|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
42-1199 |
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: 970.89 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 42 VQPHIGSFNALTegpDGGLLNLgVKDIGEKVIFDGKPlnsedeisnsgylgnKLSVSVEQVSIAKPMSNDGvssAVERKV 121
Cdd:cd00653 2 VKQQIDSFNYFL---NVGLQEI-VKSIPPITDTDDDG---------------RLKLKFGDIYLGKPKVEEG---GVTRKL 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 122 YPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQSNRCHLNKMSPYELVQHKEESDEIGGYFIVNGIEK 201
Cdd:cd00653 60 TPNECRLRDLTYSAPLYVDIRLTVNDKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEK 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 202 LIRMLIVQRRNHP----MAIIRPSFANRGASYSHYGIQIRSVRPDQTSQTN-VLHYLNdgqvtfrfswrkneylvpvvmi 276
Cdd:cd00653 140 VIINQEQRSPNVIivedSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIyVRIDLK---------------------- 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 277 lkalchtsdreifdgiigndvkdsfltdrlelllrgfkkryphlqNRTQVLQYLGDKFRvvfqaspdqsdlevgqevldr 356
Cdd:cd00653 198 ---------------------------------------------RQEEALKYIGKRFE--------------------- 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 357 ivlvhlgkdgsqdkfrMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRgm 436
Cdd:cd00653 212 ----------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSK-- 273
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 437 ainfkdKRYMSRVLMRVNENIGSKMQYFLSTGNLVSQSGLdlQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTT 516
Cdd:cd00653 274 ------KKDLTPQLLINSKPITSGIKEFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFE 345
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 517 VRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRIStqqsdvsripsilyslgvapashtfaagpslccvqidgkiigwv 596
Cdd:cd00653 346 VRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 597 sheqgkiiadtlrywkvegktpglpidleigyvppstrgqypglylfgghsrmlrpvrylpldkedivGPFEQVYMNIAv 676
Cdd:cd00653 382 --------------------------------------------------------------------GRIERPYRIVE- 392
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 677 tpqeiqnNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANL 756
Cdd:cd00653 393 -------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGI 465
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 757 YDDYGMDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITqhfGFGNDEWPKEW 836
Cdd:cd00653 466 EEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT---RGDIPNVSEEK 542
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 837 LEKLDEDGLPYIGTYVEEGDPICAYFDDTLN--------------KTKIKTYHSSEPAYIEEVNLIGDESNKfQELQTVS 902
Cdd:cd00653 543 LKNLDEDGIIRPGARVEPGDILVGKITPKGEtestpifgekardvRDTSLKYPGGEKGIVDDVKIFSRELND-GGNKLVK 621
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 903 IKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDST 982
Cdd:cd00653 622 VYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDAT 701
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 983 PWIFNEDDTPADYFGEqlakAGYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKG 1062
Cdd:cd00653 702 PFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKG 777
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1063 RKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQsvprigsistvcCRRCSmrfedakkll 1142
Cdd:cd00653 778 RSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANL------------CRLCK---------- 835
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*..
gi 6325267 1143 tksedgekifiddsqiwedgqgnkfvGGNETTTVAIPFVLKYLDSELSAMGIRLRYN 1199
Cdd:cd00653 836 --------------------------KGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
42-1203 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 583.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 42 VQPHIGSFNALtegpdgglLNLGVKDIgekvifdgkpLNSEDEISNSGYlgnKLSVSVEQVSIAKPMSNDgvSSAVERKV 121
Cdd:PRK08565 15 VRQHLDSYNDF--------IERGLQEI----------VDEFGEIKTEIP---GLKIVLGKIRVGEPEIKE--ADGSERPI 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 122 YPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRdCGGLPVMLQSNRCHLNKMSPYELVQHKEESDEIGGYFIVNGIEK 201
Cdd:PRK08565 72 TPMEARLRNLTYAAPLYLTMIPVENGIEYEPEEVK-IGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSER 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 202 LIRMLIVQRRNHPMAiirpSFANRGASYSHYGiQIRSVRPDQTSQTnVLHYLNDGqvTFRFSWRKNEYLVPVVMILKALC 281
Cdd:PRK08565 151 VIVSQEDLAPNRVLV----DKGEAGSSITHTA-KVISSRAGYRAQV-TVERRKDG--TIYVSFPAVPGKIPFVILMRALG 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 282 HTSDREIFDGIIGNDVKDSFLTDRLELLLRGFKkryphlqNRTQVLQYLGDKFRVvfqASPDQSDLEVGQEVLDRIVLVH 361
Cdd:PRK08565 223 LETDRDIVYAVSLDPEIQQELLPSLEQASSIAA-------TVEDALDYIGKRVAI---GQPREYRIERAEQILDKYLLPH 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 362 LGKdGSQDKFR---MLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAI 438
Cdd:PRK08565 293 LGT-SPEDRIKkayFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKL 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 439 NFkdkrymsRVLMRVNEnIGSKMQYFLSTGNLVSQSgldlqqvSGYTVVAEKINFYRFISHFRMVhrgsfFAQLKTTT-- 516
Cdd:PRK08565 372 DL-------RAIVRPDI-ITERIRHALATGNWVGGR-------TGVSQLLDRTNYLSTLSHLRRV-----VSPLSRGQph 431
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 517 --VRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQqSDVSRIPSILYSLGVAPASHTFAA-GPSLCCVQIDGKII 593
Cdd:PRK08565 432 feARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVG-VDEEEVEEILYELGVVPVEEAREEeYISWSRVYLNGRLI 510
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 594 GWvsHEQGKIIADTLRYWKVEGKtpgLPIDLEIGYVPPSTRGQypgLYLFGGHSRMLRPV-----RYLPLDKEDI----- 663
Cdd:PRK08565 511 GY--HPDGEELAEKIRELRRSGK---ISDEVNVAYIETGEINE---VYVNCDSGRVRRPLivvenGKPKLTREHVeklkk 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 664 ----------------VGPFEQVYMNIAVTPQEIQNNvHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMG 727
Cdd:PRK08565 583 geltfddlvkmgvieyLDAEEEENAYVALDPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 728 TPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGT---MY 804
Cdd:PRK08565 662 LYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTffrTY 741
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 805 KTEKVdlalnrnrgdpitQHFGFGNDEW-----------PKEWLEKLDEDGLPYIGTYVEEGDPIcayfddtLNKTkikt 873
Cdd:PRK08565 742 ETEER-------------KYPGGQEDKIeipepnvrgyrGEEYYRKLDEDGIVSPEVEVKGGDVL-------IGKT---- 797
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 874 yhsSEPAYIEEVNLIGDESNKFQE----------------LQTVS------IKYRIR--RTPQIGDKFSSRHGQKGVCSR 929
Cdd:PRK08565 798 ---SPPRFLEELEELSLGLQERRDtsvtvrhgekgivdtvLITESpegnklVKVRVRdlRIPELGDKFASRHGQKGVIGM 874
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 930 KWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWIfnedDTPADYFGEQLAKAGYNYHG 1009
Cdd:PRK08565 875 LVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFY----GEPEEELRKELLKLGYKPDG 950
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1010 NEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQ 1089
Cdd:PRK08565 951 TEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLK 1030
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1090 DRLLNSSDYTQASVCRECGSIlttqqsvprigsistvccrrcsmRFEDAKKlltksedgekifiddsqiwedgqgNKF-- 1167
Cdd:PRK08565 1031 ERLLDSSDKTTIYVCELCGHI-----------------------AWYDRRK------------------------NKYvc 1063
|
1210 1220 1230
....*....|....*....|....*....|....*....
gi 6325267 1168 -VGGNETT--TVAIPFVLKYLDSELSAMGIRLRYNVEPK 1203
Cdd:PRK08565 1064 pIHGDKGNisPVEVSYAFKLLLQELMSMGISPRLKLGDK 1102
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
700-1065 |
2.89e-169 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 505.14 E-value: 2.89e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 700 LANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYT 779
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 780 GYDMDDAMIINKSADERGFGYGTMYKTEKVdlalNRNRGDPITQHFGFGNDEwPKEWLEKLDEDGLPYIGTYVEEGDPIC 859
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA----RKTKLGPIEEITRDIPNV-SEEALKKLDEDGIVRVGAEVKPGDILV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 860 -------------AYFDDTLNKTKIK--TYHSSEPAYIEEVnLIGDESNKFqeLQTVSIKYRIRRTPQIGDKFSSRHGQK 924
Cdd:pfam00562 156 gkvgpteltkllrAIFGEKARDVKDTslKVPPGEEGVVDDV-IVFELPPGG--IKMVKVYIRQKRKPEVGDKFASRHGQK 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 925 GVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPwiFNEDDTPADYFGEQLAKAG 1004
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATP--FDGASTEVEDIGELLEKAG 310
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6325267 1005 YNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKR 1065
Cdd:pfam00562 311 YNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
586-1203 |
8.19e-136 |
|
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: 426.37 E-value: 8.19e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 586 VQIDGKIIGWvsHEQGKIIADTLRYWKVEGKtpgLPIDLEIGYVppSTRGQypgLYLFGGHSRMLRP------------- 652
Cdd:TIGR03670 1 VYLNGRLIGY--HDDPEELVEEVRKLRRSGK---LSQEVNVAYY--EETNE---VYINCDAGRIRRPlivvengkpkltr 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 653 ---------------------VRYLPLDKEdivgpfEQVYmnIAVTPQEIQNNvHTHVEFTPTNILSILANLTPFSDFNQ 711
Cdd:TIGR03670 71 ehveklkegeltwddlvkqgvIEYLDAEEE------ENAY--IALDPEELTPE-HTHLEIDPSAILGIIASTIPYPEHNQ 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 712 SPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMDDAMIINK 791
Cdd:TIGR03670 142 SPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNK 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 792 SADERGFGYGTMYKTEKvdlALNRNRGDPITQHFGFGNDEW----PKEWLEKLDEDGLPYIGTYVEEGDPICAY------ 861
Cdd:TIGR03670 222 ASIERGLARSTFFRTYE---AEERRYPGGQEDRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtspprf 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 862 ---FDDTLNKTKIK-----TYHSSEPAYIEEVNLI-GDESNKFqelqtVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWP 932
Cdd:TIGR03670 299 leeLREFGLVTERRrdtsvTVRHGEKGIVDKVIITeTEEGNKL-----VKVRVRDLRIPELGDKFASRHGQKGVIGMIVP 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 933 TIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWifneDDTPADYFGEQLAKAGYNYHGNEP 1012
Cdd:TIGR03670 374 QEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF----EGEPEEELRKELLKLGFKPDGKEV 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1013 MYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRL 1092
Cdd:TIGR03670 450 MYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERL 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1093 LNSSDYTQASVCRECGSIlttqqsvprigsistvccrrcsmrfedakklltksedgekifiddsqIWEDGQGNKF---VG 1169
Cdd:TIGR03670 530 LDESDKYVVYVCENCGHI-----------------------------------------------AWEDKRKGTAycpVC 562
|
650 660 670
....*....|....*....|....*....|....*.
gi 6325267 1170 GNETT--TVAIPFVLKYLDSELSAMGIRLRYNVEPK 1203
Cdd:TIGR03670 563 GETGDisPVEMSYAFKLLLDELKSLGISPRLELGDK 598
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
45-1097 |
1.62e-101 |
|
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: 345.56 E-value: 1.62e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 45 HIGSFNALTEGpdgGLLNLgVKDIGEKVIFDGKplnsedeisnsgylgnkLSVSVEQVSIAKPmsndgvssaverKVYPS 124
Cdd:COG0085 20 QLDSFNWFLEE---GLQEI-FDEISPIEDFTGN-----------------LSLEFGDYRLGEP------------KYTPE 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 125 ESRQRLTSYRGKLLLKLKWsVNNG-----EENLFevrdCGGLPVMLQSnrchlnkmspyelvqhkeesdeigGYFIVNGI 199
Cdd:COG0085 67 ECKERDLTYAAPLYVKVRL-VNKEtgeikEQEVF----MGDFPLMTDS------------------------GTFIINGT 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 200 EKLIRMLIV-----------QRRNHPM--AIIRPsfaNRGAsyshygiqirsvrpdqtsqtnvlhYL-----NDGQVTFR 261
Cdd:COG0085 118 ERVIVSQLVrspgvyfveeeDKSGKDLysAKVIP---SRGA------------------------WLefetdKDGTIYVR 170
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 262 FSwRKNEylVPVVMILKALCHTSDREIFDgIIGNDVKDSFLTDRLElllrgfkKRypHLQNRTQVLQYLGDKFRvvfqas 341
Cdd:COG0085 171 ID-RKRK--IPVTVLLRALGLETDEEILE-AFGDDPIQEYILATLE-------KD--NTKTQEEALLEIYRKLR------ 231
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 342 P-DQSDLEVGQEVLD-------RIVLVHLGKDGSQDKFRM-------------LLFMIRKLYSLVAGECSPDNPDATQHQ 400
Cdd:COG0085 232 PgEPPTIERAEQLLDnlffdpkRYDLAHVGRYKINKKLGLdvppedrvltaedIVATIKYLLELHLGEREPDDIDHLGNR 311
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 401 EVLLGGflygmilkekidEYLQNiiaQVRMDINRgMAINFKDKryMSRVLMRVNE-----NIG---SKMQYFLSTGNLvS 472
Cdd:COG0085 312 RVRLVG------------ELLQN---QFRVGLSR-MERVVRER--MTTQDVEAITpqsliNIRpvvAAIKEFFGSSQL-S 372
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 473 QSgldLQQVSgytVVAEkinfyrfISHFRMV----------HRGSFfaqlkttTVRKLLPESWGFLCPVHTPDGSPCGLL 542
Cdd:COG0085 373 QF---MDQTN---PLSE-------LTHKRRLsalgpgglsrERAGF-------EVRDVHPSHYGRMCPIETPEGPNIGLI 432
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 543 NHFAHKCRIStqqsDVSRI--PSIlyslgvapashtfaagpslccVQIDGKI---IGWVS--HEQGKIIADTlrywkveg 615
Cdd:COG0085 433 GSLALYARVN----EYGFIetPYR---------------------KVENGKVtdeIEYLTadEEENYYIAQA-------- 479
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 616 ktpGLPIDLEIGYVPPSTrgqypglylfgghsrmlrPVRYlpldKEDIVgpfeqvymniAVTPQEiqnnvHTHVEFTPTN 695
Cdd:COG0085 480 ---NAPLDEDGNFLEERV------------------LVRY----RGEEV----------LVPPEE-----VDYMDVSPKQ 519
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 696 ILSILANLTPFSDFNQSPRNMYQCQMGKQTMGtpgvalCHRSDNKL--YRLQT----------GQTPIVKAN-------- 755
Cdd:COG0085 520 IVSVATSLIPFLEHDDANRALMGANMQRQAVP------LLRPEAPLlhYPLQKfqrsnqgtciNQRPIVRVGdrvekgdv 593
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 756 LYDDYGMDN--FPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLalNRNRGDP--ITQhfgfgndE 831
Cdd:COG0085 594 LADGPATDNgeLALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEA--RDTKLGPeeITR-------D 664
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 832 WP---KEWLEKLDEDGLPYIGTYVEEGD-------P------------ICAYFDDTLNK---TKIKTYHSsEPAYIEEVN 886
Cdd:COG0085 665 IPnvsEEALRNLDEDGIIRIGAEVKGGDilvgkvtPkgeteltpeerlLRAIFGEKAREvrdTSLRVPHG-EKGKVIDVK 743
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 887 LI----GDEsNKFQELQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGM 962
Cdd:COG0085 744 VFsreeGDE-LPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQ 822
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 963 FVESLAGKAGALHGIAQDSTPwiFNEddTPADYFGEQLAKAGYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVND 1042
Cdd:COG0085 823 VLETHLGWAAALLGRRVATPV--FDG--APEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDD 898
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*
gi 6325267 1043 KFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSD 1097
Cdd:COG0085 899 KIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD 953
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
210-403 |
1.96e-41 |
|
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: 150.58 E-value: 1.96e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 210 RRNHPMAIIRPSFANRgasyshygiqIRSVRPDQTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSDREIF 289
Cdd:pfam04561 1 RSNGIYVEKELDKNGI----------IATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREIL 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 290 DGIIGndvkdSFLTDRLELLLRGFKKRYPHLQNRTQVLQYLGDkfrVVFQASPDQSDLEVGQEVLDRI-----VLVHLGK 364
Cdd:pfam04561 71 DRLCY-----DFNDPQMLELLKPELEEAENIYTQEEALDYIGK---GFALRRGEEPRLQRAREILYSRdpkynLNKHLGL 142
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 6325267 365 DGSQD----KFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVL 403
Cdd:pfam04561 143 NEPFEnerlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
593-651 |
1.06e-28 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
Pssm-ID: 462028 Cd Length: 58 Bit Score: 109.50 E-value: 1.06e-28
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 6325267 593 IGWVSHEQGKIIADTLRYWKVEGKtPGLPIDLEIGYVPPSTRGQYPGLYLFGGHSRMLR 651
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGE-HGVPLTLEIGYVPPSNGGQYPGLYLFTSPARMMR 58
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
42-1199 |
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: 970.89 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 42 VQPHIGSFNALTegpDGGLLNLgVKDIGEKVIFDGKPlnsedeisnsgylgnKLSVSVEQVSIAKPMSNDGvssAVERKV 121
Cdd:cd00653 2 VKQQIDSFNYFL---NVGLQEI-VKSIPPITDTDDDG---------------RLKLKFGDIYLGKPKVEEG---GVTRKL 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 122 YPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQSNRCHLNKMSPYELVQHKEESDEIGGYFIVNGIEK 201
Cdd:cd00653 60 TPNECRLRDLTYSAPLYVDIRLTVNDKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEK 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 202 LIRMLIVQRRNHP----MAIIRPSFANRGASYSHYGIQIRSVRPDQTSQTN-VLHYLNdgqvtfrfswrkneylvpvvmi 276
Cdd:cd00653 140 VIINQEQRSPNVIivedSKGKRIYTKTSIPSYSPYRGSWLEVKSDKKKDRIyVRIDLK---------------------- 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 277 lkalchtsdreifdgiigndvkdsfltdrlelllrgfkkryphlqNRTQVLQYLGDKFRvvfqaspdqsdlevgqevldr 356
Cdd:cd00653 198 ---------------------------------------------RQEEALKYIGKRFE--------------------- 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 357 ivlvhlgkdgsqdkfrMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRgm 436
Cdd:cd00653 212 ----------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSK-- 273
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 437 ainfkdKRYMSRVLMRVNENIGSKMQYFLSTGNLVSQSGLdlQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTT 516
Cdd:cd00653 274 ------KKDLTPQLLINSKPITSGIKEFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFE 345
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 517 VRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRIStqqsdvsripsilyslgvapashtfaagpslccvqidgkiigwv 596
Cdd:cd00653 346 VRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 597 sheqgkiiadtlrywkvegktpglpidleigyvppstrgqypglylfgghsrmlrpvrylpldkedivGPFEQVYMNIAv 676
Cdd:cd00653 382 --------------------------------------------------------------------GRIERPYRIVE- 392
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 677 tpqeiqnNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANL 756
Cdd:cd00653 393 -------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGI 465
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 757 YDDYGMDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITqhfGFGNDEWPKEW 836
Cdd:cd00653 466 EEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEIT---RGDIPNVSEEK 542
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 837 LEKLDEDGLPYIGTYVEEGDPICAYFDDTLN--------------KTKIKTYHSSEPAYIEEVNLIGDESNKfQELQTVS 902
Cdd:cd00653 543 LKNLDEDGIIRPGARVEPGDILVGKITPKGEtestpifgekardvRDTSLKYPGGEKGIVDDVKIFSRELND-GGNKLVK 621
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 903 IKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDST 982
Cdd:cd00653 622 VYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDAT 701
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 983 PWIFNEDDTPADYFGEqlakAGYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKG 1062
Cdd:cd00653 702 PFDGAEEEDISELLGE----AGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKG 777
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1063 RKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQsvprigsistvcCRRCSmrfedakkll 1142
Cdd:cd00653 778 RSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSANL------------CRLCK---------- 835
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*..
gi 6325267 1143 tksedgekifiddsqiwedgqgnkfvGGNETTTVAIPFVLKYLDSELSAMGIRLRYN 1199
Cdd:cd00653 836 --------------------------KGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
42-1203 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 583.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 42 VQPHIGSFNALtegpdgglLNLGVKDIgekvifdgkpLNSEDEISNSGYlgnKLSVSVEQVSIAKPMSNDgvSSAVERKV 121
Cdd:PRK08565 15 VRQHLDSYNDF--------IERGLQEI----------VDEFGEIKTEIP---GLKIVLGKIRVGEPEIKE--ADGSERPI 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 122 YPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRdCGGLPVMLQSNRCHLNKMSPYELVQHKEESDEIGGYFIVNGIEK 201
Cdd:PRK08565 72 TPMEARLRNLTYAAPLYLTMIPVENGIEYEPEEVK-IGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSER 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 202 LIRMLIVQRRNHPMAiirpSFANRGASYSHYGiQIRSVRPDQTSQTnVLHYLNDGqvTFRFSWRKNEYLVPVVMILKALC 281
Cdd:PRK08565 151 VIVSQEDLAPNRVLV----DKGEAGSSITHTA-KVISSRAGYRAQV-TVERRKDG--TIYVSFPAVPGKIPFVILMRALG 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 282 HTSDREIFDGIIGNDVKDSFLTDRLELLLRGFKkryphlqNRTQVLQYLGDKFRVvfqASPDQSDLEVGQEVLDRIVLVH 361
Cdd:PRK08565 223 LETDRDIVYAVSLDPEIQQELLPSLEQASSIAA-------TVEDALDYIGKRVAI---GQPREYRIERAEQILDKYLLPH 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 362 LGKdGSQDKFR---MLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAI 438
Cdd:PRK08565 293 LGT-SPEDRIKkayFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKL 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 439 NFkdkrymsRVLMRVNEnIGSKMQYFLSTGNLVSQSgldlqqvSGYTVVAEKINFYRFISHFRMVhrgsfFAQLKTTT-- 516
Cdd:PRK08565 372 DL-------RAIVRPDI-ITERIRHALATGNWVGGR-------TGVSQLLDRTNYLSTLSHLRRV-----VSPLSRGQph 431
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 517 --VRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQqSDVSRIPSILYSLGVAPASHTFAA-GPSLCCVQIDGKII 593
Cdd:PRK08565 432 feARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVG-VDEEEVEEILYELGVVPVEEAREEeYISWSRVYLNGRLI 510
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 594 GWvsHEQGKIIADTLRYWKVEGKtpgLPIDLEIGYVPPSTRGQypgLYLFGGHSRMLRPV-----RYLPLDKEDI----- 663
Cdd:PRK08565 511 GY--HPDGEELAEKIRELRRSGK---ISDEVNVAYIETGEINE---VYVNCDSGRVRRPLivvenGKPKLTREHVeklkk 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 664 ----------------VGPFEQVYMNIAVTPQEIQNNvHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMG 727
Cdd:PRK08565 583 geltfddlvkmgvieyLDAEEEENAYVALDPEDLTPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLG 661
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 728 TPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGT---MY 804
Cdd:PRK08565 662 LYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTffrTY 741
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 805 KTEKVdlalnrnrgdpitQHFGFGNDEW-----------PKEWLEKLDEDGLPYIGTYVEEGDPIcayfddtLNKTkikt 873
Cdd:PRK08565 742 ETEER-------------KYPGGQEDKIeipepnvrgyrGEEYYRKLDEDGIVSPEVEVKGGDVL-------IGKT---- 797
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 874 yhsSEPAYIEEVNLIGDESNKFQE----------------LQTVS------IKYRIR--RTPQIGDKFSSRHGQKGVCSR 929
Cdd:PRK08565 798 ---SPPRFLEELEELSLGLQERRDtsvtvrhgekgivdtvLITESpegnklVKVRVRdlRIPELGDKFASRHGQKGVIGM 874
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 930 KWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWIfnedDTPADYFGEQLAKAGYNYHG 1009
Cdd:PRK08565 875 LVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFY----GEPEEELRKELLKLGYKPDG 950
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1010 NEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQ 1089
Cdd:PRK08565 951 TEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLK 1030
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1090 DRLLNSSDYTQASVCRECGSIlttqqsvprigsistvccrrcsmRFEDAKKlltksedgekifiddsqiwedgqgNKF-- 1167
Cdd:PRK08565 1031 ERLLDSSDKTTIYVCELCGHI-----------------------AWYDRRK------------------------NKYvc 1063
|
1210 1220 1230
....*....|....*....|....*....|....*....
gi 6325267 1168 -VGGNETT--TVAIPFVLKYLDSELSAMGIRLRYNVEPK 1203
Cdd:PRK08565 1064 pIHGDKGNisPVEVSYAFKLLLQELMSMGISPRLKLGDK 1102
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
700-1065 |
2.89e-169 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 505.14 E-value: 2.89e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 700 LANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYT 779
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 780 GYDMDDAMIINKSADERGFGYGTMYKTEKVdlalNRNRGDPITQHFGFGNDEwPKEWLEKLDEDGLPYIGTYVEEGDPIC 859
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA----RKTKLGPIEEITRDIPNV-SEEALKKLDEDGIVRVGAEVKPGDILV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 860 -------------AYFDDTLNKTKIK--TYHSSEPAYIEEVnLIGDESNKFqeLQTVSIKYRIRRTPQIGDKFSSRHGQK 924
Cdd:pfam00562 156 gkvgpteltkllrAIFGEKARDVKDTslKVPPGEEGVVDDV-IVFELPPGG--IKMVKVYIRQKRKPEVGDKFASRHGQK 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 925 GVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPwiFNEDDTPADYFGEQLAKAG 1004
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATP--FDGASTEVEDIGELLEKAG 310
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6325267 1005 YNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKR 1065
Cdd:pfam00562 311 YNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
40-459 |
2.74e-152 |
|
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: 461.85 E-value: 2.74e-152
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 40 EAVQPHIGSFNALtegpdggllnlgVKDIGEKVIFDGKPLNSEDEISNSGYLGNKLSVSVEQVSIAKPMSNDGVSSAveR 119
Cdd:pfam04563 1 GLVRQQLDSFNEF------------VDNDLQKIIDENALIESEFEIQHPGENGDKLSLKFGQIRLGKPMFDETDGST--R 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 120 KVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQSNRCHLNKMSPYELVQHKEESDEIGGYFIVNGI 199
Cdd:pfam04563 67 EIYPQECRLRNLTYSAPLYVDLELSVYNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGS 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 200 EKLIRMLIVQRRNHPMAIIRPSFANRGASYSHYGIQIRSVRPDQTSQTNVLHYLNDGQVTFRFSWRKNEylVPVVMILKA 279
Cdd:pfam04563 147 EKVIVAQEHRSRNHPIVFKKADPKKRGSVASVRSSAEISVRPDSTSWVNVLEYLSNGTIYFKFPYIKKE--IPIVIILRA 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 280 LCHTSDREIFDGIIGnDVKDSFLTDRLEL-LLRGFKKRYphlQNRTQVLQYLGDKFRVVFQAS-PDQSDLEVGQEVLDRI 357
Cdd:pfam04563 225 LGFTSDREIFELICY-DVNDQQLQEELLPsLEEGFKIRI---QTQEQALDYIGGRGRAIFRMGrPREPRIKYAEEILQKE 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 358 VLVHLGKDGS--QDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRG 435
Cdd:pfam04563 301 VLPHLGTYELdeTKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSP 380
|
410 420
....*....|....*....|....
gi 6325267 436 MainfkdkRYMSRVLMRVNeNIGS 459
Cdd:pfam04563 381 D-------DLMLQLLVNAK-PITS 396
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
586-1203 |
8.19e-136 |
|
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: 426.37 E-value: 8.19e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 586 VQIDGKIIGWvsHEQGKIIADTLRYWKVEGKtpgLPIDLEIGYVppSTRGQypgLYLFGGHSRMLRP------------- 652
Cdd:TIGR03670 1 VYLNGRLIGY--HDDPEELVEEVRKLRRSGK---LSQEVNVAYY--EETNE---VYINCDAGRIRRPlivvengkpkltr 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 653 ---------------------VRYLPLDKEdivgpfEQVYmnIAVTPQEIQNNvHTHVEFTPTNILSILANLTPFSDFNQ 711
Cdd:TIGR03670 71 ehveklkegeltwddlvkqgvIEYLDAEEE------ENAY--IALDPEELTPE-HTHLEIDPSAILGIIASTIPYPEHNQ 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 712 SPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMDDAMIINK 791
Cdd:TIGR03670 142 SPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNK 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 792 SADERGFGYGTMYKTEKvdlALNRNRGDPITQHFGFGNDEW----PKEWLEKLDEDGLPYIGTYVEEGDPICAY------ 861
Cdd:TIGR03670 222 ASIERGLARSTFFRTYE---AEERRYPGGQEDRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKtspprf 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 862 ---FDDTLNKTKIK-----TYHSSEPAYIEEVNLI-GDESNKFqelqtVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWP 932
Cdd:TIGR03670 299 leeLREFGLVTERRrdtsvTVRHGEKGIVDKVIITeTEEGNKL-----VKVRVRDLRIPELGDKFASRHGQKGVIGMIVP 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 933 TIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWifneDDTPADYFGEQLAKAGYNYHGNEP 1012
Cdd:TIGR03670 374 QEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF----EGEPEEELRKELLKLGFKPDGKEV 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1013 MYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRL 1092
Cdd:TIGR03670 450 MYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERL 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1093 LNSSDYTQASVCRECGSIlttqqsvprigsistvccrrcsmrfedakklltksedgekifiddsqIWEDGQGNKF---VG 1169
Cdd:TIGR03670 530 LDESDKYVVYVCENCGHI-----------------------------------------------AWEDKRKGTAycpVC 562
|
650 660 670
....*....|....*....|....*....|....*.
gi 6325267 1170 GNETT--TVAIPFVLKYLDSELSAMGIRLRYNVEPK 1203
Cdd:TIGR03670 563 GETGDisPVEMSYAFKLLLDELKSLGISPRLELGDK 598
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
668-1110 |
4.15e-129 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 408.58 E-value: 4.15e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 668 EQVYmnIAVTPQEIQNNvHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTG 747
Cdd:PRK07225 107 ENAY--IAVYEEDLTEE-HTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYP 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 748 QTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKT-EKVDlalnrnRGDPITQ--H 824
Cdd:PRK07225 184 QVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTyEGEE------RRYPGGQedR 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 825 FGFGNDEW----PKEWLEKLDEDGLPYIGTYVEEGDPICAY---------FDDTL------NKTKIkTYHSSEPAYIEEV 885
Cdd:PRK07225 258 FEIPDKDVrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKtspprfleePDDFGispekrRETSV-TMRSGEEGIVDTV 336
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 886 NLI-GDESNKFqelqtVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFV 964
Cdd:PRK07225 337 ILTeTEEGSRL-----VKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVL 411
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 965 ESLAGKAGALHGIAQDSTPWifneDDTPADYFGEQLAKAGYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKF 1044
Cdd:PRK07225 412 EMIGGKVGSLEGRRVDGTAF----SGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKL 487
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6325267 1045 QVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSDYTQASVCRECGSI 1110
Cdd:PRK07225 488 HARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMI 553
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
45-1097 |
1.62e-101 |
|
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: 345.56 E-value: 1.62e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 45 HIGSFNALTEGpdgGLLNLgVKDIGEKVIFDGKplnsedeisnsgylgnkLSVSVEQVSIAKPmsndgvssaverKVYPS 124
Cdd:COG0085 20 QLDSFNWFLEE---GLQEI-FDEISPIEDFTGN-----------------LSLEFGDYRLGEP------------KYTPE 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 125 ESRQRLTSYRGKLLLKLKWsVNNG-----EENLFevrdCGGLPVMLQSnrchlnkmspyelvqhkeesdeigGYFIVNGI 199
Cdd:COG0085 67 ECKERDLTYAAPLYVKVRL-VNKEtgeikEQEVF----MGDFPLMTDS------------------------GTFIINGT 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 200 EKLIRMLIV-----------QRRNHPM--AIIRPsfaNRGAsyshygiqirsvrpdqtsqtnvlhYL-----NDGQVTFR 261
Cdd:COG0085 118 ERVIVSQLVrspgvyfveeeDKSGKDLysAKVIP---SRGA------------------------WLefetdKDGTIYVR 170
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 262 FSwRKNEylVPVVMILKALCHTSDREIFDgIIGNDVKDSFLTDRLElllrgfkKRypHLQNRTQVLQYLGDKFRvvfqas 341
Cdd:COG0085 171 ID-RKRK--IPVTVLLRALGLETDEEILE-AFGDDPIQEYILATLE-------KD--NTKTQEEALLEIYRKLR------ 231
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 342 P-DQSDLEVGQEVLD-------RIVLVHLGKDGSQDKFRM-------------LLFMIRKLYSLVAGECSPDNPDATQHQ 400
Cdd:COG0085 232 PgEPPTIERAEQLLDnlffdpkRYDLAHVGRYKINKKLGLdvppedrvltaedIVATIKYLLELHLGEREPDDIDHLGNR 311
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 401 EVLLGGflygmilkekidEYLQNiiaQVRMDINRgMAINFKDKryMSRVLMRVNE-----NIG---SKMQYFLSTGNLvS 472
Cdd:COG0085 312 RVRLVG------------ELLQN---QFRVGLSR-MERVVRER--MTTQDVEAITpqsliNIRpvvAAIKEFFGSSQL-S 372
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 473 QSgldLQQVSgytVVAEkinfyrfISHFRMV----------HRGSFfaqlkttTVRKLLPESWGFLCPVHTPDGSPCGLL 542
Cdd:COG0085 373 QF---MDQTN---PLSE-------LTHKRRLsalgpgglsrERAGF-------EVRDVHPSHYGRMCPIETPEGPNIGLI 432
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 543 NHFAHKCRIStqqsDVSRI--PSIlyslgvapashtfaagpslccVQIDGKI---IGWVS--HEQGKIIADTlrywkveg 615
Cdd:COG0085 433 GSLALYARVN----EYGFIetPYR---------------------KVENGKVtdeIEYLTadEEENYYIAQA-------- 479
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 616 ktpGLPIDLEIGYVPPSTrgqypglylfgghsrmlrPVRYlpldKEDIVgpfeqvymniAVTPQEiqnnvHTHVEFTPTN 695
Cdd:COG0085 480 ---NAPLDEDGNFLEERV------------------LVRY----RGEEV----------LVPPEE-----VDYMDVSPKQ 519
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 696 ILSILANLTPFSDFNQSPRNMYQCQMGKQTMGtpgvalCHRSDNKL--YRLQT----------GQTPIVKAN-------- 755
Cdd:COG0085 520 IVSVATSLIPFLEHDDANRALMGANMQRQAVP------LLRPEAPLlhYPLQKfqrsnqgtciNQRPIVRVGdrvekgdv 593
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 756 LYDDYGMDN--FPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLalNRNRGDP--ITQhfgfgndE 831
Cdd:COG0085 594 LADGPATDNgeLALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEA--RDTKLGPeeITR-------D 664
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 832 WP---KEWLEKLDEDGLPYIGTYVEEGD-------P------------ICAYFDDTLNK---TKIKTYHSsEPAYIEEVN 886
Cdd:COG0085 665 IPnvsEEALRNLDEDGIIRIGAEVKGGDilvgkvtPkgeteltpeerlLRAIFGEKAREvrdTSLRVPHG-EKGKVIDVK 743
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 887 LI----GDEsNKFQELQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGM 962
Cdd:COG0085 744 VFsreeGDE-LPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQ 822
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 963 FVESLAGKAGALHGIAQDSTPwiFNEddTPADYFGEQLAKAGYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVND 1042
Cdd:COG0085 823 VLETHLGWAAALLGRRVATPV--FDG--APEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDD 898
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*
gi 6325267 1043 KFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSD 1097
Cdd:COG0085 899 KIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSD 953
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
417-1101 |
2.37e-45 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 178.75 E-value: 2.37e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 417 IDEYLQNiiaQVRMDINRgmaINFKDKRYMSRV---LMRVNENIGSKMQYFLSTGNLVSQsgldlqQVSGYTvvaEKINF 493
Cdd:CHL00207 311 VGELLQN---QFRIGLKR---LERILRNRMTICdidSLSKFNLINPKPLIALIREFFGSS------QLSQYM---DQTNP 375
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 494 YRFISHFRMVH---RGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQsdvsripsilyslgv 570
Cdd:CHL00207 376 LSELTHKRRISilgPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFG--------------- 440
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 571 apashtFAAGPslCCVQIDGKIIgwvshEQGKII---ADTLRYWKVegkTPGLPIDLEIGYVppstrgqypglylfgghS 647
Cdd:CHL00207 441 ------FIETP--FYKVINGKVK-----KFGNPIyltADSEDLYRI---APNDINLNKNNYF-----------------K 487
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 648 RMLRPVRYlpldKED--IVGPFEQVYMNIavtpqeiqnnvhthvefTPTNILSILANLTPFSDFNQSPR-----NM---- 716
Cdd:CHL00207 488 KNIIPVRY----KQEfkTVNPSKVDFIAI-----------------SPIQVFSIAESLIPFLEHNDANRalmgsNMqrqa 546
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 717 --------------YQCQMGKQTmGTPGVALC-----HRSDNKL-----------YRLQ----------TGQTPIV---- 752
Cdd:CHL00207 547 vpllypekpivgtgYEKQIALDS-GMTIISLTegivvSVSAYKIiiqddnnryihYYLQkyqrsnqntcINYRPIVwvge 625
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 753 KAN----LYDDYGMDN--FPNGFNAVVAVISYTGYDMDDAMIINKSadergFGYGTMYKT---EKVDLALNRNRGDP--I 821
Cdd:CHL00207 626 KINigqiLADGSDIDNseLALGQNVLVAYMPWEGYNFEDAILINKR-----LVYEDLFTSihiEKYEIELRQTKLGSeeI 700
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 822 TQH---FGFGNdewpkewLEKLDEDGLPYIGTYVEEGDPIC-------------------AYFDDTLNKTKIKTYHSSEP 879
Cdd:CHL00207 701 TRNipnVSEYS-------LKNLDENGIISIGSKVLAGDILVgkitpkgesdqlpegkllrAIFGEKAKDVKDTSLRMPNG 773
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 880 AYIEEVNLIGDESNKFQELQT-VSIKYRI----RRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAF 954
Cdd:CHL00207 774 GYGRVIKVEIFSRSKGDELKFgYYLKIRVfiaqIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGV 853
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 955 PSRMTIGMFVESLAGKAGALHGIAQDSTPwiFNEddtpadYFGEQLAKA---------------GYNYHGNEP----MYS 1015
Cdd:CHL00207 854 PSRMNVGQLFECLLGLAGDNLNKRFKILP--FDE------MYGSEYSRIlinnklnqasiknneYWLFNSYHPgkmvLRD 925
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1016 GATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNS 1095
Cdd:CHL00207 926 GRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIK 1005
|
....*.
gi 6325267 1096 SDYTQA 1101
Cdd:CHL00207 1006 SDDMQG 1011
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
748-1097 |
2.29e-43 |
|
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: 172.15 E-value: 2.29e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 748 QTPIVKAN--------LYDDYGMDN--FPNGFNAVVAVISYTGYDMDDAMIINKSADERGFgYGTMYKTEKVDLALNRNR 817
Cdd:TIGR02013 644 QRPIVSVGdrveagdvLADGPSTDLgeLALGRNVLVAFMPWNGYNYEDAILISERLVKDDV-FTSIHIEEYEVEARDTKL 722
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 818 GDP-ITQhfgfgndEWP---KEWLEKLDEDGLPYIGTYVEEGDPIC-------------------AYFDDT---LNKTKI 871
Cdd:TIGR02013 723 GPEeITR-------DIPnvsEEALRNLDENGIVRIGAEVKAGDILVgkvtpkgeteltpeekllrAIFGEKardVRDTSL 795
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 872 KTYHSSEPAYIEeVNL----IGDESNKfQELQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDI 947
Cdd:TIGR02013 796 RVPPGVEGTVID-VKVfsreQGDELPP-GVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDI 873
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 948 IINPHAFPSRMTIGMFVES---LAGKAGALHGIaQDSTPwIFneDDTPADYFGEQLAKAGYNYHGNEPMYSGATGEELRA 1024
Cdd:TIGR02013 874 VLNPLGVPSRMNIGQILEThlgWAGKRLGRKGV-PIATP-VF--DGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDR 949
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6325267 1025 DIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSD 1097
Cdd:TIGR02013 950 PVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
210-403 |
1.96e-41 |
|
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: 150.58 E-value: 1.96e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 210 RRNHPMAIIRPSFANRgasyshygiqIRSVRPDQTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSDREIF 289
Cdd:pfam04561 1 RSNGIYVEKELDKNGI----------IATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREIL 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 290 DGIIGndvkdSFLTDRLELLLRGFKKRYPHLQNRTQVLQYLGDkfrVVFQASPDQSDLEVGQEVLDRI-----VLVHLGK 364
Cdd:pfam04561 71 DRLCY-----DFNDPQMLELLKPELEEAENIYTQEEALDYIGK---GFALRRGEEPRLQRAREILYSRdpkynLNKHLGL 142
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 6325267 365 DGSQD----KFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVL 403
Cdd:pfam04561 143 NEPFEnerlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
42-572 |
3.61e-33 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 135.08 E-value: 3.61e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 42 VQPHIGSFNALTegpDGGLlnlgvkdigEKVIFDGKPLnsEDEISNSGYlgnklsVSVEQVSIAKPMSNDGVSSavERKV 121
Cdd:PRK09606 19 VRHHIDSYNDFV---DNGL---------QKIIDEQGPI--ETEIEDGVY------VELGKIRVGKPVVKEADGS--EREI 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 122 YPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRdCGGLPVMLQSNRCHLNKMSPYELVQHKEESDEIGGYFIVNGIEk 201
Cdd:PRK09606 77 YPMEARLRNLTYSAPLYLEMSPVEGGEEEEPEEVY-IGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSE- 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 202 liRMLIVQRRNHPMAIIrpsfANRGASYSHYgIQIRSVrpdqTSQTN------VLHYLNDG--QVTF-RFSWRkneylVP 272
Cdd:PRK09606 155 --RVLMTLEDLAPNKIL----VEKDERYGDR-IEVAKV----FSQRRgyralvTVERNRDGllEVSFpSVPGS-----IP 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 273 VVMILKALCHTSDREIFDGiIGND---VKdsFLTDRLELLlrgfkkrypHLQNRTQVLQYLGDkfRVVfqasPDQSD--- 346
Cdd:PRK09606 219 FVILMRALGLETDEEIVEA-VSDDpeiVK--FMLENLEEA---------EVDTQEEALEYIGK--RVA----PGQTKeyr 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 347 LEVGQEVLDRIVLVHLGKDGS--QDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNI 424
Cdd:PRK09606 281 IKRAEYVIDRYLLPHLGVEPEvrRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDV 360
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 425 IAQVRMDINRGmainfkdkRYMS-RVLMR---VNENIGSKMqyflSTGNLvsqsgldlqqVSGYTVVA---EKINFYRFI 497
Cdd:PRK09606 361 KYQLERANMRN--------RELSiKTAVRsdvLTERLEHAM----ATGNW----------VGGRTGVSqllDRTDYMATL 418
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 498 SHFRMV------HRGSFFAqlktttvRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQsDVSRIPSILYSLGVA 571
Cdd:PRK09606 419 SHLRRVvsplsrSQPHFEA-------RDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGE-DEEEVKEILKELGVE 490
|
.
gi 6325267 572 P 572
Cdd:PRK09606 491 P 491
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
486-550 |
3.18e-32 |
|
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: 119.55 E-value: 3.18e-32
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6325267 486 VVAEKINFYRFISHFRMVH--RGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCR 550
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNspRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
907-1089 |
4.10e-32 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 136.00 E-value: 4.10e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 907 IRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIaQDSTPwIF 986
Cdd:PRK00405 876 QKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGI-KFATP-VF 953
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 987 ---NEDDtpadyFGEQLAKAGYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVnSL-TMQPVKG 1062
Cdd:PRK00405 954 dgaKEEE-----IKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPY-SLvTQQPLGG 1027
|
170 180
....*....|....*....|....*..
gi 6325267 1063 RKRHGGIRVGEMERDALIGHGTSFLLQ 1089
Cdd:PRK00405 1028 KAQFGGQRFGEMEVWALEAYGAAYTLQ 1054
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
908-1101 |
2.77e-30 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 130.02 E-value: 2.77e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 908 RRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHG----IA----- 978
Cdd:CHL00001 811 KREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNrhyrIApfder 890
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 979 -------------------QDSTPWIFnEDDTPadyfgeqlakagynyhGNEPMYSGATGEELRADIYVGVVYYQRLRHM 1039
Cdd:CHL00001 891 yeqeasrklvfselyeaskQTANPWVF-EPEYP----------------GKSRLFDGRTGDPFEQPVTIGKAYILKLIHQ 953
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6325267 1040 VNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSDYTQA 1101
Cdd:CHL00001 954 VDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRA 1015
|
|
| RNA_pol_Rpa2_4 |
pfam06883 |
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ... |
593-651 |
1.06e-28 |
|
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.
Pssm-ID: 462028 Cd Length: 58 Bit Score: 109.50 E-value: 1.06e-28
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 6325267 593 IGWVSHEQGKIIADTLRYWKVEGKtPGLPIDLEIGYVPPSTRGQYPGLYLFGGHSRMLR 651
Cdd:pfam06883 1 IGYVSPKLAKRIADTLRYLKVEGE-HGVPLTLEIGYVPPSNGGQYPGLYLFTSPARMMR 58
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
898-1097 |
4.24e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 123.88 E-value: 4.24e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 898 LQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHG- 976
Cdd:PRK09603 1075 IKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGk 1154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 977 -----IAQDSTPW-------------IFNEDDTPADYFGEQLAK-----------------------------------A 1003
Cdd:PRK09603 1155 qiasmLEDKTKDFakelrakmleianAINEKDPLTIHALENCSDeelleyakdwskgvkmaipvfegisqekfyklfelA 1234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 1004 GYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHG 1083
Cdd:PRK09603 1235 KIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYG 1314
|
250
....*....|....
gi 6325267 1084 TSFLLQDRLLNSSD 1097
Cdd:PRK09603 1315 AAHTLKEMLTIKSD 1328
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
898-1097 |
3.21e-20 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 97.77 E-value: 3.21e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 898 LQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAG----KAGA 973
Cdd:PRK14844 1068 SMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackKLGE 1147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 974 LHGIAQDSTPWI-------------------------------FNED-------DTP-------------ADYFG----- 997
Cdd:PRK14844 1148 KVGNILDEINKIksafckgirslnddnftkfaaayldnkkienIDDDeitasvlNTPnknalndelnelvENYLNscksa 1227
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325267 998 -------------------------------------------------------EQLAK----AGYNYHGNEPMYSGAT 1018
Cdd:PRK14844 1228 ysnlrnflievyscgsnvsicnnirdisdnnliefarklrdgipvaapvfegpkdEQIAKlfelAGLDNSGQAVLYDGCS 1307
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6325267 1019 GEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSD 1097
Cdd:PRK14844 1308 GEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1067-1108 |
2.72e-15 |
|
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: 72.24 E-value: 2.72e-15
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 6325267 1067 GGIRVGEMERDALIGHGTSFLLQDRLLNSSDYTQASVCRECG 1108
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCG 42
|
|
| |
