|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
7-1097 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1239.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 7 PRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYC 86
Cdd:PRK08565 45 PGLKIVLGKIRVGEPEIKEADGSERPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKIC 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 87 LLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTGECRSCLENSSRPTstiwvsML 165
Cdd:PRK08565 120 PLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TV 193
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 166 ARGGQGAkksaigqrIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALN 244
Cdd:PRK08565 194 ERRKDGT--------IYVSFPAVPGKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALD 262
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 245 FIGSRGAkPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPL 324
Cdd:PRK08565 263 YIGKRVA-IGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDL 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 325 LAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTL 404
Cdd:PRK08565 342 LAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTL 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 405 SHLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPA 484
Cdd:PRK08565 416 SHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE 495
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 485 AIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKK 562
Cdd:PRK08565 496 EYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTR 574
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 563 RHIDQLKEREynnYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHN 642
Cdd:PRK08565 575 EHVEKLKKGE---LTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHN 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 643 QSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMN 722
Cdd:PRK08565 645 QSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMN 724
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 723 RSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---L 798
Cdd:PRK08565 725 KASIERGLARSTFFRTYETEERKYPGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfL 803
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 799 PENEDELESTNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQED 878
Cdd:PRK08565 804 EELEELSLGLQER---RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQED 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 879 MPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFT 958
Cdd:PRK08565 881 MPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRT 959
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 959 GRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDP 1038
Cdd:PRK08565 960 GEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDK 1039
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*....
gi 740087257 1039 YQVHVCNLCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1097
Cdd:PRK08565 1040 TTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLK 1098
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
7-1097 |
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: 1214.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 7 PRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMLRSTYC 86
Cdd:cd00653 34 GRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDLTYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLC 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 87 LLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAytgECRSCLENSSRPTSTIWVSMLA 166
Cdd:cd00653 109 NLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVEDSKGKRIY---TKTSIPSYSPYRGSWLEVKSDK 185
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 167 RGgqgakksaigQRIVATLPYIKQEVpiiivfralgfvsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFI 246
Cdd:cd00653 186 KK----------DRIYVRIDLKRQEE-------------------------------------------------ALKYI 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 247 GSRGakpgvtkekrikyakevlqkemlphvgvsdfcetkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLA 326
Cdd:cd00653 207 GKRF-------------------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQ 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 327 FLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSH 406
Cdd:cd00653 250 NLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSH 328
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 407 LRRLNS-PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaa 485
Cdd:cd00653 329 KRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--------------------------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 486 iadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirereiriytdaGRICRPLLIVEKQklllkkrhi 565
Cdd:cd00653 382 ----------------------------------------------------------GRIERPYRIVEKE--------- 394
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 566 dqlkereynnyswqdlvasgvveyidtleeetvmlamtpddlqekevaycstYTHCEIHPSMILGVCASIIPFPDHNQSP 645
Cdd:cd00653 395 ----------------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSP 422
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 646 RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSA 725
Cdd:cd00653 423 RNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSS 502
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 726 VDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 805
Cdd:cd00653 503 VDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP 578
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 806 ESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFT 882
Cdd:cd00653 579 IFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFT 658
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 883 CEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKI 962
Cdd:cd00653 659 EDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPL 737
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 963 TSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVH 1042
Cdd:cd00653 738 EAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVAR 817
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*
gi 740087257 1043 VCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1097
Cdd:cd00653 818 VCVKCGIILSAN------LCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
492-1096 |
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: 786.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 492 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKER 571
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 572 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 651
Cdd:TIGR03670 80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 652 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 731
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 732 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 807
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 808 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGIT 887
Cdd:TIGR03670 309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 888 PDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIF 967
Cdd:TIGR03670 386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF-EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 968 IGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLC 1047
Cdd:TIGR03670 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 740087257 1048 GIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRM 1096
Cdd:TIGR03670 545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
11-1098 |
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: 671.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 11 LKFEQIYLSKPTHwerdgapspmMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMLRStycllng 90
Cdd:COG0085 51 LEFGDYRLGEPKY----------TPEECKERDLTYAAPLYVKVRLVNKETGEIKEQE----VFMGDFPLMTDS------- 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 91 ltdrdlcelnecpldpgGYFIINGSEKVLIAQEKMATNTVYVFAK-KDSKYAYTGECRSclensSRPTstiWVSMLARgg 169
Cdd:COG0085 110 -----------------GTFIINGTERVIVSQLVRSPGVYFVEEEdKSGKDLYSAKVIP-----SRGA---WLEFETD-- 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 170 qgaKKSAIGQRIVAtlpyiKQEVPIIIVFRALGFVSDRDILEHiiydFEDPEMMEMVKPSLDEAFVI-QEQnvALNFIGS 248
Cdd:COG0085 163 ---KDGTIYVRIDR-----KRKIPVTVLLRALGLETDEEILEA----FGDDPIQEYILATLEKDNTKtQEE--ALLEIYR 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 249 RgAKPGvtKEKRIKYAKEVL-------QKEMLPHVG-----------VSDFCETKKAYFLGYMVHRLLLAALGRRELDDR 310
Cdd:COG0085 229 K-LRPG--EPPTIERAEQLLdnlffdpKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDI 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 311 DHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRiyaqkfiDR-----GKDFNLELAIKTRIISDGLKYSLATGnwgdqkkah 385
Cdd:COG0085 306 DHLGNRRVRLVGELLQNQFRVGLSRMERVVR-------ERmttqdVEAITPQSLINIRPVVAAIKEFFGSS--------- 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 386 qaraGVSQVLNRLTFASTLSHLRRLN----SPIGRDgklaKP----RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYI 457
Cdd:COG0085 370 ----QLSQFMDQTNPLSELTHKRRLSalgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV 441
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 458 SvgsqpspilEFleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirerei 537
Cdd:COG0085 442 N---------EY-------------------------------------------------------------------- 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 538 riytdaGRICRPLLIVEKQKLLLKkrhidqlkereynnyswqdlvasgvVEYIDTLEEETVMLAMTPDDLQEK------- 610
Cdd:COG0085 445 ------GFIETPYRKVENGKVTDE-------------------------IEYLTADEEENYYIAQANAPLDEDgnfleer 493
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 611 -------EVAYCST--YTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNfhvrmdtlAHVLYYP-- 679
Cdd:COG0085 494 vlvryrgEEVLVPPeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlq 565
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 680 ------------QKPLVttRSMEYLR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVF 735
Cdd:COG0085 566 kfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIH 643
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 736 YRSY--KEQESKKGfdQEEVfekpTREtcqgmrhaI-------YDKLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDELE 806
Cdd:COG0085 644 IEEYeiEARDTKLG--PEEI----TRD--------IpnvseeaLRNLDEDGIIRIGAEVKGGDILVGK-VT-PKGETELT 707
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 807 STNR----------RYtKRDCSTFLRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGT 869
Cdd:COG0085 708 PEERllraifgekaRE-VRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGV 786
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 870 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRG 949
Cdd:COG0085 787 ISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIRELLEKAGLPPDG 865
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 950 NEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLR 1029
Cdd:COG0085 866 KEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQ 945
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 740087257 1030 ERLFEASDPYqvhvcnlCGimaiantRTHTYECRgcRNKTQISLVRMPYACKLLFQELMSMSIAPRMMS 1098
Cdd:COG0085 946 ERLTIKSDDV-------CG-------RVKVYEAI--VKGENIPEPGIPESFKVLLKELQSLGLDVEVLS 998
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
632-1005 |
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: 552.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 632 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYT 711
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 712 GYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGfDQEEVFEKPTREtcqgmRHAIYDKLDDDGLIAPGVRVSGDDVI 791
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-PIEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 792 IGKTV-TLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV-TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 869
Cdd:pfam00562 155 VGKVGpTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 870 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA-VNVQKISNLLSDYGYHLR 948
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAsTEVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 740087257 949 GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR 1005
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
7-1097 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1239.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 7 PRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYC 86
Cdd:PRK08565 45 PGLKIVLGKIRVGEPEIKEADGSERPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKIC 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 87 LLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTGECRSCLENSSRPTstiwvsML 165
Cdd:PRK08565 120 PLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TV 193
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 166 ARGGQGAkksaigqrIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALN 244
Cdd:PRK08565 194 ERRKDGT--------IYVSFPAVPGKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALD 262
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 245 FIGSRGAkPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPL 324
Cdd:PRK08565 263 YIGKRVA-IGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDL 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 325 LAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTL 404
Cdd:PRK08565 342 LAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTL 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 405 SHLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPA 484
Cdd:PRK08565 416 SHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREE 495
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 485 AIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKK 562
Cdd:PRK08565 496 EYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTR 574
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 563 RHIDQLKEREynnYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHN 642
Cdd:PRK08565 575 EHVEKLKKGE---LTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHN 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 643 QSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMN 722
Cdd:PRK08565 645 QSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMN 724
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 723 RSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---L 798
Cdd:PRK08565 725 KASIERGLARSTFFRTYETEERKYPGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfL 803
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 799 PENEDELESTNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQED 878
Cdd:PRK08565 804 EELEELSLGLQER---RDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQED 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 879 MPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFT 958
Cdd:PRK08565 881 MPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRT 959
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 959 GRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDP 1038
Cdd:PRK08565 960 GEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDK 1039
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*....
gi 740087257 1039 YQVHVCNLCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1097
Cdd:PRK08565 1040 TTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLK 1098
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
7-1097 |
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: 1214.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 7 PRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMLRSTYC 86
Cdd:cd00653 34 GRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDLTYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLC 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 87 LLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAytgECRSCLENSSRPTSTIWVSMLA 166
Cdd:cd00653 109 NLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVEDSKGKRIY---TKTSIPSYSPYRGSWLEVKSDK 185
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 167 RGgqgakksaigQRIVATLPYIKQEVpiiivfralgfvsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFI 246
Cdd:cd00653 186 KK----------DRIYVRIDLKRQEE-------------------------------------------------ALKYI 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 247 GSRGakpgvtkekrikyakevlqkemlphvgvsdfcetkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLA 326
Cdd:cd00653 207 GKRF-------------------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQ 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 327 FLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSH 406
Cdd:cd00653 250 NLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSH 328
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 407 LRRLNS-PIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaa 485
Cdd:cd00653 329 KRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--------------------------- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 486 iadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirereiriytdaGRICRPLLIVEKQklllkkrhi 565
Cdd:cd00653 382 ----------------------------------------------------------GRIERPYRIVEKE--------- 394
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 566 dqlkereynnyswqdlvasgvveyidtleeetvmlamtpddlqekevaycstYTHCEIHPSMILGVCASIIPFPDHNQSP 645
Cdd:cd00653 395 ----------------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSP 422
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 646 RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSA 725
Cdd:cd00653 423 RNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSS 502
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 726 VDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDEL 805
Cdd:cd00653 503 VDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP 578
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 806 ESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFT 882
Cdd:cd00653 579 IFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFT 658
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 883 CEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKI 962
Cdd:cd00653 659 EDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPL 737
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 963 TSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVH 1042
Cdd:cd00653 738 EAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVAR 817
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*
gi 740087257 1043 VCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1097
Cdd:cd00653 818 VCVKCGIILSAN------LCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
492-1096 |
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: 786.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 492 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKER 571
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 572 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 651
Cdd:TIGR03670 80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 652 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 731
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 732 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 807
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 808 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGIT 887
Cdd:TIGR03670 309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 888 PDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIF 967
Cdd:TIGR03670 386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF-EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 968 IGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLC 1047
Cdd:TIGR03670 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 740087257 1048 GIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRM 1096
Cdd:TIGR03670 545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
490-1097 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 752.18 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 490 TKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIiVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLK 569
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEI-SEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLK 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 570 EREYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTY 649
Cdd:PRK07225 84 NGEL---TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE-------HTHLEIDPSLILGIGAGMIPYPEHNASPRITM 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 650 QSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRG 729
Cdd:PRK07225 154 GAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERG 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 730 FFRSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDEL 805
Cdd:PRK07225 234 LGRSHFFRTYEGEERRYPGGQEDRFEIPDKDV-RGYRGEeAYRHLDEDGLVNPETEVKEGDVLIGKTSPprfLEEPDDFG 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 806 ESTNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG 885
Cdd:PRK07225 313 ISPEKR---RETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESG 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 886 ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDaVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQ 965
Cdd:PRK07225 390 VVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSG-EDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAE 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 966 IFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCN 1045
Cdd:PRK07225 469 IFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCA 548
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 740087257 1046 LCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1097
Cdd:PRK07225 549 KCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLE 600
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
11-1098 |
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: 671.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 11 LKFEQIYLSKPTHwerdgapspmMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMLRStycllng 90
Cdd:COG0085 51 LEFGDYRLGEPKY----------TPEECKERDLTYAAPLYVKVRLVNKETGEIKEQE----VFMGDFPLMTDS------- 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 91 ltdrdlcelnecpldpgGYFIINGSEKVLIAQEKMATNTVYVFAK-KDSKYAYTGECRSclensSRPTstiWVSMLARgg 169
Cdd:COG0085 110 -----------------GTFIINGTERVIVSQLVRSPGVYFVEEEdKSGKDLYSAKVIP-----SRGA---WLEFETD-- 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 170 qgaKKSAIGQRIVAtlpyiKQEVPIIIVFRALGFVSDRDILEHiiydFEDPEMMEMVKPSLDEAFVI-QEQnvALNFIGS 248
Cdd:COG0085 163 ---KDGTIYVRIDR-----KRKIPVTVLLRALGLETDEEILEA----FGDDPIQEYILATLEKDNTKtQEE--ALLEIYR 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 249 RgAKPGvtKEKRIKYAKEVL-------QKEMLPHVG-----------VSDFCETKKAYFLGYMVHRLLLAALGRRELDDR 310
Cdd:COG0085 229 K-LRPG--EPPTIERAEQLLdnlffdpKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDI 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 311 DHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRiyaqkfiDR-----GKDFNLELAIKTRIISDGLKYSLATGnwgdqkkah 385
Cdd:COG0085 306 DHLGNRRVRLVGELLQNQFRVGLSRMERVVR-------ERmttqdVEAITPQSLINIRPVVAAIKEFFGSS--------- 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 386 qaraGVSQVLNRLTFASTLSHLRRLN----SPIGRDgklaKP----RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYI 457
Cdd:COG0085 370 ----QLSQFMDQTNPLSELTHKRRLSalgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV 441
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 458 SvgsqpspilEFleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirerei 537
Cdd:COG0085 442 N---------EY-------------------------------------------------------------------- 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 538 riytdaGRICRPLLIVEKQKLLLKkrhidqlkereynnyswqdlvasgvVEYIDTLEEETVMLAMTPDDLQEK------- 610
Cdd:COG0085 445 ------GFIETPYRKVENGKVTDE-------------------------IEYLTADEEENYYIAQANAPLDEDgnfleer 493
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 611 -------EVAYCST--YTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNfhvrmdtlAHVLYYP-- 679
Cdd:COG0085 494 vlvryrgEEVLVPPeeVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlq 565
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 680 ------------QKPLVttRSMEYLR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVF 735
Cdd:COG0085 566 kfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIH 643
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 736 YRSY--KEQESKKGfdQEEVfekpTREtcqgmrhaI-------YDKLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDELE 806
Cdd:COG0085 644 IEEYeiEARDTKLG--PEEI----TRD--------IpnvseeaLRNLDEDGIIRIGAEVKGGDILVGK-VT-PKGETELT 707
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 807 STNR----------RYtKRDCSTFLRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGT 869
Cdd:COG0085 708 PEERllraifgekaRE-VRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGV 786
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 870 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRG 949
Cdd:COG0085 787 ISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIRELLEKAGLPPDG 865
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 950 NEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLR 1029
Cdd:COG0085 866 KEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQ 945
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 740087257 1030 ERLFEASDPYqvhvcnlCGimaiantRTHTYECRgcRNKTQISLVRMPYACKLLFQELMSMSIAPRMMS 1098
Cdd:COG0085 946 ERLTIKSDDV-------CG-------RVKVYEAI--VKGENIPEPGIPESFKVLLKELQSLGLDVEVLS 998
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
632-1005 |
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: 552.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 632 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYT 711
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 712 GYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGfDQEEVFEKPTREtcqgmRHAIYDKLDDDGLIAPGVRVSGDDVI 791
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-PIEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 792 IGKTV-TLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV-TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 869
Cdd:pfam00562 155 VGKVGpTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 870 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA-VNVQKISNLLSDYGYHLR 948
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAsTEVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 740087257 949 GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR 1005
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
5-366 |
6.63e-162 |
|
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: 484.19 E-value: 6.63e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 5 NQPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQlqtqHQKTFIGKIPIMLRST 84
Cdd:pfam04563 40 NGDKLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRNLTYSAPLYVDLELSVYNGEDIK----PIEVFIGRLPIMLRSN 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 85 YCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKD-SKYAYTGECRSCLENSSRPTSTIWVS 163
Cdd:pfam04563 116 ACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNHPIVFKKADpKKRGSVASVRSSAEISVRPDSTSWVN 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 164 MLARggqgakksAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVI--QEQNV 241
Cdd:pfam04563 196 VLEY--------LSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQ 267
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 242 ALNFIGSRGAKP---GVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRL 318
Cdd:pfam04563 268 ALDYIGGRGRAIfrmGRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRL 347
|
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 740087257 319 DLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIIS 366
Cdd:pfam04563 348 RLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPIT 395
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
7-472 |
3.32e-124 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 389.69 E-value: 3.32e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 7 PRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYC 86
Cdd:PRK09606 50 DGVYVELGKIRVGKPVVKEADGSEREIYPMEARLRNLTYSAPLYLEMS--PVEGGEEE---EPEEVYIGELPVMVGSKIC 124
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 87 LLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVfaKKDSKYAYTGECRSCLenSSRPTSTIWVSmLA 166
Cdd:PRK09606 125 NLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKILV--EKDERYGDRIEVAKVF--SQRRGYRALVT-VE 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 167 RGGQGakksaigqRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAfVIQEQNVALNFI 246
Cdd:PRK09606 200 RNRDG--------LLEVSFPSVPGSIPFVILMRALGLETDEEIVEAV---SDDPEIVKFMLENLEEA-EVDTQEEALEYI 267
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 247 GSRGAkPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLA 326
Cdd:PRK09606 268 GKRVA-PGQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLME 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 327 FLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNW-GdqkkahqARAGVSQVLNRLTFASTLS 405
Cdd:PRK09606 347 DLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNWvG-------GRTGVSQLLDRTDYMATLS 419
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 740087257 406 HLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEE 472
Cdd:PRK09606 420 HLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKE 486
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
35-1037 |
9.89e-69 |
|
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: 250.74 E-value: 9.89e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 35 PNEARLRNLTYSAPLYVDiTKTVIKEGEEQLQTQHQKTFIGKIPIMlrstycllnglTDRdlcelnecpldpgGYFIING 114
Cdd:TIGR02013 79 VEECKERGLTYSAPLKVK-LRLINKEEDGTKEIKEQDVYMGDIPLM-----------TDR-------------GTFIING 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 115 SEKVLIAQEKMATNTVYVFAKKDSKyaytgecRSCLENSSR--PTSTIWVSMlarggQGAKKSAIGQRIVAtlpyiKQEV 192
Cdd:TIGR02013 134 AERVVVSQLHRSPGVFFSSEKDTTK-------SGKVLFSARiiPYRGSWLEF-----ETDKKDVLYVRIDR-----KRKL 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 193 PIIIVFRALGFVSDRDILEHiiydFEDPEMME---MVKPSL--DEAFVIQeqnvalnfigSRGAKPG--VTKEKrikyAK 265
Cdd:TIGR02013 197 PATVLLRALGYTIDTLILNR----LGSGEYIRntlRKDPTNseEEALVEI----------YRKLRPGepPTVEA----AR 258
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 266 EVLQKEM-------LPHVG---VSDFCETKKAYFLGYMVHRLLLAAL--------GRRELDDRDHYGNKRLDLAGPLLAF 327
Cdd:TIGR02013 259 SLLENLFfdpkrydLGRVGrykLNKKLGLDVPESIGVLTKEDIIATIkyliklrnGKGEIDDIDHLGNRRIRSVGELLQN 338
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 328 LFRGMFKNLLKEVRiyaqkfiDRGKDFNLELA-----IKTRIISDGLKYSLATGNwgdqkkahqaragVSQVLNRLTFAS 402
Cdd:TIGR02013 339 QFRVGLARMERIVR-------ERMSTQDTDTLtpqdlINAKPISAAIKEFFGSSQ-------------LSQFMDQTNPLA 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 403 TLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVgsqpspiLEFLEewsmenl 478
Cdd:TIGR02013 399 ELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE-------YGFIE------- 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 479 eeiSPAAIADATKIFVNGCWVGIHKDPEQlmntlRKLRRQMDIIVSEVSMIRDirereiriytdagricrpllivekqkl 558
Cdd:TIGR02013 465 ---TPYRKVKDGKVVVTDEIDYLTADEED-----NYVIAQANAPLDENGRFVE--------------------------- 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 559 llkkrhidqlkereynnyswqDLVASGVVEYIDTLEEETVmlamtpddlqekevaycstyTHCEIHPSMILGVCASIIPF 638
Cdd:TIGR02013 510 ---------------------DLVVARYRGEITLVSPDQV--------------------DYMDVSPKQVVSVAASLIPF 548
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 639 PDHNQSPRNTYQSAMGKQAM-------------------------------GV---------YITNFHVRMDTLAHVLYY 678
Cdd:TIGR02013 549 LEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVveyvdakriVIRYDEDEEEPDGGIDIY 628
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 679 P--------------QKPLVTT-------------RSMEylrFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 731
Cdd:TIGR02013 629 RllkyqrsnqdtcinQRPIVSVgdrveagdvladgPSTD---LGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVF 705
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 732 RSVFYRSYK--EQESKKGfdQEEVfekpTRETCQGMRHAIyDKLDDDGLIAPGVRVSGDDVIIGKTVtlPENEDELESTN 809
Cdd:TIGR02013 706 TSIHIEEYEveARDTKLG--PEEI----TRDIPNVSEEAL-RNLDENGIVRIGAEVKAGDILVGKVT--PKGETELTPEE 776
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 810 RRYTK---------RDCSTFLRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQ 873
Cdd:TIGR02013 777 KLLRAifgekardvRDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKI 856
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 874 YRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD--ATPFNDAVNVQKISNLLSDYGYHLRGNE 951
Cdd:TIGR02013 857 LPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPVFDGASEEEIKEYLEKAGLPRDGKV 936
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 952 VLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRER 1031
Cdd:TIGR02013 937 RLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1016
|
....*.
gi 740087257 1032 LFEASD 1037
Cdd:TIGR02013 1017 LTVKSD 1022
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
5-1041 |
8.47e-57 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 214.57 E-value: 8.47e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 5 NQPRYLLKFEQIYLSKPthwerdgapsPMMPNEARLRNLTYSAPLYVDITKTVIKEGeeqlQTQHQKTFIGKIPIMlrst 84
Cdd:CHL00207 41 GNLELLLFGKNYKLKYP----------KYNLLSAKSYDSNYSIQIYLPLKFINLKTN----KIKFINYLIGNLPKM---- 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 85 ycllnglTDRdlcelnecpldpgGYFIINGSEKVLIAQeKMATNTVYVFAKKDSKYaytgecRSCLENSSRPTSTIWVSM 164
Cdd:CHL00207 103 -------TQR-------------GTFIINGLERVIVSQ-IIRSPGIYFKKEIKKNS------NKIYSATLIPNRGSWIKF 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 165 LARggqgaKKSAIGQRIVATLpyikqEVPIIIVFRALGfVSDRDILEHIIYDFEDP-------------------EMMEM 225
Cdd:CHL00207 156 ELD-----KNKEIWIRIDKNR-----KKPLIIFLKALG-LTDQDIYSRLTKSEFLKklkpillnsnsytneeillEIYKN 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 226 VKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCEtkkayflgyMVHRLLLAALGRR 305
Cdd:CHL00207 225 LSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILS---------IIDKLINLKINKG 295
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 306 ELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKF-IDRGKDFNLelaIKTRIISDGLKYSLATGNwgdqkka 384
Cdd:CHL00207 296 NFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICdIDSLSKFNL---INPKPLIALIREFFGSSQ------- 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 385 hqaragVSQVLNRLTFASTLSHLRRLNS--PIGRDgKLAKP---RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISv 459
Cdd:CHL00207 366 ------LSQYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLATNARIN- 437
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 460 gsqpspILEFLEE--WSMENLeeispaaiadatKIFVNGCWVGIHKDPEQLMNTLrklrrqmdiivsevsmIRDIREREI 537
Cdd:CHL00207 438 ------KFGFIETpfYKVING------------KVKKFGNPIYLTADSEDLYRIA----------------PNDINLNKN 483
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 538 RiytdagricrpllivekqklLLKKRHIdqlkEREYNNyswqdlvasgvvEYIDTLEEETVMLAMTPDDlqekevaycst 617
Cdd:CHL00207 484 N--------------------YFKKNII----PVRYKQ------------EFKTVNPSKVDFIAISPIQ----------- 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 618 ythceihpsmILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG---------------------------------VYITN 664
Cdd:CHL00207 517 ----------VFSIAESLIPFLEHNDANRALMGSNMQRQAVPllypekpivgtgyekqialdsgmtiisltegivVSVSA 586
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 665 F--HVRMDTLAHVLYYPQK-------------PLV----------TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSV 719
Cdd:CHL00207 587 YkiIIQDDNNRYIHYYLQKyqrsnqntcinyrPIVwvgekinigqILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAI 666
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 720 IMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETCQGMRHAIYdKLDDDGLIAPGVRVSGDDVIIGKTVTLP 799
Cdd:CHL00207 667 LINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEI----TRNIPNVSEYSLK-NLDENGIISIGSKVLAGDILVGKITPKG 741
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 800 ENEDELEST--------NRRYTKrDCSTFLRTSETGIVDQVMVTLNQEG--YKF-----CKIRVRSVRIPQIGDKFASRH 864
Cdd:CHL00207 742 ESDQLPEGKllraifgeKAKDVK-DTSLRMPNGGYGRVIKVEIFSRSKGdeLKFgyylkIRVFIAQIRKIQVGDKLAGRH 820
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 865 GQKGTCG-IQYRQeDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA------------- 930
Cdd:CHL00207 821 GNKGIISrILPRQ-DMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMygseysrilinnk 899
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 931 -VNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGL 1009
Cdd:CHL00207 900 lNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQ 979
|
1130 1140 1150
....*....|....*....|....*....|..
gi 740087257 1010 RFGEMERDCQIAHGAAQFLRERLFEASDPYQV 1041
Cdd:CHL00207 980 RFGEMEVWALEAFGAAYTLKELLTIKSDDMQG 1011
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
126-319 |
5.72e-56 |
|
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 191.79 E-value: 5.72e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 126 ATNTVYVFAKKDSKyaytgecrsclenssrPTSTIWVSMLARGGQGAKKSAIGQR-IVATLPYIKQEVPIIIVFRALGFV 204
Cdd:pfam04561 1 RSNGIYVEKELDKN----------------GIIATYTSSLISNRGSWLKLEIDGKtLIWSRPSKKRKIPIVIFLKALGLV 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 205 SDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSrGAKPGVTKEKRIKYAKEVLQK-----EMLPHVGVS 279
Cdd:pfam04561 65 SDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLN 143
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 740087257 280 DFCETK--KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLD 319
Cdd:pfam04561 144 EPFENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
8-1032 |
6.17e-45 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 177.22 E-value: 6.17e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 8 RYLLKFEQIYLSKPTHWERdgapspmmpnEARLRNLTYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMlrstycl 87
Cdd:PRK00405 66 NLSLEFVSYELGEPKYDVE----------ECKERGLTYSAPLRVKLRLINKETGE----IKEQEVYMGDIPLM------- 124
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 88 lnglTDRdlcelnecpldpgGYFIINGSEKVLIAQekmatnTVY---VFAKKDSKYAYTGEcrscLENSSR--PTstiwv 162
Cdd:PRK00405 125 ----TEN-------------GTFIINGTERVIVSQ------LHRspgVYFDHDKDKTSSGK----LLYSARiiPY----- 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 163 smlaRGG----QGAKKSAIGQRIVatlpyIKQEVPIIIVFRALGFvSDRDILEhIIYDFED-PEMMEMVKPSLDEAFVIQ 237
Cdd:PRK00405 173 ----RGSwlefEFDPKDILYVRID-----RRRKLPVTVLLRALGY-SDEEILD-LFYEKEEfGKEIEVPVEYLLGKVLAE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 238 EQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKE--------------ML-----PHVgvsdfcETKKAYF--------- 289
Cdd:PRK00405 242 DIVDEETGEVLAEANDEITEELDGPYIRNTLEKDptssreealveiyrRLrpgepPTV------EAARSLLenlffdpkr 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 290 --LG----YMV-HRL---------------LLAAL--------GRRELDDRDHYGNKRLDLAGPLLAFLFR-GMfknllk 338
Cdd:PRK00405 316 ydLSkvgrYKLnKKLgldededvrvltkedIIATIkylinlrnGKGEVDDIDHLGNRRVRSVGELLQNQFRiGL------ 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 339 eVRIyaQKFI-DR--GKDFN----LELaIKTRIISDGLKYSLATgnwgdqkkaHQaragVSQVL---NRLtfaSTLSHLR 408
Cdd:PRK00405 390 -SRM--ERAVrERmsLQDLDtltpQDL-INAKPVVAAIKEFFGS---------SQ----LSQFMdqtNPL---SELTHKR 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 409 RLNS--PIG----------RDgklakprqLHNTLWGMVCPAETPEGHAVGLVKNLALMAYI-SVGsqpspileFLEewsm 475
Cdd:PRK00405 450 RLSAlgPGGltreragfevRD--------VHPTHYGRICPIETPEGPNIGLINSLATYARVnEYG--------FIE---- 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 476 enleeiSPaaiadaTKIFVNGcwvgihkdpeqlmntlrklrrqmdIIVSEVSMIRDIREREIRI------YTDAGRICRP 549
Cdd:PRK00405 510 ------TP------YRKVVDG------------------------KVTDEIVYLTADEEDNYVIaqanapLDEDGRFVDE 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 550 LLIVekqklllkkrhidqlkeREYNNYswqDLVASGVVEYIDtleeetvmlamtpddlqekevaycstythceIHPSMIL 629
Cdd:PRK00405 554 LVTA-----------------RYKGEF---VLVPPEEVDYMD-------------------------------VSPKQVV 582
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 630 GVCASIIPFPDHNQSPRNTYQSAMGKQA--------------M-----------------GV---------YITNFHVRM 669
Cdd:PRK00405 583 SVAASLIPFLEHDDANRALMGSNMQRQAvpllrpeaplvgtgMerrvardsgavvvakrdGVveyvdasriVVRVEELDP 662
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 670 DTLAHVLY-------------YPQKPLVTTR-------------SMEYlrfRELPAGINSIVAIASYTGYNQEDSVIMNR 723
Cdd:PRK00405 663 GEDGVDIYnlikfqrsnqntcINQRPIVKVGdrvekgdvladgpSTDN---GELALGQNVLVAFMPWNGYNFEDAILISE 739
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 724 SAVDRGFFRSVfyrSYKEQE-----SKKGfdQEEVfekpTREtcqgmrhaIYD-------KLDDDGLIAPGVRVSGDDVI 791
Cdd:PRK00405 740 RLVKEDVFTSI---HIEEYEieardTKLG--PEEI----TRD--------IPNvseealrNLDESGIVRIGAEVKPGDIL 802
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 792 IGKtVTlPENEDEL------------EstnrrytK----RDCStfLR--TSETGIVDQVMV-TLNQEGY-------KFCK 845
Cdd:PRK00405 803 VGK-VT-PKGETELtpeekllraifgE-------KardvKDTS--LRvpHGEEGTVIDVKVfTRIEQGDelppgvnKLVK 871
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 846 IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGiTP-DIIINPHAIPSRMTIGHLIECLQGKVSANKGE-Igd 923
Cdd:PRK00405 872 VYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDG-TPvDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIkF-- 948
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 924 ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGR 1003
Cdd:PRK00405 949 ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGK 1028
|
1210 1220 1230
....*....|....*....|....*....|...
gi 740087257 1004 SRDGGLRFGEMErdcqI----AHGAAQFLRERL 1032
Cdd:PRK00405 1029 AQFGGQRFGEME----VwaleAYGAAYTLQEML 1057
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1007-1099 |
3.32e-42 |
|
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 148.89 E-value: 3.32e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 1007 GGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYACKLLFQE 1086
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYN------KCPICKGETDISPGYIPESFKLLFQE 74
|
90
....*....|...
gi 740087257 1087 LMSMSIAPRMMSV 1099
Cdd:pfam04560 75 LQSLGIDPRLLLE 87
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
14-1037 |
5.79e-36 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 148.13 E-value: 5.79e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 14 EQIYLSKPTHWERDgapspmmpneARLRNLTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMlrstycllngltd 93
Cdd:CHL00001 55 ETYQLVEPLIKERD----------AVYESLTYSSELYVPAGLIWKKSRDMQEQT----VFIGNIPLM------------- 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 94 rdlcelnecplDPGGYFIINGSEKVLIAQeKMATNTVYVFAKKDSK--YAYTG----ECRSCLENSSRPTSTIWVsmlar 167
Cdd:CHL00001 108 -----------NSLGTFIINGIYRVVINQ-ILRSPGIYYRSELDHNgiSVYTGtiisDWGGRLELEIDRKARIWA----- 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 168 ggqgakksaigqRIVAtlpyiKQEVPIIIVFRALGFvSDRDILEHIIYdfedPEMMemvkpsldeafviqeqnvaLNFIG 247
Cdd:CHL00001 171 ------------RVSR-----KQKISILVLLSAMGL-NLREILDNVCY----PEIF-------------------LSFLN 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 248 SRGAKPGVTKEKRIkyakeVLQKEMLPHVGV------SDFCETKKAYF-----LGY-----MVHRL-------------- 297
Cdd:CHL00001 210 DKEKKKIGSKENAI-----LEFYQQFACVGGdpvfseSLCKELQKKFFqqrceLGRigrrnMNRKLnldipenntfllpq 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 298 -LLAA--------LGRRELDDRDHYGNKRLDLAGPLLaflfRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDG 368
Cdd:CHL00001 285 dVLAAadyligmkFGMGTLDDIDHLKNKRIRSVADLL----QDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTP 360
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 369 LkyslaTGNWGDQKKAHQaragVSQVLNRLTFASTLSHLRRLNS--PIGRDGKLA--KPRQLHNTLWGMVCPAETPEGHA 444
Cdd:CHL00001 361 L-----TTTYESFFGSHP----LSQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGIN 431
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 445 VGLVKNLALMAYI-SVGSQPSPILEFLEEWSMENLEEISPAaiadatkifvngcwvgihKDpEQLMntlrklrrqmdiIV 523
Cdd:CHL00001 432 AGLIGSLAIHARIgHWGSLESPFYEISERSKEERMVYLSPS------------------ED-EYYM------------IA 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 524 SEVSMI--RDIREREIriyTDAgricrpllivekqklllkkRHidqlkEREYNNYSWQdlvasgvveyidtleeetvmla 601
Cdd:CHL00001 481 AGNSLAlnQGIQEEQV---VPA-------------------RY-----RQEFLTIAWE---------------------- 511
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 602 mtpddlqekEVAYCStythceIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM----------------------G 659
Cdd:CHL00001 512 ---------QIHLRS------IFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVplsrsekcivgtglerqvaldsG 576
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 660 V-----------YI-------------TNFHVRM------DTLAHvlyypQKPLVttRSMEYLRFRELPA---------- 699
Cdd:CHL00001 577 VvaiaehegkiiYTdtdkiilsgngdtLSIPLVMyqrsnkNTCMH-----QKPQV--RRGKCVKKGQILAdgaatvggel 649
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 700 --GINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQ--ESKKGFdqeevfEKPTRETCQ----GMRHaiyd 771
Cdd:CHL00001 650 alGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQthVTSQGP------ERITKEIPHleahLLRN---- 719
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 772 kLDDDGLIAPGVRVSGDDVIIGKtVTLPENEDELESTNRR----------YTKRDCSTFLRTSETGIVDQVMvTLNQEGY 841
Cdd:CHL00001 720 -LDKNGIVMLGSWVETGDILVGK-LTPQEAEESSYAPEGRllraifgiqvSTSKETCLKLPIGGRGRVIDVR-WIQKKGG 796
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 842 KFCKIRVRSVRIPQ-----IGDKFASRHGQKGTCG-IQYRQeDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVS 915
Cdd:CHL00001 797 SSYNPETIHVYILQkreiqVGDKVAGRHGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAG 875
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 916 ANKGEIGDATPFnDAVNVQKIS-NLLSDYGYHLR--------------GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMV 980
Cdd:CHL00001 876 DLLNRHYRIAPF-DERYEQEASrKLVFSELYEASkqtanpwvfepeypGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQV 954
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*..
gi 740087257 981 DDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1037
Cdd:CHL00001 955 DDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
303-1037 |
7.59e-35 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 145.45 E-value: 7.59e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 303 GRRELDDRDHYGNKRLDLAGPLLAflfrgmfkNLLKEVRIYAQKFIdRGKDFNLELAIKTRIISDGLKYSLATGNWGDQK 382
Cdd:PRK09603 450 NQGKIDDRDHLGNRRIRAVGELLA--------NELHSGLVKMQKTI-KDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFF 520
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 383 KAHQaragVSQVLNRLTFASTLSHLRRLnSPIGrDGKLAK------PRQLHNTLWGMVCPAETPEGHAVGLVKNLAlmAY 456
Cdd:PRK09603 521 MGGQ----LSQFMDQTNPLSEVTHKRRL-SALG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS--TF 592
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 457 ISVGSqpspiLEFLEewsmenleeispaaiADATKIfVNGcwvgihkdpeqlmntlrklrrqmdIIVSEVSMIRDIRERE 536
Cdd:PRK09603 593 TRVND-----LGFIE---------------APYKKV-VDG------------------------KVVGETIYLTAIQEDS 627
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 537 IRIYTDAGRIcrpllivekqklllkkrhidqlkerEYNNYSWQDLvasgvveyIDTLEEETVMLAmtpddlqEKevaycS 616
Cdd:PRK09603 628 HIIAPASTPI-------------------------DEEGNILGDL--------IETRVEGEIVLN-------EK-----S 662
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 617 TYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------------- 658
Cdd:PRK09603 663 KVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgtgiekiiardswgaikanragvvekid 742
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 659 ------------GVYITNFHVRMDTLAHV-LYYPQKPLVTT-------------RSMEYlrfRELPAGINSIVAIASYTG 712
Cdd:PRK09603 743 skniyilgegkeEAYIDAYSLQKNLRTNQnTSFNQVPIVKVgdkveagqiiadgPSMDR---GELALGKNVRVAFMPWNG 819
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 713 YNQEDSVIMNRSAVDRGFFRSV--FYRSYKEQESKKGFdqeevfEKPTRETcQGMRHAIYDKLDDDGLIAPGVRVSGDDV 790
Cdd:PRK09603 820 YNFEDAIVVSERITKDDIFTSThiYEKEVDARELKHGV------EEFTADI-PDVKEEALAHLDESGIVKVGTYVSAGMI 892
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 791 IIGKTV------TLPENE---------------------DELEST---------------------------------NR 810
Cdd:PRK09603 893 LVGKTSpkgeikSTPEERllraifgdkaghvvnkslycpPSLEGTvidvkvftkkgyekdarvlsayeeekakldmehFD 972
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 811 RYTKRDCSTFLRT----------SETGIVDQVM----------------VTLN----------QEGY------------- 841
Cdd:PRK09603 973 RLTMLNREELLRVssllsqaileEPFSHNGKDYkegdqipkeeiasinrFTLAslvkkyskevQNHYeitknnfleqkkv 1052
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 842 -----------------------KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIP 898
Cdd:PRK09603 1053 lgeeheeklsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVP 1132
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 899 SRMTIGHLIECLQGKVSANKG-----------------------EIGD-------------------------------- 923
Cdd:PRK09603 1133 SRMNIGQILEMHLGLVGKEFGkqiasmledktkdfakelrakmlEIANainekdpltihalencsdeelleyakdwskgv 1212
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 924 --ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPME 1001
Cdd:PRK09603 1213 kmAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVG 1292
|
970 980 990
....*....|....*....|....*....|....*.
gi 740087257 1002 GRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1037
Cdd:PRK09603 1293 GKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
492-554 |
5.12e-30 |
|
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: 113.23 E-value: 5.12e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 740087257 492 IFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIvSEVSMIRDIREREIRIYTDAGRICRPLLIVE 554
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKIS-EEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
293-1037 |
2.30e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 124.35 E-value: 2.30e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 293 MVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFR-GMFKNLLKEVRIYAQKFIDR--GKDFnlelaIKTRIISDGL 369
Cdd:PRK14844 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRtGLLKLERAVVDSMSTSSLDKvsPSDF-----INPKVLTNVL 523
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 370 KyslatgnwgDQKKAHQaragVSQVLNRLTFASTLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMVCPAETPEGHAV 445
Cdd:PRK14844 524 R---------DFFNSSQ----LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 446 GLVKNLALMAYIS-VGSQPSPILEFLEEWSMENLEEISPA-----AIADAT-KIFVNGCWVgihkdpeQLMNTLRKLRRQ 518
Cdd:PRK14844 591 GLINSLAIYARINkYGFIESPYRKVVNRVVTDQIEYLSAIdeglyYIADTSaKLDENNCFV-------DDMLYCRYAGSF 663
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 519 MDIIVSEVSMIrDIREREIrIYTDAGRIcrPLLivekqklllkkrhidqlkereYNNYSWQDLVASGVVEYIDTLEEETV 598
Cdd:PRK14844 664 VMVSSDQVSYI-DVSPKQV-ISVAASLI--PFL---------------------ENDDANRALMGSNMQRQAVPLLKPTA 718
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 599 MLAMTPddlQEKEVAYCSTythceihpSMILGVCASIIPFPDHNQSPRNTYQSAmGKQAMGVYItnFHVR-MDTLAHVLY 677
Cdd:PRK14844 719 PLVATG---MESFVASGSG--------AVVLAKRDGIVDSSDSNSIVIRAFDKE-RVNYLDVDI--YHLRkFQRSNHNTC 784
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 678 YPQKPLVttRSMEYLR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVfyrsYKEQESK 745
Cdd:PRK14844 785 INQKPLV--CVGDYVKegdviadgpainSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSI----HIEEFEC 858
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 746 KGFDQEEVFEKPTRETCQGMRHAIYdKLDDDGLIAPGVRVSGDDVIIGK-----TVTLP--------------------- 799
Cdd:PRK14844 859 VVHDTPLGSEKITRAIPGVNEENLY-HLDDSGIVKIGTRVGPGYILVGKvtpkpSLSLPpetkllmtifgeksfdcadss 937
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 800 -----------------------ENE-----------------------------DELE-------STNRR--------- 811
Cdd:PRK14844 938 lytspdvegtvidvqvftrrgveENErallikqkeindfekerdyiinvtseyfyDELKkllinsgSQDREkfdsiereq 1017
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 812 -----YTKRDCSTFLRTSETGIVDQVMVTLNQ---------EGYKFCKIRVRSVRI-------PQIGDKFASRHGQKGTC 870
Cdd:PRK14844 1018 wwgigLKNQSISEQVKSLKKDFDEKVSHAIAQfkrkveklhEGYDLPQGVSMSVKVfiavkhsLQPGDKMAGRHGNKGVI 1097
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 871 GIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQG--------KVS--------------------------- 915
Cdd:PRK14844 1098 SRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgeKVGnildeinkiksafckgirslnddnftk 1177
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 916 -------------ANKGEIGDA---TPFNDAVN----------------------------------------VQKIS-N 938
Cdd:PRK14844 1178 faaayldnkkienIDDDEITASvlnTPNKNALNdelnelvenylnscksaysnlrnflievyscgsnvsicnnIRDISdN 1257
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740087257 939 LLSDYGYHLR------------------------------GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRA 988
Cdd:PRK14844 1258 NLIEFARKLRdgipvaapvfegpkdeqiaklfelagldnsGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARS 1337
|
970 980 990 1000
....*....|....*....|....*....|....*....|....*....
gi 740087257 989 RGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1037
Cdd:PRK14844 1338 VGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
393-456 |
4.61e-28 |
|
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: 107.61 E-value: 4.61e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 740087257 393 QVLNRLTFASTLSHLRRLNSPIG---RDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAY 456
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
578-625 |
1.68e-23 |
|
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: 94.14 E-value: 1.68e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 740087257 578 WQDLVASGVVEYIDTLEEETVMLAMTPDDL-----QEKEVAYCSTYTHCEIHP 625
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLeessrEEREGPYAHTYTHCEIHP 53
|
|
| |
