|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
27-1172 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1284.13 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhaSGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 105
Cdd:PRK08565 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 106 SPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 185
Cdd:PRK08565 69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 186 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTGECRSCLENSSRPTstiwvsMLARGGQGAkksaigqrIVATLPYIK 264
Cdd:PRK08565 144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 265 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 343
Cdd:PRK08565 210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 344 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 423
Cdd:PRK08565 286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 424 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 503
Cdd:PRK08565 366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 504 TLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 583
Cdd:PRK08565 440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 584 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREynnYSWQDLVASGV 661
Cdd:PRK08565 520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 662 VEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 741
Cdd:PRK08565 596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 742 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821
Cdd:PRK08565 669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 822 GFDQEEVFEKPTrETCQGMRHA-IYEKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 897
Cdd:PRK08565 749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 898 TSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 977
Cdd:PRK08565 825 HGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMT 904
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 978 IGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDD 1057
Cdd:PRK08565 905 VGQLLESIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1058 KIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC 1137
Cdd:PRK08565 984 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVC 1063
|
1130 1140 1150
....*....|....*....|....*....|....*
gi 226958589 1138 RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1172
Cdd:PRK08565 1064 PIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLK 1098
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
39-1172 |
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: 1253.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 39 LVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEaqhasgeveePPRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNL 118
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 119 TYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQE 198
Cdd:cd00653 70 TYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQE 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 199 KMATNTVYVFAKKDSKYAytgECRSCLENSSRPTSTIWVSMLARGgqgakksaigQRIVATLPYIKQEVpiiivfralgf 278
Cdd:cd00653 146 QRSPNVIIVEDSKGKRIY---TKTSIPSYSPYRGSWLEVKSDKKK----------DRIYVRIDLKRQEE----------- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 279 vsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFIGSRGakpgvtkekrikyakevlqkemlphvgvsdfce 358
Cdd:cd00653 202 --------------------------------------ALKYIGKRF--------------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 359 tkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTR 438
Cdd:cd00653 211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSK 286
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 439 IISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSHLRRLNS-PIGRDGKLAKPRQLHNTLWGMVCPAETPEG 517
Cdd:cd00653 287 PITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEG 365
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 518 HAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdii 597
Cdd:cd00653 366 ENCGLVKNLALMARIS---------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 598 vsevsmirdirereiriytdaGRICRPLLIVEKQklllkkrhidqlkereynnyswqdlvasgvveyidtleeetvmlam 677
Cdd:cd00653 382 ---------------------GRIERPYRIVEKE---------------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 678 tpddlqekevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKP 757
Cdd:cd00653 395 ---------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKP 459
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 758 LVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETC 837
Cdd:cd00653 460 LVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDI 535
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 838 QGMRHAIYEKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQE 914
Cdd:cd00653 536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDG 615
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 915 GYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKG 994
Cdd:cd00653 616 GNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLG 695
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 995 EIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQP 1074
Cdd:cd00653 696 KFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQP 774
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1075 MEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYA 1154
Cdd:cd00653 775 LKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYA 848
|
1130
....*....|....*...
gi 226958589 1155 CKLLFQELMSMSIAPRMM 1172
Cdd:cd00653 849 FKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
567-1171 |
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 226958589 567 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKER 646
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 647 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 726
Cdd:TIGR03670 80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 727 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 806
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 807 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYEKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 882
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 883 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGIT 962
Cdd:TIGR03670 309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 963 PDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIF 1042
Cdd:TIGR03670 386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF-EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1043 IGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLC 1122
Cdd:TIGR03670 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 226958589 1123 GIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRM 1171
Cdd:TIGR03670 545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
30-1173 |
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: 701.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 30 ISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQaeaqhaSGEVEepprylLKFEQIYLSKPTHwerdgapspmM 109
Cdd:COG0085 7 IKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDF------TGNLS------LEFGDYRLGEPKY----------T 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 110 PNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMLRStycllngltdrdlcelnecpldpgGYFIING 189
Cdd:COG0085 65 PEECKERDLTYAAPLYVKVRLVNKETGEIKEQE----VFMGDFPLMTDS------------------------GTFIING 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 190 SEKVLIAQEKMATNTVYVFAK-KDSKYAYTGECRSclensSRPTstiWVSMLARggqgaKKSAIGQRIVAtlpyiKQEVP 268
Cdd:COG0085 117 TERVIVSQLVRSPGVYFVEEEdKSGKDLYSAKVIP-----SRGA---WLEFETD-----KDGTIYVRIDR-----KRKIP 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 269 IIIVFRALGFVSDRDILEHiiydFEDPEMMEMVKPSLDEAFVI-QEQnvALNFIGSRgAKPGvtKEKRIKYAKEVL---- 343
Cdd:COG0085 179 VTVLLRALGLETDEEILEA----FGDDPIQEYILATLEKDNTKtQEE--ALLEIYRK-LRPG--EPPTIERAEQLLdnlf 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 344 ---QKEMLPHVG-----------VSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFK 409
Cdd:COG0085 250 fdpKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 410 NLLKEVRiyaqkfiDR-----GKDFNLELAIKTRIISDGLKYSLATGnwgdqkkahqaraGVSQVLNRLTFASTLSHLRR 484
Cdd:COG0085 330 RMERVVR-------ERmttqdVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRR 389
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 485 LN----SPIGRDgklaKP----RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqpspilEFleewsmenleei 556
Cdd:COG0085 390 LSalgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY------------ 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 557 spaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirereiriytdaGRICRPLLIVEKQKLLLK 636
Cdd:COG0085 445 --------------------------------------------------------------GFIETPYRKVENGKVTDE 462
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 637 krhidqlkereynnyswqdlvasgvVEYIDTLEEETVMLAMTPDDLQEK--------------EVAYCST--YTHCEIHP 700
Cdd:COG0085 463 -------------------------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryrgEEVLVPPeeVDYMDVSP 517
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 701 SMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNfhvrmdtlAHVLYYP--------------QKPLVttRSMEY 766
Cdd:COG0085 518 KQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPIV--RVGDR 587
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 767 LR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSY--KEQESKKGfdQEEVfekp 832
Cdd:COG0085 588 VEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYeiEARDTKLG--PEEI---- 661
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 833 TREtcqgmrhaI-------YEKLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDELESTNR----------RYtKRDCSTF 895
Cdd:COG0085 662 TRD--------IpnvseeaLRNLDEDGIIRIGAEVKGGDILVGK-VT-PKGETELTPEERllraifgekaRE-VRDTSLR 730
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 896 LRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIIN 968
Cdd:COG0085 731 VPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLN 810
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 969 PHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYY 1048
Cdd:COG0085 811 PLGVPSRMNVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYY 889
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1049 QRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYqvhvcnlCGimaia 1128
Cdd:COG0085 890 LKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDV-------CG----- 957
|
1210 1220 1230 1240
....*....|....*....|....*....|....*....|....*
gi 226958589 1129 ntRTHTYECRgcRNKTQISLVRMPYACKLLFQELMSMSIAPRMMS 1173
Cdd:COG0085 958 --RVKVYEAI--VKGENIPEPGIPESFKVLLKELQSLGLDVEVLS 998
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
707-1080 |
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: 553.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 707 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYT 786
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 787 GYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGfDQEEVFEKPTREtcqgmRHAIYEKLDDDGLIAPGVRVSGDDVI 866
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-PIEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 867 IGKTV-TLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV-TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 944
Cdd:pfam00562 155 VGKVGpTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 945 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA-VNVQKISNLLSDYGYHLR 1023
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAsTEVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 226958589 1024 GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR 1080
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
27-1172 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1284.13 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhaSGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 105
Cdd:PRK08565 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 106 SPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 185
Cdd:PRK08565 69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 186 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTGECRSCLENSSRPTstiwvsMLARGGQGAkksaigqrIVATLPYIK 264
Cdd:PRK08565 144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 265 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 343
Cdd:PRK08565 210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 344 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 423
Cdd:PRK08565 286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 424 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 503
Cdd:PRK08565 366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 504 TLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 583
Cdd:PRK08565 440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 584 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREynnYSWQDLVASGV 661
Cdd:PRK08565 520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 662 VEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 741
Cdd:PRK08565 596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 742 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 821
Cdd:PRK08565 669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 822 GFDQEEVFEKPTrETCQGMRHA-IYEKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 897
Cdd:PRK08565 749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 898 TSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 977
Cdd:PRK08565 825 HGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMT 904
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 978 IGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDD 1057
Cdd:PRK08565 905 VGQLLESIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1058 KIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC 1137
Cdd:PRK08565 984 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVC 1063
|
1130 1140 1150
....*....|....*....|....*....|....*
gi 226958589 1138 RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1172
Cdd:PRK08565 1064 PIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLK 1098
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
39-1172 |
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: 1253.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 39 LVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEaqhasgeveePPRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNL 118
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 119 TYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQE 198
Cdd:cd00653 70 TYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQE 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 199 KMATNTVYVFAKKDSKYAytgECRSCLENSSRPTSTIWVSMLARGgqgakksaigQRIVATLPYIKQEVpiiivfralgf 278
Cdd:cd00653 146 QRSPNVIIVEDSKGKRIY---TKTSIPSYSPYRGSWLEVKSDKKK----------DRIYVRIDLKRQEE----------- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 279 vsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFIGSRGakpgvtkekrikyakevlqkemlphvgvsdfce 358
Cdd:cd00653 202 --------------------------------------ALKYIGKRF--------------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 359 tkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTR 438
Cdd:cd00653 211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSK 286
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 439 IISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSHLRRLNS-PIGRDGKLAKPRQLHNTLWGMVCPAETPEG 517
Cdd:cd00653 287 PITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEG 365
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 518 HAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdii 597
Cdd:cd00653 366 ENCGLVKNLALMARIS---------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 598 vsevsmirdirereiriytdaGRICRPLLIVEKQklllkkrhidqlkereynnyswqdlvasgvveyidtleeetvmlam 677
Cdd:cd00653 382 ---------------------GRIERPYRIVEKE---------------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 678 tpddlqekevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKP 757
Cdd:cd00653 395 ---------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKP 459
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 758 LVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETC 837
Cdd:cd00653 460 LVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDI 535
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 838 QGMRHAIYEKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQE 914
Cdd:cd00653 536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDG 615
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 915 GYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKG 994
Cdd:cd00653 616 GNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLG 695
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 995 EIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQP 1074
Cdd:cd00653 696 KFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQP 774
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1075 MEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYA 1154
Cdd:cd00653 775 LKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYA 848
|
1130
....*....|....*...
gi 226958589 1155 CKLLFQELMSMSIAPRMM 1172
Cdd:cd00653 849 FKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
567-1171 |
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 226958589 567 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKER 646
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 647 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 726
Cdd:TIGR03670 80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 727 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 806
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 807 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYEKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 882
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 883 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGIT 962
Cdd:TIGR03670 309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 963 PDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIF 1042
Cdd:TIGR03670 386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF-EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1043 IGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLC 1122
Cdd:TIGR03670 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 226958589 1123 GIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRM 1171
Cdd:TIGR03670 545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
565-1172 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 750.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 565 TKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIiVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLK 644
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEI-SEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLK 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 645 EREYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTY 724
Cdd:PRK07225 84 NGEL---TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE-------HTHLEIDPSLILGIGAGMIPYPEHNASPRITM 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 725 QSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRG 804
Cdd:PRK07225 154 GAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERG 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 805 FFRSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYEKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDEL 880
Cdd:PRK07225 234 LGRSHFFRTYEGEERRYPGGQEDRFEIPDKDV-RGYRGEeAYRHLDEDGLVNPETEVKEGDVLIGKTSPprfLEEPDDFG 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 881 ESTNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG 960
Cdd:PRK07225 313 ISPEKR---RETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESG 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 961 ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDaVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQ 1040
Cdd:PRK07225 390 VVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSG-EDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAE 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1041 IFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCN 1120
Cdd:PRK07225 469 IFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCA 548
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 226958589 1121 LCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1172
Cdd:PRK07225 549 KCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLE 600
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
30-1173 |
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: 701.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 30 ISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQaeaqhaSGEVEepprylLKFEQIYLSKPTHwerdgapspmM 109
Cdd:COG0085 7 IKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDF------TGNLS------LEFGDYRLGEPKY----------T 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 110 PNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMLRStycllngltdrdlcelnecpldpgGYFIING 189
Cdd:COG0085 65 PEECKERDLTYAAPLYVKVRLVNKETGEIKEQE----VFMGDFPLMTDS------------------------GTFIING 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 190 SEKVLIAQEKMATNTVYVFAK-KDSKYAYTGECRSclensSRPTstiWVSMLARggqgaKKSAIGQRIVAtlpyiKQEVP 268
Cdd:COG0085 117 TERVIVSQLVRSPGVYFVEEEdKSGKDLYSAKVIP-----SRGA---WLEFETD-----KDGTIYVRIDR-----KRKIP 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 269 IIIVFRALGFVSDRDILEHiiydFEDPEMMEMVKPSLDEAFVI-QEQnvALNFIGSRgAKPGvtKEKRIKYAKEVL---- 343
Cdd:COG0085 179 VTVLLRALGLETDEEILEA----FGDDPIQEYILATLEKDNTKtQEE--ALLEIYRK-LRPG--EPPTIERAEQLLdnlf 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 344 ---QKEMLPHVG-----------VSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFK 409
Cdd:COG0085 250 fdpKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 410 NLLKEVRiyaqkfiDR-----GKDFNLELAIKTRIISDGLKYSLATGnwgdqkkahqaraGVSQVLNRLTFASTLSHLRR 484
Cdd:COG0085 330 RMERVVR-------ERmttqdVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRR 389
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 485 LN----SPIGRDgklaKP----RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqpspilEFleewsmenleei 556
Cdd:COG0085 390 LSalgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY------------ 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 557 spaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirereiriytdaGRICRPLLIVEKQKLLLK 636
Cdd:COG0085 445 --------------------------------------------------------------GFIETPYRKVENGKVTDE 462
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 637 krhidqlkereynnyswqdlvasgvVEYIDTLEEETVMLAMTPDDLQEK--------------EVAYCST--YTHCEIHP 700
Cdd:COG0085 463 -------------------------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryrgEEVLVPPeeVDYMDVSP 517
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 701 SMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNfhvrmdtlAHVLYYP--------------QKPLVttRSMEY 766
Cdd:COG0085 518 KQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPIV--RVGDR 587
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 767 LR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSY--KEQESKKGfdQEEVfekp 832
Cdd:COG0085 588 VEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYeiEARDTKLG--PEEI---- 661
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 833 TREtcqgmrhaI-------YEKLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDELESTNR----------RYtKRDCSTF 895
Cdd:COG0085 662 TRD--------IpnvseeaLRNLDEDGIIRIGAEVKGGDILVGK-VT-PKGETELTPEERllraifgekaRE-VRDTSLR 730
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 896 LRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIIN 968
Cdd:COG0085 731 VPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLN 810
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 969 PHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYY 1048
Cdd:COG0085 811 PLGVPSRMNVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYY 889
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1049 QRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYqvhvcnlCGimaia 1128
Cdd:COG0085 890 LKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDV-------CG----- 957
|
1210 1220 1230 1240
....*....|....*....|....*....|....*....|....*
gi 226958589 1129 ntRTHTYECRgcRNKTQISLVRMPYACKLLFQELMSMSIAPRMMS 1173
Cdd:COG0085 958 --RVKVYEAI--VKGENIPEPGIPESFKVLLKELQSLGLDVEVLS 998
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
707-1080 |
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: 553.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 707 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYT 786
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 787 GYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGfDQEEVFEKPTREtcqgmRHAIYEKLDDDGLIAPGVRVSGDDVI 866
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-PIEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 867 IGKTV-TLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV-TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 944
Cdd:pfam00562 155 VGKVGpTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 945 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA-VNVQKISNLLSDYGYHLR 1023
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAsTEVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 226958589 1024 GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR 1080
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
38-441 |
6.94e-178 |
|
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: 527.72 E-value: 6.94e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 38 GLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEeppRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRN 117
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGD---KLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 118 LTYSAPLYVDITKTVIKEGEEQlqtqHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQ 197
Cdd:pfam04563 78 LTYSAPLYVDLELSVYNGEDIK----PIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQ 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 198 EKMATNTVYVFAKKD-SKYAYTGECRSCLENSSRPTSTIWVSMLARggqgakksAIGQRIVATLPYIKQEVPIIIVFRAL 276
Cdd:pfam04563 154 EHRSRNHPIVFKKADpKKRGSVASVRSSAEISVRPDSTSWVNVLEY--------LSNGTIYFKFPYIKKEIPIVIILRAL 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 277 GFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVI--QEQNVALNFIGSRGAKP---GVTKEKRIKYAKEVLQKEMLPHV 351
Cdd:pfam04563 226 GFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQKEVLPHL 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 352 GVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNL 431
Cdd:pfam04563 306 GTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLML 385
|
410
....*....|
gi 226958589 432 ELAIKTRIIS 441
Cdd:pfam04563 386 QLLVNAKPIT 395
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
27-547 |
5.50e-138 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 427.44 E-value: 5.50e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 27 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaqhasgEVEEPPRYLLKFEQIYLSKPTHWERDGAPS 106
Cdd:PRK09606 6 RVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPI-----------ETEIEDGVYVELGKIRVGKPVVKEADGSER 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 107 PMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFI 186
Cdd:PRK09606 75 EIYPMEARLRNLTYSAPLYLEMS--PVEGGEEE---EPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFI 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 187 INGSEKVLIAQEKMATNTVYVfaKKDSKYAYTGECRSCLenSSRPTSTIWVSmLARGGQGakksaigqRIVATLPYIKQE 266
Cdd:PRK09606 150 VNGSERVLMTLEDLAPNKILV--EKDERYGDRIEVAKVF--SQRRGYRALVT-VERNRDG--------LLEVSFPSVPGS 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 267 VPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAfVIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVLQKE 346
Cdd:PRK09606 217 IPFVILMRALGLETDEEIVEAV---SDDPEIVKFMLENLEEA-EVDTQEEALEYIGKRVA-PGQTKEYRIKRAEYVIDRY 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 347 MLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 426
Cdd:PRK09606 292 LLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRN 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 427 KDFNLELAIKTRIISDGLKYSLATGNW-GdqkkahqARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTL 505
Cdd:PRK09606 372 RELSIKTAVRSDVLTERLEHAMATGNWvG-------GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQ 444
|
490 500 510 520
....*....|....*....|....*....|....*....|..
gi 226958589 506 WGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEE 547
Cdd:PRK09606 445 WGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKE 486
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
30-1112 |
1.26e-70 |
|
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: 257.28 E-value: 1.26e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 30 ISSYFDEKGLVRQQLDSFDEFIQMS----------VQRIVEDAPPIdlqaeaQHASGeveeppRYLLKFEQIYLSKPTHw 99
Cdd:TIGR02013 11 IPEVLEVPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPI------EDYTG------NIELEYLSYRLGEPKY- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 100 erdgapspmMPNEARLRNLTYSAPLYVDiTKTVIKEGEEQLQTQHQKTFIGKIPIMlrstycllnglTDRdlcelnecpl 179
Cdd:TIGR02013 78 ---------SVEECKERGLTYSAPLKVK-LRLINKEEDGTKEIKEQDVYMGDIPLM-----------TDR---------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 180 dpgGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKyaytgecRSCLENSSR--PTSTIWVSMlarggQGAKKSAIGQRIV 257
Cdd:TIGR02013 127 ---GTFIINGAERVVVSQLHRSPGVFFSSEKDTTK-------SGKVLFSARiiPYRGSWLEF-----ETDKKDVLYVRID 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 258 AtlpyiKQEVPIIIVFRALGFVSDRDILEHiiydFEDPEMME---MVKPSL--DEAFVIQeqnvalnfigSRGAKPG--V 330
Cdd:TIGR02013 192 R-----KRKLPATVLLRALGYTIDTLILNR----LGSGEYIRntlRKDPTNseEEALVEI----------YRKLRPGepP 252
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 331 TKEKrikyAKEVLQKEM-------LPHVG---VSDFCETKKAYFLGYMVHRLLLAAL--------GRRELDDRDHYGNKR 392
Cdd:TIGR02013 253 TVEA----ARSLLENLFfdpkrydLGRVGrykLNKKLGLDVPESIGVLTKEDIIATIkyliklrnGKGEIDDIDHLGNRR 328
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 393 LDLAGPLLAFLFRGMFKNLLKEVRiyaqkfiDRGKDFNLELA-----IKTRIISDGLKYSLATGNwgdqkkahqaragVS 467
Cdd:TIGR02013 329 IRSVGELLQNQFRVGLARMERIVR-------ERMSTQDTDTLtpqdlINAKPISAAIKEFFGSSQ-------------LS 388
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 468 QVLNRLTFASTLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVgsqpspiLE 543
Cdd:TIGR02013 389 QFMDQTNPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE-------YG 461
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 544 FLEewsmenleeiSPAAIADATKIFVNGCWVGIHKDPEQlmntlRKLRRQMDIIVSEVSMIRDirereiriytdagricr 623
Cdd:TIGR02013 462 FIE----------TPYRKVKDGKVVVTDEIDYLTADEED-----NYVIAQANAPLDENGRFVE----------------- 509
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 624 pllivekqklllkkrhidqlkereynnyswqDLVASGVVEYIDTLEEETVmlamtpddlqekevaycstyTHCEIHPSMI 703
Cdd:TIGR02013 510 -------------------------------DLVVARYRGEITLVSPDQV--------------------DYMDVSPKQV 538
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 704 LGVCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------GV---------YITNFHVR 743
Cdd:TIGR02013 539 VSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVveyvdakriVIRYDEDE 618
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 744 MDTLAHVLYYP--------------QKPLVTT-------------RSMEylrFRELPAGINSIVAIASYTGYNQEDSVIM 796
Cdd:TIGR02013 619 EEPDGGIDIYRllkyqrsnqdtcinQRPIVSVgdrveagdvladgPSTD---LGELALGRNVLVAFMPWNGYNYEDAILI 695
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 797 NRSAVDRGFFRSVFYRSYK--EQESKKGfdQEEVfekpTRETCQGMRHAIyEKLDDDGLIAPGVRVSGDDVIIGKTVtlP 874
Cdd:TIGR02013 696 SERLVKDDVFTSIHIEEYEveARDTKLG--PEEI----TRDIPNVSEEAL-RNLDENGIVRIGAEVKAGDILVGKVT--P 766
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 875 ENEDELESTNRRYTK---------RDCSTFLRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASR 938
Cdd:TIGR02013 767 KGETELTPEEKLLRAifgekardvRDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGR 846
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 939 HGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD--ATPFNDAVNVQKISNLLS 1016
Cdd:TIGR02013 847 HGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPVFDGASEEEIKEYLE 926
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1017 DYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIA 1096
Cdd:TIGR02013 927 KAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1006
|
1210
....*....|....*.
gi 226958589 1097 HGAAQFLRERLFEASD 1112
Cdd:TIGR02013 1007 YGAAYTLQEMLTVKSD 1022
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
84-1116 |
2.72e-57 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 216.50 E-value: 2.72e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 84 YLLKFEQIYLSKPthwerdgapsPMMPNEARLRNLTYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMlrstycll 163
Cdd:CHL00207 45 LLLFGKNYKLKYP----------KYNLLSAKSYDSNYSIQIYLPLKFINLKTNK----IKFINYLIGNLPKM-------- 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 164 nglTDRdlcelnecpldpgGYFIINGSEKVLIAQeKMATNTVYVFAKKDSKYaytgecRSCLENSSRPTSTIWVSMLARg 243
Cdd:CHL00207 103 ---TQR-------------GTFIINGLERVIVSQ-IIRSPGIYFKKEIKKNS------NKIYSATLIPNRGSWIKFELD- 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 244 gqgaKKSAIGQRIVATLpyikqEVPIIIVFRALGfVSDRDILEHIIYDFEDP-------------------EMMEMVKPS 304
Cdd:CHL00207 159 ----KNKEIWIRIDKNR-----KKPLIIFLKALG-LTDQDIYSRLTKSEFLKklkpillnsnsytneeillEIYKNLSPI 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 305 LDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCEtkkayflgyMVHRLLLAALGRRELDD 384
Cdd:CHL00207 229 EPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILS---------IIDKLINLKINKGNFDD 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 385 RDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKF-IDRGKDFNLelaIKTRIISDGLKYSLATGNwgdqkkahqar 463
Cdd:CHL00207 300 IDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICdIDSLSKFNL---INPKPLIALIREFFGSSQ----------- 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 464 agVSQVLNRLTFASTLSHLRRLNS--PIGRDgKLAKP---RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqp 538
Cdd:CHL00207 366 --LSQYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLATNARIN----- 437
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 539 spILEFLEE--WSMENLeeispaaiadatKIFVNGCWVGIHKDPEQLMNTLrklrrqmdiivsevsmIRDIREREIRiyt 616
Cdd:CHL00207 438 --KFGFIETpfYKVING------------KVKKFGNPIYLTADSEDLYRIA----------------PNDINLNKNN--- 484
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 617 dagricrpllivekqklLLKKRHIdqlkEREYNNyswqdlvasgvvEYIDTLEEETVMLAMTPDDlqekevaycstythc 696
Cdd:CHL00207 485 -----------------YFKKNII----PVRYKQ------------EFKTVNPSKVDFIAISPIQ--------------- 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 697 eihpsmILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG---------------------------------VYITNF--H 741
Cdd:CHL00207 517 ------VFSIAESLIPFLEHNDANRALMGSNMQRQAVPllypekpivgtgyekqialdsgmtiisltegivVSVSAYkiI 590
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 742 VRMDTLAHVLYYPQK-------------PLV----------TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNR 798
Cdd:CHL00207 591 IQDDNNRYIHYYLQKyqrsnqntcinyrPIVwvgekinigqILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINK 670
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 799 SAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETCQGMRHAIYeKLDDDGLIAPGVRVSGDDVIIGKTVTLPENED 878
Cdd:CHL00207 671 RLVYEDLFTSIHIEKYEIELRQTKLGSEEI----TRNIPNVSEYSLK-NLDENGIISIGSKVLAGDILVGKITPKGESDQ 745
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 879 ELEST--------NRRYTKrDCSTFLRTSETGIVDQVMVTLNQEG--YKF-----CKIRVRSVRIPQIGDKFASRHGQKG 943
Cdd:CHL00207 746 LPEGKllraifgeKAKDVK-DTSLRMPNGGYGRVIKVEIFSRSKGdeLKFgyylkIRVFIAQIRKIQVGDKLAGRHGNKG 824
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 944 TCG-IQYRQeDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA--------------VNV 1008
Cdd:CHL00207 825 IISrILPRQ-DMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMygseysrilinnklNQA 903
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1009 QKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGE 1088
Cdd:CHL00207 904 SIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGE 983
|
1130 1140
....*....|....*....|....*...
gi 226958589 1089 MERDCQIAHGAAQFLRERLFEASDPYQV 1116
Cdd:CHL00207 984 MEVWALEAFGAAYTLKELLTIKSDDMQG 1011
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
201-394 |
6.06e-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: 192.18 E-value: 6.06e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 201 ATNTVYVFAKKDSKyaytgecrsclenssrPTSTIWVSMLARGGQGAKKSAIGQR-IVATLPYIKQEVPIIIVFRALGFV 279
Cdd:pfam04561 1 RSNGIYVEKELDKN----------------GIIATYTSSLISNRGSWLKLEIDGKtLIWSRPSKKRKIPIVIFLKALGLV 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 280 SDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSrGAKPGVTKEKRIKYAKEVLQK-----EMLPHVGVS 354
Cdd:pfam04561 65 SDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLN 143
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 226958589 355 DFCETK--KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLD 394
Cdd:pfam04561 144 EPFENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
43-1107 |
4.21e-47 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 184.15 E-value: 4.21e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 43 QLDSFDEFIQMSV-------QRIVEDAPPIdlqaeaQHASGeveeppRYLLKFEQIYLSKPTHWERdgapspmmpnEARL 115
Cdd:PRK00405 31 QLDSFDWFLQLDVppedeglEEVFRSIFPI------EDFNG------NLSLEFVSYELGEPKYDVE----------ECKE 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 116 RNLTYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMlrstycllnglTDRdlcelnecpldpgGYFIINGSEKVLI 195
Cdd:PRK00405 89 RGLTYSAPLRVKLRLINKETGE----IKEQEVYMGDIPLM-----------TEN-------------GTFIINGTERVIV 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 196 AQekmatnTVY---VFAKKDSKYAYTGEcrscLENSSR--PTstiwvsmlaRGG----QGAKKSAIGQRIVatlpyIKQE 266
Cdd:PRK00405 141 SQ------LHRspgVYFDHDKDKTSSGK----LLYSARiiPY---------RGSwlefEFDPKDILYVRID-----RRRK 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 267 VPIIIVFRALGFvSDRDILEhIIYDFED-PEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQK 345
Cdd:PRK00405 197 LPVTVLLRALGY-SDEEILD-LFYEKEEfGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTLEK 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 346 E--------------ML-----PHVgvsdfcETKKAYF-----------LG----YMV-HRL---------------LLA 375
Cdd:PRK00405 275 DptssreealveiyrRLrpgepPTV------EAARSLLenlffdpkrydLSkvgrYKLnKKLgldededvrvltkedIIA 348
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 376 AL--------GRRELDDRDHYGNKRLDLAGPLLAFLFR-GMfknllkeVRIyaQKFI-DR--GKDFN----LELaIKTRI 439
Cdd:PRK00405 349 TIkylinlrnGKGEVDDIDHLGNRRVRSVGELLQNQFRiGL-------SRM--ERAVrERmsLQDLDtltpQDL-INAKP 418
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 440 ISDGLKYSLATgnwgdqkkaHQaragVSQVL---NRLtfaSTLSHLRRLNS--PIG----------RDgklakprqLHNT 504
Cdd:PRK00405 419 VVAAIKEFFGS---------SQ----LSQFMdqtNPL---SELTHKRRLSAlgPGGltreragfevRD--------VHPT 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 505 LWGMVCPAETPEGHAVGLVKNLALMAYI-SVGsqpspileFLEewsmenleeiSPaaiadaTKIFVNGcwvgihkdpeql 583
Cdd:PRK00405 475 HYGRICPIETPEGPNIGLINSLATYARVnEYG--------FIE----------TP------YRKVVDG------------ 518
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 584 mntlrklrrqmdIIVSEVSMIRDIREREIRI------YTDAGRICRPLLIVekqklllkkrhidqlkeREYNNYswqDLV 657
Cdd:PRK00405 519 ------------KVTDEIVYLTADEEDNYVIaqanapLDEDGRFVDELVTA-----------------RYKGEF---VLV 566
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 658 ASGVVEYIDtleeetvmlamtpddlqekevaycstythceIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQA----- 732
Cdd:PRK00405 567 PPEEVDYMD-------------------------------VSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAvpllr 615
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 733 ---------M-----------------GV---------YITNFHVRMDTLAHVLY-------------YPQKPLVTTR-- 762
Cdd:PRK00405 616 peaplvgtgMerrvardsgavvvakrdGVveyvdasriVVRVEELDPGEDGVDIYnlikfqrsnqntcINQRPIVKVGdr 695
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 763 -----------SMEYlrfRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVfyrSYKEQE-----SKKGfdQE 826
Cdd:PRK00405 696 vekgdvladgpSTDN---GELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSI---HIEEYEieardTKLG--PE 767
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 827 EVfekpTREtcqgmrhaIY-------EKLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDEL------------Estnrry 887
Cdd:PRK00405 768 EI----TRD--------IPnvseealRNLDESGIVRIGAEVKPGDILVGK-VT-PKGETELtpeekllraifgE------ 827
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 888 tK----RDCStfLR--TSETGIVDQVMV-TLNQEGY-------KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQED 953
Cdd:PRK00405 828 -KardvKDTS--LRvpHGEEGTVIDVKVfTRIEQGDelppgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVED 904
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 954 MPFTCEGiTP-DIIINPHAIPSRMTIGHLIECLQGKVSANKGE-IgdATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNG 1031
Cdd:PRK00405 905 MPYLEDG-TPvDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIkF--ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDG 981
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1032 FTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMErdcqI----AHGAAQFLRERL 1107
Cdd:PRK00405 982 RTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEME----VwaleAYGAAYTLQEML 1057
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1082-1174 |
3.11e-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: 3.11e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1082 GGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYACKLLFQE 1161
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYN------KCPICKGETDISPGYIPESFKLLFQE 74
|
90
....*....|...
gi 226958589 1162 LMSMSIAPRMMSV 1174
Cdd:pfam04560 75 LQSLGIDPRLLLE 87
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
38-1112 |
1.58e-38 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 156.60 E-value: 1.58e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 38 GLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaQHASGEVEepprYLLKFEQIYLSKPTHWERDgapspmmpneARLRN 117
Cdd:CHL00001 14 GFNQIQFEGFCRFIDQGLTEELSKFPKI------EDTDQEIE----FQLFVETYQLVEPLIKERD----------AVYES 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 118 LTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMlrstycllngltdrdlcelnecplDPGGYFIINGSEKVLIAQ 197
Cdd:CHL00001 74 LTYSSELYVPAGLIWKKSRDMQEQT----VFIGNIPLM------------------------NSLGTFIINGIYRVVINQ 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 198 eKMATNTVYVFAKKDSK--YAYTG----ECRSCLENSSRPTSTIWVsmlarggqgakksaigqRIVAtlpyiKQEVPIII 271
Cdd:CHL00001 126 -ILRSPGIYYRSELDHNgiSVYTGtiisDWGGRLELEIDRKARIWA-----------------RVSR-----KQKISILV 182
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 272 VFRALGFvSDRDILEHIIYdfedPEMMemvkpsldeafviqeqnvaLNFIGSRGAKPGVTKEKRIkyakeVLQKEMLPHV 351
Cdd:CHL00001 183 LLSAMGL-NLREILDNVCY----PEIF-------------------LSFLNDKEKKKIGSKENAI-----LEFYQQFACV 233
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 352 GV------SDFCETKKAYF-----LGY-----MVHRL---------------LLAA--------LGRRELDDRDHYGNKR 392
Cdd:CHL00001 234 GGdpvfseSLCKELQKKFFqqrceLGRigrrnMNRKLnldipenntfllpqdVLAAadyligmkFGMGTLDDIDHLKNKR 313
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 393 LDLAGPLLaflfRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLkyslaTGNWGDQKKAHQaragVSQVLNR 472
Cdd:CHL00001 314 IRSVADLL----QDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPL-----TTTYESFFGSHP----LSQFLDQ 380
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 473 LTFASTLSHLRRLNS--PIGRDGKLA--KPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYI-SVGSQPSPILEFLEE 547
Cdd:CHL00001 381 TNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIgHWGSLESPFYEISER 460
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 548 WSMENLEEISPAaiadatkifvngcwvgihKDpEQLMntlrklrrqmdiIVSEVSMI--RDIREREIriyTDAgricrpl 625
Cdd:CHL00001 461 SKEERMVYLSPS------------------ED-EYYM------------IAAGNSLAlnQGIQEEQV---VPA------- 499
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 626 livekqklllkkRHidqlkEREYNNYSWQdlvasgvveyidtleeetvmlamtpddlqekEVAYCStythceIHPSMILG 705
Cdd:CHL00001 500 ------------RY-----RQEFLTIAWE-------------------------------QIHLRS------IFPFQYFS 525
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 706 VCASIIPFPDHNQSPRNTYQSAMGKQAM----------------------GV-----------YI-------------TN 739
Cdd:CHL00001 526 IGASLIPFLEHNDANRALMGSNMQRQAVplsrsekcivgtglerqvaldsGVvaiaehegkiiYTdtdkiilsgngdtLS 605
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 740 FHVRM------DTLAHvlyypQKPLVttRSMEYLRFRELPA------------GINSIVAIASYTGYNQEDSVIMNRSAV 801
Cdd:CHL00001 606 IPLVMyqrsnkNTCMH-----QKPQV--RRGKCVKKGQILAdgaatvggelalGKNVLVAYMPWEGYNFEDAVLISERLV 678
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 802 DRGFFRSVFYRSYKEQ--ESKKGFdqeevfEKPTRETCQ----GMRHaiyekLDDDGLIAPGVRVSGDDVIIGKtVTLPE 875
Cdd:CHL00001 679 YEDIYTSFHIRKYEIQthVTSQGP------ERITKEIPHleahLLRN-----LDKNGIVMLGSWVETGDILVGK-LTPQE 746
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 876 NEDELESTNRR----------YTKRDCSTFLRTSETGIVDQVMvTLNQEGYKFCKIRVRSVRIPQ-----IGDKFASRHG 940
Cdd:CHL00001 747 AEESSYAPEGRllraifgiqvSTSKETCLKLPIGGRGRVIDVR-WIQKKGGSSYNPETIHVYILQkreiqVGDKVAGRHG 825
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 941 QKGTCG-IQYRQeDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKIS-NLLSDY 1018
Cdd:CHL00001 826 NKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPF-DERYEQEASrKLVFSE 903
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1019 GYHLR--------------GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGL 1084
Cdd:CHL00001 904 LYEASkqtanpwvfepeypGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQ 983
|
1210 1220
....*....|....*....|....*...
gi 226958589 1085 RFGEMERDCQIAHGAAQFLRERLFEASD 1112
Cdd:CHL00001 984 RVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
378-1112 |
1.61e-34 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 144.68 E-value: 1.61e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 378 GRRELDDRDHYGNKRLDLAGPLLAflfrgmfkNLLKEVRIYAQKFIdRGKDFNLELAIKTRIISDGLKYSLATGNWGDQK 457
Cdd:PRK09603 450 NQGKIDDRDHLGNRRIRAVGELLA--------NELHSGLVKMQKTI-KDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFF 520
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 458 KAHQaragVSQVLNRLTFASTLSHLRRLnSPIGrDGKLAK------PRQLHNTLWGMVCPAETPEGHAVGLVKNLAlmAY 531
Cdd:PRK09603 521 MGGQ----LSQFMDQTNPLSEVTHKRRL-SALG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS--TF 592
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 532 ISVGSqpspiLEFLEewsmenleeispaaiADATKIfVNGcwvgihkdpeqlmntlrklrrqmdIIVSEVSMIRDIRERE 611
Cdd:PRK09603 593 TRVND-----LGFIE---------------APYKKV-VDG------------------------KVVGETIYLTAIQEDS 627
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 612 IRIYTDAGRIcrpllivekqklllkkrhidqlkerEYNNYSWQDLvasgvveyIDTLEEETVMLAmtpddlqEKevaycS 691
Cdd:PRK09603 628 HIIAPASTPI-------------------------DEEGNILGDL--------IETRVEGEIVLN-------EK-----S 662
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 692 TYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------------- 733
Cdd:PRK09603 663 KVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgtgiekiiardswgaikanragvvekid 742
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 734 ------------GVYITNFHVRMDTLAHV-LYYPQKPLVTT-------------RSMEYlrfRELPAGINSIVAIASYTG 787
Cdd:PRK09603 743 skniyilgegkeEAYIDAYSLQKNLRTNQnTSFNQVPIVKVgdkveagqiiadgPSMDR---GELALGKNVRVAFMPWNG 819
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 788 YNQEDSVIMNRSAVDRGFFRSV--FYRSYKEQESKKGFdqeevfEKPTRETcQGMRHAIYEKLDDDGLIAPGVRVSGDDV 865
Cdd:PRK09603 820 YNFEDAIVVSERITKDDIFTSThiYEKEVDARELKHGV------EEFTADI-PDVKEEALAHLDESGIVKVGTYVSAGMI 892
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 866 IIGKTV------TLPENE---------------------DELEST---------------------------------NR 885
Cdd:PRK09603 893 LVGKTSpkgeikSTPEERllraifgdkaghvvnkslycpPSLEGTvidvkvftkkgyekdarvlsayeeekakldmehFD 972
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 886 RYTKRDCSTFLRT----------SETGIVDQVM----------------VTLN----------QEGY------------- 916
Cdd:PRK09603 973 RLTMLNREELLRVssllsqaileEPFSHNGKDYkegdqipkeeiasinrFTLAslvkkyskevQNHYeitknnfleqkkv 1052
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 917 -----------------------KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIP 973
Cdd:PRK09603 1053 lgeeheeklsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVP 1132
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 974 SRMTIGHLIECLQGKVSANKG-----------------------EIGD-------------------------------- 998
Cdd:PRK09603 1133 SRMNIGQILEMHLGLVGKEFGkqiasmledktkdfakelrakmlEIANainekdpltihalencsdeelleyakdwskgv 1212
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 999 --ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPME 1076
Cdd:PRK09603 1213 kmAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVG 1292
|
970 980 990
....*....|....*....|....*....|....*.
gi 226958589 1077 GRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1112
Cdd:PRK09603 1293 GKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
567-629 |
3.57e-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: 113.62 E-value: 3.57e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 226958589 567 IFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIvSEVSMIRDIREREIRIYTDAGRICRPLLIVE 629
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKIS-EEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
368-1112 |
2.12e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 124.73 E-value: 2.12e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 368 MVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFR-GMFKNLLKEVRIYAQKFIDR--GKDFnlelaIKTRIISDGL 444
Cdd:PRK14844 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRtGLLKLERAVVDSMSTSSLDKvsPSDF-----INPKVLTNVL 523
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 445 KyslatgnwgDQKKAHQaragVSQVLNRLTFASTLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMVCPAETPEGHAV 520
Cdd:PRK14844 524 R---------DFFNSSQ----LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 521 GLVKNLALMAYIS-VGSQPSPILEFLEEWSMENLEEISPA-----AIADAT-KIFVNGCWVgihkdpeQLMNTLRKLRRQ 593
Cdd:PRK14844 591 GLINSLAIYARINkYGFIESPYRKVVNRVVTDQIEYLSAIdeglyYIADTSaKLDENNCFV-------DDMLYCRYAGSF 663
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 594 MDIIVSEVSMIrDIREREIrIYTDAGRIcrPLLivekqklllkkrhidqlkereYNNYSWQDLVASGVVEYIDTLEEETV 673
Cdd:PRK14844 664 VMVSSDQVSYI-DVSPKQV-ISVAASLI--PFL---------------------ENDDANRALMGSNMQRQAVPLLKPTA 718
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 674 MLAMTPddlQEKEVAYCSTythceihpSMILGVCASIIPFPDHNQSPRNTYQSAmGKQAMGVYItnFHVR-MDTLAHVLY 752
Cdd:PRK14844 719 PLVATG---MESFVASGSG--------AVVLAKRDGIVDSSDSNSIVIRAFDKE-RVNYLDVDI--YHLRkFQRSNHNTC 784
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 753 YPQKPLVttRSMEYLR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVfyrsYKEQESK 820
Cdd:PRK14844 785 INQKPLV--CVGDYVKegdviadgpainSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSI----HIEEFEC 858
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 821 KGFDQEEVFEKPTReTCQGMRHAIYEKLDDDGLIAPGVRVSGDDVIIGK-----TVTLP--------------------- 874
Cdd:PRK14844 859 VVHDTPLGSEKITR-AIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKvtpkpSLSLPpetkllmtifgeksfdcadss 937
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 875 -----------------------ENE-----------------------------DELE-------STNRR--------- 886
Cdd:PRK14844 938 lytspdvegtvidvqvftrrgveENErallikqkeindfekerdyiinvtseyfyDELKkllinsgSQDREkfdsiereq 1017
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 887 -----YTKRDCSTFLRTSETGIVDQVMVTLNQ---------EGYKFCKIRVRSVRI-------PQIGDKFASRHGQKGTC 945
Cdd:PRK14844 1018 wwgigLKNQSISEQVKSLKKDFDEKVSHAIAQfkrkveklhEGYDLPQGVSMSVKVfiavkhsLQPGDKMAGRHGNKGVI 1097
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 946 GIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQG--------KVS--------------------------- 990
Cdd:PRK14844 1098 SRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgeKVGnildeinkiksafckgirslnddnftk 1177
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 991 -------------ANKGEIGDA---TPFNDAVN----------------------------------------VQKIS-N 1013
Cdd:PRK14844 1178 faaayldnkkienIDDDEITASvlnTPNKNALNdelnelvenylnscksaysnlrnflievyscgsnvsicnnIRDISdN 1257
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226958589 1014 LLSDYGYHLR------------------------------GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRA 1063
Cdd:PRK14844 1258 NLIEFARKLRdgipvaapvfegpkdeqiaklfelagldnsGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARS 1337
|
970 980 990 1000
....*....|....*....|....*....|....*....|....*....
gi 226958589 1064 RGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1112
Cdd:PRK14844 1338 VGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
468-531 |
4.92e-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: 4.92e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 226958589 468 QVLNRLTFASTLSHLRRLNSPIG---RDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAY 531
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
653-700 |
4.26e-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: 92.99 E-value: 4.26e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 226958589 653 WQDLVASGVVEYIDTLEEETVMLAMTPDDL-----QEKEVAYCSTYTHCEIHP 700
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLeessrEEREGPYAHTYTHCEIHP 53
|
|
| |
