPQRTGPDaEKMQILDDDGLATPGEIIRPNDIYINK 849
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA--RKTKLGPIEEITRDIPNVSE-EALKKLDEDGIVRVGAEVKPGDILVGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 850 QVPVDTVTKFTSALSDSQYRPAREYFKGPEGETQVVDRVALCS-DKKGQLCIKYIIRHTRRPELGDKFSSRHGQKGVCGI 928
Cdd:pfam00562 158 VGPTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFElPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSR 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 929 IIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIELLGSKAGVSCGRFHYGSAFGERSghaDKVETISATLVEKGFSYS 1008
Cdd:pfam00562 238 ILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAS---TEVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 79529842 1009 GKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSK 1065
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
28-531 |
5.23e-102 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 331.53 E-value: 5.23e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 28 STADKFQLVPEFLKVRGLVKQHLDSFNYFINVGIHKIVKANSRITSTVDPSIYLRFKKVRVGEPSIINVN-TVENINPHM 106
Cdd:PRK09606 1 MMEDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEADgSEREIYPME 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 107 CRLADMTYAAPIFVNIEYVHGSHGNKAksakDNVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFIIKGTEKV 186
Cdd:PRK09606 81 ARLRNLTYSAPLYLEMSPVEGGEEEEP----EEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERV 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 187 LLIQEQLSKNRIIIDSDKKGNIN---ASVTSSTEMTKSKTVIQMEKEKI-YLFLHRFVKKIPIIIVLKAMGMESDQEIVQ 262
Cdd:PRK09606 157 LMTLEDLAPNKILVEKDERYGDRievAKVFSQRRGYRALVTVERNRDGLlEVSFPSVPGSIPFVILMRALGLETDEEIVE 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 263 MVGRDPRFSASLLPSIEEcvsEGVNTQKQALDYLEAKVKKisyGTPPE-KDGRALSILRDLFLAHVPVPDNNFRQKCFYV 341
Cdd:PRK09606 237 AVSDDPEIVKFMLENLEE---AEVDTQEEALEYIGKRVAP---GQTKEyRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYL 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 342 GVMLRRMIEAMLNKDAMDDKDYVGNKRLELSGQlislLFEDLFKTMLSEAIKNVDHIL------NKPIRASRFDFSQCLN 415
Cdd:PRK09606 311 GRMAEACFELALGRREEDDKDHYANKRLKLAGD----LMEDLFRVAFNRLARDVKYQLeranmrNRELSIKTAVRSDVLT 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 416 KDsrysislgLERTLSTGNfdikrFRMHRKGMTQVLTRLSFIGSMGFITKI-------SPQFEKsrkvsgpRSLQPSQWG 488
Cdd:PRK09606 387 ER--------LEHAMATGN-----WVGGRTGVSQLLDRTDYMATLSHLRRVvsplsrsQPHFEA-------RDLHPTQWG 446
|
490 500 510 520
....*....|....*....|....*....|....*....|...
gi 79529842 489 MLCPCDTPEGESCGLVKNLALMTHVTTDEEEGPLVAMCYKLGV 531
Cdd:PRK09606 447 RICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGV 489
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
44-402 |
9.02e-96 |
|
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: 311.24 E-value: 9.02e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 44 GLVKQHLDSFNYFINVGIHKIVKANSRITSTVDPS--------IYLRFKKVRVGEPSI-INVNTVENINPHMCRLADMTY 114
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQhpgengdkLSLKFGQIRLGKPMFdETDGSTREIYPQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 115 AAPIFVNIEYVHGshgNKAKSAKDNVIIGRMPIMLRSCRCVLHGKDEEELARLGECPLDPGGYFIIKGTEKVLLIQEQLS 194
Cdd:pfam04563 81 SAPLYVDLELSVY---NGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRS 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 195 KNRIIIDSD---KKGNINASVTSSTEMTKSKT---VIQMEKE----KIYLFLHRFVKKIPIIIVLKAMGMESDQEIVQMV 264
Cdd:pfam04563 158 RNHPIVFKKadpKKRGSVASVRSSAEISVRPDstsWVNVLEYlsngTIYFKFPYIKKEIPIVIILRALGFTSDREIFELI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 265 ---GRDPRFSASLLPSIEECVSEGVNTQKQALDYLEAKVKKI-SYGTPPEKDGR-ALSILRDLFLAHVPVPDNNFRQKCF 339
Cdd:pfam04563 238 cydVNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIfRMGRPREPRIKyAEEILQKEVLPHLGTYELDETKKAY 317
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79529842 340 YVGVMLRRMIEAMLNKDAMDDKDYVGNKRLELSGQLISLLFEDLFKTMLSEAIKNVDHILNKP 402
Cdd:pfam04563 318 FIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSP 380
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
33-1150 |
8.07e-67 |
|
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: 245.73 E-value: 8.07e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 33 FQLVPEFLKVRGLVKQHLDSFNYFI----------NVGIHKIVKANSRITSTVDpSIYLRFKKVRVGEPsiinVNTVENi 102
Cdd:TIGR02013 8 FGKIPEVLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTG-NIELEYLSYRLGEP----KYSVEE- 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 103 nphmCRLADMTYAAPIFVNIEYVHGSHGNKAKSAKDNVIIGRMPIMLRScrcvlhgkdeeelarlgecpldpgGYFIIKG 182
Cdd:TIGR02013 82 ----CKERGLTYSAPLKVKLRLINKEEDGTKEIKEQDVYMGDIPLMTDR------------------------GTFIING 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 183 TEKVllIQEQLSKNRIIIDSDKKGNinasvTSSTEMTKSKTVI-------QME---KEKIYLFLHRfVKKIPIIIVLKAM 252
Cdd:TIGR02013 134 AERV--VVSQLHRSPGVFFSSEKDT-----TKSGKVLFSARIIpyrgswlEFEtdkKDVLYVRIDR-KRKLPATVLLRAL 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 253 GMESDQEIVQMVGRDPRFSASLLpsieecvSEGVNTQKQALDYLeakVKKISYGTPPEKDGrALSILRDLF-------LA 325
Cdd:TIGR02013 206 GYTIDTLILNRLGSGEYIRNTLR-------KDPTNSEEEALVEI---YRKLRPGEPPTVEA-ARSLLENLFfdpkrydLG 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 326 HV-----------PVPDnnfrqkcfYVGVM--------LRRMIEAMLNKDAMDDKDYVGNKRLELSGQLIsllfEDLFKT 386
Cdd:TIGR02013 275 RVgryklnkklglDVPE--------SIGVLtkediiatIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELL----QNQFRV 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 387 MLSEAIKNVDHilnkpiRASRFDFsqclnkDSRYSISLGLERTLSTGnfdIKRFRMH---RKGMTQV-----LT---RLS 455
Cdd:TIGR02013 343 GLARMERIVRE------RMSTQDT------DTLTPQDLINAKPISAA---IKEFFGSsqlSQFMDQTnplaeLThkrRLS 407
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 456 FIGSMGfITKISPQFEKsrkvsgpRSLQPSQWGMLCPCDTPEGESCGLVKNLALMTHVTtdeeegplvamcyKLGVtdle 535
Cdd:TIGR02013 408 ALGPGG-LTRERAGFEV-------RDVHPTHYGRICPIETPEGPNIGLINSLSTYARVN-------------EYGF---- 462
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 536 vlsaeeLHTPdsflvilnglilgkhsrpqyfanslrrlrragkigefvsvftnekqhcvYVasdvgrvcrplviadkgis 615
Cdd:TIGR02013 463 ------IETP-------------------------------------------------YR------------------- 468
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 616 RVKqhhmkelqDGVRTFDDfirdgLIEYLDVNEENNALIAlyesDGTTELDEGA----------------EAAKADTTHI 679
Cdd:TIGR02013 469 KVK--------DGKVVVTD-----EIDYLTADEEDNYVIA----QANAPLDENGrfvedlvvaryrgeitLVSPDQVDYM 531
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 680 EIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAM-------------------------------GNIAY------- 721
Cdd:TIGR02013 532 DVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVVEYvdakriv 611
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 722 --NQLNRMDTLLYLLVYP--------------QRPLLTtrtielVGyDKLGAGQ-----------------NATVAVMSF 768
Cdd:TIGR02013 612 irYDEDEEEPDGGIDIYRllkyqrsnqdtcinQRPIVS------VG-DRVEAGDvladgpstdlgelalgrNVLVAFMPW 684
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 769 SGYDIEDAIVMNKssldrgfgrCIVmKKIVAMS---QKYDNCTADRILIPQRTGPD-----AEKMQILDDDGLATPGEII 840
Cdd:TIGR02013 685 NGYNYEDAILISE---------RLV-KDDVFTSihiEEYEVEARDTKLGPEEITRDipnvsEEALRNLDENGIVRIGAEV 754
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 841 RPNDIYINKQVPvDTVTKFTS------ALSDSQYRPARE-YFKGPEGETQVVDRVALCSDKKG--------QLcIKYIIR 905
Cdd:TIGR02013 755 KAGDILVGKVTP-KGETELTPeekllrAIFGEKARDVRDtSLRVPPGVEGTVIDVKVFSREQGdelppgvnKL-VKVYIA 832
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 906 HTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIELLGSKAGVSCGRfhYGSAFGE 985
Cdd:TIGR02013 833 QKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGR--KGVPIAT 910
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 986 RSGHADKVETISATLVEKGFSYSGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSK 1065
Cdd:TIGR02013 911 PVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQ 990
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1066 NGGLRVGEMERDCLIAYGASMLIYERLMISSDpfEVQvcracGLLGYYNYKLKkavcttcknGDNIATMKLPYACKLLFQ 1145
Cdd:TIGR02013 991 FGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD--DVV-----GRTKAYEAIVK---------GENVPEPGIPESFNVLIK 1054
|
....*
gi 79529842 1146 ELQSM 1150
Cdd:TIGR02013 1055 ELQSL 1059
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
51-1152 |
3.86e-51 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 196.85 E-value: 3.86e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 51 DSFNYFINVGIHKIVKANSRItstVDPSIYLrfKKVRVGEPSIINVNtveNINPHMCRLADMTYAAPIFVNIEYVHGSHG 130
Cdd:CHL00207 16 TSFCWFLNEGLNEELNIFSKI---FDYTGNL--ELLLFGKNYKLKYP---KYNLLSAKSYDSNYSIQIYLPLKFINLKTN 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 131 nkaKSAKDNVIIGRMPIMLRScrcvlhgkdeeelarlgecpldpgGYFIIKGTEKVLLIQEQLSkNRIIIDSDKKgNINA 210
Cdd:CHL00207 88 ---KIKFINYLIGNLPKMTQR------------------------GTFIINGLERVIVSQIIRS-PGIYFKKEIK-KNSN 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 211 SVTSSTEMTKSKTVIQMEKEK---IYLFLHRfVKKIPIIIVLKAMGMeSDQEIVQMVgrdpRFSASLLPSIEECVSEGVN 287
Cdd:CHL00207 139 KIYSATLIPNRGSWIKFELDKnkeIWIRIDK-NRKKPLIIFLKALGL-TDQDIYSRL----TKSEFLKKLKPILLNSNSY 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 288 TQKQALDYLEAKVKKISYGTPPEKDGRALS------------ILRDLFLAHVPVPDNNFRQKCFYVGVM--LRRMIEAML 353
Cdd:CHL00207 213 TNEEILLEIYKNLSPIEPATVNDANQNLFSrffdpknydlgkVGRYKINNKLNLNIPERVRNLTYEDILsiIDKLINLKI 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 354 NKDAMDDKDYVGNKRLELSGQLISLLFEDLFKTmLSEAIKNvDHILnkpirasrFDFSQCLNKdsrysislglerTLSTG 433
Cdd:CHL00207 293 NKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKR-LERILRN-RMTI--------CDIDSLSKF------------NLINP 350
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 434 NFDIKRFRMHRkGMTQVLTRLSFIGSMGFIT---KIS----PQFEKSRKVSGPRSLQPSQWGMLCPCDTPEGESCGLVKN 506
Cdd:CHL00207 351 KPLIALIREFF-GSSQLSQYMDQTNPLSELThkrRISilgpGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGS 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 507 LALMTHVttdeeegplvamcYKLGVtdlevlsaeeLHTPdsFLVILNGLIlgkhsrpQYFANSlrrlrragkigefvsvf 586
Cdd:CHL00207 430 LATNARI-------------NKFGF----------IETP--FYKVINGKV-------KKFGNP----------------- 460
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 587 tnekqhcVYVASDVGRVCRplvIADKGISRVKQHHMKELQDGVRTFDDFIrdglieylDVNEENNALIAlyesdgtteld 666
Cdd:CHL00207 461 -------IYLTADSEDLYR---IAPNDINLNKNNYFKKNIIPVRYKQEFK--------TVNPSKVDFIA----------- 511
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 667 egaeaakadtthieIEPFTILGVVAGLIPYPHHNQSPRNTYQCAMGKQAMGNI---------AYNQLNRMDTLL------ 731
Cdd:CHL00207 512 --------------ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLypekpivgtGYEKQIALDSGMtiislt 577
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 732 ------------------------YLLVYP---------QRPL------LTTRTIELVGYD----KLGAGQNATVAVMSF 768
Cdd:CHL00207 578 egivvsvsaykiiiqddnnryihyYLQKYQrsnqntcinYRPIvwvgekINIGQILADGSDidnsELALGQNVLVAYMPW 657
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 769 SGYDIEDAIVMNKSSLDRGFGRCIVMKKI-VAMSQKYDNCTADRILIPQRTgpDAEKMQiLDDDGLATPGEIIRPNDIYI 847
Cdd:CHL00207 658 EGYNFEDAILINKRLVYEDLFTSIHIEKYeIELRQTKLGSEEITRNIPNVS--EYSLKN-LDENGIISIGSKVLAGDILV 734
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 848 NKQVPVDTVT-----KFTSALSDSQYRPAREY-FKGPEGET-QVVDRVALCSDKKGQL------CIKYIIRHTRRPELGD 914
Cdd:CHL00207 735 GKITPKGESDqlpegKLLRAIFGEKAKDVKDTsLRMPNGGYgRVIKVEIFSRSKGDELkfgyylKIRVFIAQIRKIQVGD 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 915 KFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIE-LLGSKAGVSCGRFHYGSaFGERSGH-ADK 992
Cdd:CHL00207 815 KLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFEcLLGLAGDNLNKRFKILP-FDEMYGSeYSR 893
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 993 V---ETISATLVEKGFSY------SGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGK 1063
Cdd:CHL00207 894 IlinNKLNQASIKNNEYWlfnsyhPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGK 973
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1064 SKNGGLRVGEMERDCLIAYGASMLIYERLMISSDPFEVqvcracgllgyynyklKKAVCTTCKNGDNIATMKLPYACKLL 1143
Cdd:CHL00207 974 AQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQG----------------RNETLNAIVKGQPIPKPGTPESFKVL 1037
|
....*....
gi 79529842 1144 FQELQSMNV 1152
Cdd:CHL00207 1038 MRELQSLGL 1046
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
33-1097 |
4.86e-43 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 171.05 E-value: 4.86e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 33 FQLVPEFLKVRGLVKQHLDSFNYFI-------NVGIHKIVKANSRITSTvDPSIYLRFKKVRVGEPsiinVNTVENinph 105
Cdd:PRK00405 15 FGKIKEVLELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDF-NGNLSLEFVSYELGEP----KYDVEE---- 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 106 mCRLADMTYAAPIFVNIEYVHGSHGNkAKSakDNVIIGRMPIMlrscrcvlhgkdeeelarlgecplDPGGYFIIKGTEK 185
Cdd:PRK00405 86 -CKERGLTYSAPLRVKLRLINKETGE-IKE--QEVYMGDIPLM------------------------TENGTFIINGTER 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 186 VllIQEQLskNR---IIIDSDKkgninaSVTSSTEMTKSKTVIQ-----ME-----KEKIYLFLHRfVKKIPIIIVLKAM 252
Cdd:PRK00405 138 V--IVSQL--HRspgVYFDHDK------DKTSSGKLLYSARIIPyrgswLEfefdpKDILYVRIDR-RRKLPVTVLLRAL 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 253 GMeSDQEIVQMVGRDPRFSASLLPSIEECVS--------------------------------------EGVNTQKQALD 294
Cdd:PRK00405 207 GY-SDEEILDLFYEKEEFGKEIEVPVEYLLGkvlaedivdeetgevlaeandeiteeldgpyirntlekDPTSSREEALV 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 295 YLeakVKKISYGTPPEKDGrALSILRDLF-------LAHV-----------PVPDNnfrqkcfyVGVM--------LRRM 348
Cdd:PRK00405 286 EI---YRRLRPGEPPTVEA-ARSLLENLFfdpkrydLSKVgryklnkklglDEDED--------VRVLtkediiatIKYL 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 349 IEAMLNKDAMDDKDYVGNKRLELSGQLIsllfEDLFKTMLS---------------EAIKNVDHILNKPIRASRFDF--- 410
Cdd:PRK00405 354 INLRNGKGEVDDIDHLGNRRVRSVGELL----QNQFRIGLSrmeravrermslqdlDTLTPQDLINAKPVVAAIKEFfgs 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 411 SQclnkdsrysislglertLStgnfdikRFrmhrkgMTQV-----LT---RLSFIGSMGfITKISPQFEksrkVsgpRSL 482
Cdd:PRK00405 430 SQ-----------------LS-------QF------MDQTnplseLThkrRLSALGPGG-LTRERAGFE----V---RDV 471
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 483 QPSQWGMLCPCDTPEGESCGLVKNLAlmTHVTTDEEeGPLVAMCYKL--G-VTDlEV--LSAEElhtPDSFLVILNGLIL 557
Cdd:PRK00405 472 HPTHYGRICPIETPEGPNIGLINSLA--TYARVNEY-GFIETPYRKVvdGkVTD-EIvyLTADE---EDNYVIAQANAPL 544
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 558 GKHSRpqyFANSLRRLRRAGkigEFVSVFTNE--------KQhCVYVAS---------DVGR-----------VcrPLVI 609
Cdd:PRK00405 545 DEDGR---FVDELVTARYKG---EFVLVPPEEvdymdvspKQ-VVSVAAslipflehdDANRalmgsnmqrqaV--PLLR 615
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 610 ADKGIsrvkqhhmkelqdgVRTfddfirdGlIEYLDVNEENNALIAlyESDGTTEldegaeaaKADTTHIEIEPFTILGV 689
Cdd:PRK00405 616 PEAPL--------------VGT-------G-MERRVARDSGAVVVA--KRDGVVE--------YVDASRIVVRVEELDPG 663
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 690 VAG-----LIPYPHHNQsprNTyqCamgkqamgniaYNQlnrmdtllyllvypqRPLLTtrtielVGyDKLGA------- 757
Cdd:PRK00405 664 EDGvdiynLIKFQRSNQ---NT--C-----------INQ---------------RPIVK------VG-DRVEKgdvladg 705
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 758 ----------GQNATVAVMSFSGYDIEDAIVMNK--------SSLDrgfgrcIVMKKIVAMSQK--YDNCTADrilIPQr 817
Cdd:PRK00405 706 pstdngelalGQNVLVAFMPWNGYNFEDAILISErlvkedvfTSIH------IEEYEIEARDTKlgPEEITRD---IPN- 775
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 818 TGPDAEKMqiLDDDGLATPGEIIRPNDIYINKqvpvdtVTkftsalsdsqyrpareyfkgPEGETQ-------------- 883
Cdd:PRK00405 776 VSEEALRN--LDESGIVRIGAEVKPGDILVGK------VT--------------------PKGETEltpeekllraifge 827
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 884 ----VVD---RValcsdKKGQ----LCIKYIIRHTRRPEL--------------------GDKFSSRHGQKGVCGIIIQQ 932
Cdd:PRK00405 828 kardVKDtslRV-----PHGEegtvIDVKVFTRIEQGDELppgvnklvkvyiaqkrkiqvGDKMAGRHGNKGVVSRILPV 902
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 933 EDFPFSELGICPDLIMNPHGFPSRMTVGKMIELlgskagvscgrfHYGSAfGERSGhaDKVET----------ISATLVE 1002
Cdd:PRK00405 903 EDMPYLEDGTPVDIVLNPLGVPSRMNIGQILET------------HLGWA-AKGLG--IKFATpvfdgakeeeIKELLEE 967
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1003 KGFSYSGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAY 1082
Cdd:PRK00405 968 AGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1047
|
1290
....*....|....*
gi 79529842 1083 GASMLIYERLMISSD 1097
Cdd:PRK00405 1048 GAAYTLQEMLTVKSD 1062
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1067-1158 |
1.74e-39 |
|
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: 141.19 E-value: 1.74e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1067 GGLRVGEMERDCLIAYGASMLIYERLMISSDPFEVQVCRACGLLGYYNYklkkavCTTCKNGDNIATMKLPYACKLLFQE 1146
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNK------CPICKGETDISPGYIPESFKLLFQE 74
|
90
....*....|..
gi 79529842 1147 LQSMNVVPRLKL 1158
Cdd:pfam04560 75 LQSLGIDPRLLL 86
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
37-1097 |
8.28e-39 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 157.37 E-value: 8.28e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 37 PEFLKVRglvkqhLDSFNYFINVGIHKIVKANSRITSTvDPSIYLRF--KKVRVGEPSIinvntveniNPHMCRLADMTY 114
Cdd:CHL00001 13 PGFNQIQ------FEGFCRFIDQGLTEELSKFPKIEDT-DQEIEFQLfvETYQLVEPLI---------KERDAVYESLTY 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 115 AAPIFVNieyVHGSHGNKAKSAKDNVIIGRMPIMlrscrcvlhgkdeeelarlgecplDPGGYFIIKGTEKVLLIQeqls 194
Cdd:CHL00001 77 SSELYVP---AGLIWKKSRDMQEQTVFIGNIPLM------------------------NSLGTFIINGIYRVVINQ---- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 195 knriIIDS---------DKKGNinaSVTSSTEMTKSKTVIQME---KEKIYLFLHRfVKKIPIIIVLKAMGMESDqEIVQ 262
Cdd:CHL00001 126 ----ILRSpgiyyrselDHNGI---SVYTGTIISDWGGRLELEidrKARIWARVSR-KQKISILVLLSAMGLNLR-EILD 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 263 MVgRDPRFsasLLPSIEECVSEGVNTQKQALdyLEAKVKKISYGTPPEKDGRALSILRDLFlahvpvpdnnFRQKCfYVG 342
Cdd:CHL00001 197 NV-CYPEI---FLSFLNDKEKKKIGSKENAI--LEFYQQFACVGGDPVFSESLCKELQKKF----------FQQRC-ELG 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 343 VMLRRMIeamlnkdamddkdyvgNKRLEL--SGQLISLLFEDLfktmLSEA---IK---------NVDHILNKPIRaSRF 408
Cdd:CHL00001 260 RIGRRNM----------------NRKLNLdiPENNTFLLPQDV----LAAAdylIGmkfgmgtldDIDHLKNKRIR-SVA 318
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 409 DFSQ-----CLNKdsrysislgLERTLSTgnfDIKRFRMHRKGMT-------QVLTRL--SFIGS---MGFITKISP--Q 469
Cdd:CHL00001 319 DLLQdqfglALNR---------LENAVRG---TICGAIRRKLIPTpqnlvtsTPLTTTyeSFFGShplSQFLDQTNPltE 386
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 470 FEKSRKVS--GP------------RSLQPSQWGMLCPCDTPEGESCGLVKNLAlmTHVTTDEE---EGPLVAMCYKLGVT 532
Cdd:CHL00001 387 IVHGRKLSslGPggltgrtasfrvRDIHPSHYGRICPIDTSEGINAGLIGSLA--IHARIGHWgslESPFYEISERSKEE 464
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 533 DLEVLSAEElhtpDSFLVILNGLILGKHSRPQYFANSLRRLRRagkigEFVSVftnekqhcvyvasdvgrvcrplviadk 612
Cdd:CHL00001 465 RMVYLSPSE----DEYYMIAAGNSLALNQGIQEEQVVPARYRQ-----EFLTI--------------------------- 508
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 613 gisRVKQHHMKelqdGVRTFDDF-IRDGLIEYLDVNEENNAL---------IALYESD----GT-----TELDEGAEA-A 672
Cdd:CHL00001 509 ---AWEQIHLR----SIFPFQYFsIGASLIPFLEHNDANRALmgsnmqrqaVPLSRSEkcivGTglerqVALDSGVVAiA 581
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 673 KADTTHIEIEPFTILGVVAGlipypHHNQSPRNTYQCAmgkqamgniayNQlnrmDTLLYllvypQRPllttrTIELVGY 752
Cdd:CHL00001 582 EHEGKIIYTDTDKIILSGNG-----DTLSIPLVMYQRS-----------NK----NTCMH-----QKP-----QVRRGKC 631
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 753 DK---------------LGAGQNATVAVMSFSGYDIEDAIVMNKssldrgfgrCIVMKKIVAmS---QKYD------NCT 808
Cdd:CHL00001 632 VKkgqiladgaatvggeLALGKNVLVAYMPWEGYNFEDAVLISE---------RLVYEDIYT-SfhiRKYEiqthvtSQG 701
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 809 ADRIL--IPQRtgpDAEKMQILDDDGLATPGEIIRPNDIYINKQVPVDTVT-------KFTSALSDSQYRPAREY-FKGP 878
Cdd:CHL00001 702 PERITkeIPHL---EAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEEssyapegRLLRAIFGIQVSTSKETcLKLP 778
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 879 EG-ETQVVDrVALCSDKKGQLCIKYIIR----HTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGF 953
Cdd:CHL00001 779 IGgRGRVID-VRWIQKKGGSSYNPETIHvyilQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGV 857
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 954 PSRMTVGKMIE-LLGSkAGVSCGRfHYGSA-FGERSGhadkvETISATLVekgFS------------------YSGKDLL 1013
Cdd:CHL00001 858 PSRMNVGQIFEcLLGL-AGDLLNR-HYRIApFDERYE-----QEASRKLV---FSelyeaskqtanpwvfepeYPGKSRL 927
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1014 YSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLM 1093
Cdd:CHL00001 928 FDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLT 1007
|
....
gi 79529842 1094 ISSD 1097
Cdd:CHL00001 1008 YKSD 1011
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
900-1150 |
2.36e-26 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 117.72 E-value: 2.36e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 900 IKYIIRHTRRPELGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIE----LLGSKAGVSCG 975
Cdd:PRK09603 1078 VKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEmhlgLVGKEFGKQIA 1157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 976 RF------------------------HYGSAFGERSGHADKVETIS-----------ATLVEKGFS-------------- 1006
Cdd:PRK09603 1158 SMledktkdfakelrakmleianainEKDPLTIHALENCSDEELLEyakdwskgvkmAIPVFEGISqekfyklfelakia 1237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 1007 YSGKDLLYSGISGEPVEAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASM 1086
Cdd:PRK09603 1238 MDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAH 1317
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 79529842 1087 LIYERLMISSDPFEvqvcracGLLGYYnyklkKAVcttcKNGDNIATMKLPYACKLLFQELQSM 1150
Cdd:PRK09603 1318 TLKEMLTIKSDDIR-------GRENAY-----RAI----AKGEQVGESEIPETFYVLTKELQSL 1365
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
550-611 |
5.92e-25 |
|
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: 98.59 E-value: 5.92e-25
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 79529842 550 VILNGLILGKHSRPQYFANSLRRLRRAGKIGEFVSVFTNEKQHCVYVASDVGRVCRPLVIAD 611
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
194-370 |
8.30e-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: 102.81 E-value: 8.30e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 194 SKNRIIIDSDK-KGNINASVTSSTEMTKSKTVIQMEKEKIYLFLHRFVK-KIPIIIVLKAMGMESDQEIVQMV---GRDP 268
Cdd:pfam04561 1 RSNGIYVEKELdKNGIIATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKrKIPIVIFLKALGLVSDREILDRLcydFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 269 RFSASLLPSIEECvsEGVNTQKQALDYLEAKVKKIS---YGTPPEKDGRALSILRDLFLAHVPV--PDNNFRQKCFYVGV 343
Cdd:pfam04561 81 QMLELLKPELEEA--ENIYTQEEALDYIGKGFALRRgeePRLQRAREILYSRDPKYNLNKHLGLnePFENERLKAQDILY 158
|
170 180
....*....|....*....|....*..
gi 79529842 344 MLRRMIEAMLNKDAMDDKDYVGNKRLE 370
Cdd:pfam04561 159 MIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
904-1097 |
3.68e-21 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 100.85 E-value: 3.68e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 904 IRHTRRPelGDKFSSRHGQKGVCGIIIQQEDFPFSELGICPDLIMNPHGFPSRMTVGKMIEL--------LGSKAGV--- 972
Cdd:PRK14844 1077 VKHSLQP--GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILEThvgwackkLGEKVGNild 1154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 973 --------------------------------------------------------------------SCGRFH------ 978
Cdd:PRK14844 1155 einkiksafckgirslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenylnSCKSAYsnlrnf 1234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79529842 979 ------YGS-------------------AFGERSG--------HADKVETISATLVEKGFSYSGKDLLYSGISGEPVEAY 1025
Cdd:PRK14844 1235 lievysCGSnvsicnnirdisdnnliefARKLRDGipvaapvfEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRK 1314
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 79529842 1026 IFMGPIYYQKLKHMVLDKMHARGSGPRVMMTRQPTEGKSKNGGLRVGEMERDCLIAYGASMLIYERLMISSD 1097
Cdd:PRK14844 1315 VTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
449-512 |
7.67e-19 |
|
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: 81.42 E-value: 7.67e-19
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79529842 449 QVLTRLSFIGSMGFITKISP---QFEKSRKVSGPRSLQPSQWGMLCPCDTPEGESCGLVKNLALMTH 512
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSprgGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
632-683 |
1.12e-13 |
|
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: 66.41 E-value: 1.12e-13
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 79529842 632 FDDFIRDGLIEYLDVNEENNALIALYESDGTTELDEGAEAAKADT-THIEIEP 683
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREGPYAHTyTHCEIHP 53
|
|
| |
