|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
20-1165 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1282.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 20 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhaSGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 98
Cdd:PRK08565 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 99 SPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 178
Cdd:PRK08565 69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 179 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTGECRSCLENSSRPTstiwvsMLARGGQGAkksaigqrIVATLPYIK 257
Cdd:PRK08565 144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 258 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 336
Cdd:PRK08565 210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 337 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 416
Cdd:PRK08565 286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 417 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 496
Cdd:PRK08565 366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 497 TLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 576
Cdd:PRK08565 440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 577 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREynnYSWQDLVASGV 654
Cdd:PRK08565 520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 655 VEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 734
Cdd:PRK08565 596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 735 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 814
Cdd:PRK08565 669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 815 GFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 890
Cdd:PRK08565 749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 891 TSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 970
Cdd:PRK08565 825 HGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMT 904
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 971 IGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDD 1050
Cdd:PRK08565 905 VGQLLESIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1051 KIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC 1130
Cdd:PRK08565 984 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVC 1063
|
1130 1140 1150
....*....|....*....|....*....|....*
gi 740086795 1131 RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1165
Cdd:PRK08565 1064 PIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLK 1098
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
32-1165 |
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: 1254.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 32 LVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEaqhasgeveePPRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNL 111
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 112 TYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQE 191
Cdd:cd00653 70 TYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQE 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 192 KMATNTVYVFAKKDSKYAytgECRSCLENSSRPTSTIWVSMLARGgqgakksaigQRIVATLPYIKQEVpiiivfralgf 271
Cdd:cd00653 146 QRSPNVIIVEDSKGKRIY---TKTSIPSYSPYRGSWLEVKSDKKK----------DRIYVRIDLKRQEE----------- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 272 vsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFIGSRGakpgvtkekrikyakevlqkemlphvgvsdfce 351
Cdd:cd00653 202 --------------------------------------ALKYIGKRF--------------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 352 tkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTR 431
Cdd:cd00653 211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSK 286
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 432 IISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSHLRRLNS-PIGRDGKLAKPRQLHNTLWGMVCPAETPEG 510
Cdd:cd00653 287 PITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEG 365
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 511 HAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdii 590
Cdd:cd00653 366 ENCGLVKNLALMARIS---------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 591 vsevsmirdirereiriytdaGRICRPLLIVEKQklllkkrhidqlkereynnyswqdlvasgvveyidtleeetvmlam 670
Cdd:cd00653 382 ---------------------GRIERPYRIVEKE---------------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 671 tpddlqekevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKP 750
Cdd:cd00653 395 ---------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKP 459
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 751 LVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETC 830
Cdd:cd00653 460 LVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDI 535
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 831 QGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQE 907
Cdd:cd00653 536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDG 615
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 908 GYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKG 987
Cdd:cd00653 616 GNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLG 695
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 988 EIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQP 1067
Cdd:cd00653 696 KFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQP 774
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1068 MEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYA 1147
Cdd:cd00653 775 LKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYA 848
|
1130
....*....|....*...
gi 740086795 1148 CKLLFQELMSMSIAPRMM 1165
Cdd:cd00653 849 FKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
560-1164 |
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: 786.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 560 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKER 639
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 640 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 719
Cdd:TIGR03670 80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 720 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 799
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 800 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 875
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 876 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGIT 955
Cdd:TIGR03670 309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 956 PDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIF 1035
Cdd:TIGR03670 386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF-EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1036 IGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLC 1115
Cdd:TIGR03670 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 740086795 1116 GIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRM 1164
Cdd:TIGR03670 545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
23-1166 |
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: 701.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 23 ISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQaeaqhaSGEVEepprylLKFEQIYLSKPTHwerdgapspmM 102
Cdd:COG0085 7 IKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDF------TGNLS------LEFGDYRLGEPKY----------T 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 103 PNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMLRStycllngltdrdlcelnecpldpgGYFIING 182
Cdd:COG0085 65 PEECKERDLTYAAPLYVKVRLVNKETGEIKEQE----VFMGDFPLMTDS------------------------GTFIING 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 183 SEKVLIAQEKMATNTVYVFAK-KDSKYAYTGECRSclensSRPTstiWVSMLARggqgaKKSAIGQRIVAtlpyiKQEVP 261
Cdd:COG0085 117 TERVIVSQLVRSPGVYFVEEEdKSGKDLYSAKVIP-----SRGA---WLEFETD-----KDGTIYVRIDR-----KRKIP 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 262 IIIVFRALGFVSDRDILEHiiydFEDPEMMEMVKPSLDEAFVI-QEQnvALNFIGSRgAKPGvtKEKRIKYAKEVL---- 336
Cdd:COG0085 179 VTVLLRALGLETDEEILEA----FGDDPIQEYILATLEKDNTKtQEE--ALLEIYRK-LRPG--EPPTIERAEQLLdnlf 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 337 ---QKEMLPHVG-----------VSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFK 402
Cdd:COG0085 250 fdpKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 403 NLLKEVRiyaqkfiDR-----GKDFNLELAIKTRIISDGLKYSLATGnwgdqkkahqaraGVSQVLNRLTFASTLSHLRR 477
Cdd:COG0085 330 RMERVVR-------ERmttqdVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRR 389
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 478 LN----SPIGRDgklaKP----RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqpspilEFleewsmenleei 549
Cdd:COG0085 390 LSalgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY------------ 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 550 spaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirereiriytdaGRICRPLLIVEKQKLLLK 629
Cdd:COG0085 445 --------------------------------------------------------------GFIETPYRKVENGKVTDE 462
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 630 krhidqlkereynnyswqdlvasgvVEYIDTLEEETVMLAMTPDDLQEK--------------EVAYCST--YTHCEIHP 693
Cdd:COG0085 463 -------------------------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryrgEEVLVPPeeVDYMDVSP 517
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 694 SMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNfhvrmdtlAHVLYYP--------------QKPLVttRSMEY 759
Cdd:COG0085 518 KQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPIV--RVGDR 587
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 760 LR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSY--KEQESKKGfdQEEVfekp 825
Cdd:COG0085 588 VEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYeiEARDTKLG--PEEI---- 661
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 826 TREtcqgmrhaI-------YDKLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDELESTNR----------RYtKRDCSTF 888
Cdd:COG0085 662 TRD--------IpnvseeaLRNLDEDGIIRIGAEVKGGDILVGK-VT-PKGETELTPEERllraifgekaRE-VRDTSLR 730
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 889 LRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIIN 961
Cdd:COG0085 731 VPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLN 810
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 962 PHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYY 1041
Cdd:COG0085 811 PLGVPSRMNVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYY 889
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1042 QRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYqvhvcnlCGimaia 1121
Cdd:COG0085 890 LKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDV-------CG----- 957
|
1210 1220 1230 1240
....*....|....*....|....*....|....*....|....*
gi 740086795 1122 ntRTHTYECRgcRNKTQISLVRMPYACKLLFQELMSMSIAPRMMS 1166
Cdd:COG0085 958 --RVKVYEAI--VKGENIPEPGIPESFKVLLKELQSLGLDVEVLS 998
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
700-1073 |
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 740086795 700 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYT 779
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 780 GYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGfDQEEVFEKPTREtcqgmRHAIYDKLDDDGLIAPGVRVSGDDVI 859
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-PIEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 860 IGKTV-TLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV-TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 937
Cdd:pfam00562 155 VGKVGpTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 938 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA-VNVQKISNLLSDYGYHLR 1016
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAsTEVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 740086795 1017 GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR 1073
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
20-1165 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1282.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 20 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDappidlqaeaqhaSGEVEEP-PRYLLKFEQIYLSKPTHWERDGAP 98
Cdd:PRK08565 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDE-------------FGEIKTEiPGLKIVLGKIRVGEPEIKEADGSE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 99 SPMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF 178
Cdd:PRK08565 69 RPITPMEARLRNLTYAAPLYLTMI--PVENGIEY---EPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYF 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 179 IINGSEKVLIAQEKMATNTVYV-FAKKDSKYAYTGECRSCLENSSRPTstiwvsMLARGGQGAkksaigqrIVATLPYIK 257
Cdd:PRK08565 144 IINGSERVIVSQEDLAPNRVLVdKGEAGSSITHTAKVISSRAGYRAQV------TVERRKDGT--------IYVSFPAVP 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 258 QEVPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAF-VIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVL 336
Cdd:PRK08565 210 GKIPFVILMRALGLETDRDIVYAV---SLDPEIQQELLPSLEQASsIAATVEDALDYIGKRVA-IGQPREYRIERAEQIL 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 337 QKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFI 416
Cdd:PRK08565 286 DKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 417 DRGKDFNLELAIKTRIISDGLKYSLATGNWGdqkkahQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHN 496
Cdd:PRK08565 366 ARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHG 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 497 TLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQL 576
Cdd:PRK08565 440 TQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEEL 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 577 MNTLRKLRRQMDI--IVSeVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREynnYSWQDLVASGV 654
Cdd:PRK08565 520 AEKIRELRRSGKIsdEVN-VAYIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGE---LTFDDLVKMGV 595
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 655 VEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFH 734
Cdd:PRK08565 596 IEYLDAEEEENAYVALDPEDLTPE-------HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFR 668
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 735 VRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKK 814
Cdd:PRK08565 669 IRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKY 748
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 815 GFDQEEVFEKPTrETCQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELESTNRRytkRDCSTFLR 890
Cdd:PRK08565 749 PGGQEDKIEIPE-PNVRGYRGEeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQER---RDTSVTVR 824
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 891 TSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMT 970
Cdd:PRK08565 825 HGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMT 904
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 971 IGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDD 1050
Cdd:PRK08565 905 VGQLLESIAGKVAALEGRFVDATPF-YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVAD 983
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1051 KIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYEC 1130
Cdd:PRK08565 984 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVC 1063
|
1130 1140 1150
....*....|....*....|....*....|....*
gi 740086795 1131 RGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1165
Cdd:PRK08565 1064 PIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLK 1098
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
32-1165 |
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: 1254.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 32 LVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEaqhasgeveePPRYLLKFEQIYLSKPTHWErDGAPSPMMPNEARLRNL 111
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDD----------DGRLKLKFGDIYLGKPKVEE-GGVTRKLTPNECRLRDL 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 112 TYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQE 191
Cdd:cd00653 70 TYSAPLYVDIRLTVNDKGK----IKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQE 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 192 KMATNTVYVFAKKDSKYAytgECRSCLENSSRPTSTIWVSMLARGgqgakksaigQRIVATLPYIKQEVpiiivfralgf 271
Cdd:cd00653 146 QRSPNVIIVEDSKGKRIY---TKTSIPSYSPYRGSWLEVKSDKKK----------DRIYVRIDLKRQEE----------- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 272 vsdrdilehiiydfedpemmemvkpsldeafviqeqnvALNFIGSRGakpgvtkekrikyakevlqkemlphvgvsdfce 351
Cdd:cd00653 202 --------------------------------------ALKYIGKRF--------------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 352 tkkaYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTR 431
Cdd:cd00653 211 ----EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSK 286
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 432 IISDGLKYSLATGNWGDQKKaHQARAGVSQVLNRLTFASTLSHLRRLNS-PIGRDGKLAKPRQLHNTLWGMVCPAETPEG 510
Cdd:cd00653 287 PITSGIKEFLATGNWGSKRF-LMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEG 365
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 511 HAVGLVKNLALMAYISvgsqpspilefleewsmenleeispaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdii 590
Cdd:cd00653 366 ENCGLVKNLALMARIS---------------------------------------------------------------- 381
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 591 vsevsmirdirereiriytdaGRICRPLLIVEKQklllkkrhidqlkereynnyswqdlvasgvveyidtleeetvmlam 670
Cdd:cd00653 382 ---------------------GRIERPYRIVEKE---------------------------------------------- 394
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 671 tpddlqekevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKP 750
Cdd:cd00653 395 ---------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKP 459
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 751 LVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETC 830
Cdd:cd00653 460 LVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI----TRGDI 535
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 831 QGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVT---LNQE 907
Cdd:cd00653 536 PNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFsreLNDG 615
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 908 GYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKG 987
Cdd:cd00653 616 GNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLG 695
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 988 EIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQP 1067
Cdd:cd00653 696 KFGDATPF-DGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQP 774
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1068 MEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYA 1147
Cdd:cd00653 775 LKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN------LCRLCKKGTNISKVGIPYA 848
|
1130
....*....|....*...
gi 740086795 1148 CKLLFQELMSMSIAPRMM 1165
Cdd:cd00653 849 FKLLFQELQSMNIDPRLK 866
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
560-1164 |
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: 786.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 560 IFVNGCWVGIHKDPEQLMNTLRKLRRQmDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKER 639
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRS-GKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 640 EYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQS 719
Cdd:TIGR03670 80 EL---TWDDLVKQGVIEYLDAEEEENAYIALDPEELTPE-------HTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGA 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 720 AMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFF 799
Cdd:TIGR03670 150 AMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 800 RSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDELES 875
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPGGQEDRFEIPEPDV-RGYRGEeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLV 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 876 TNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGIT 955
Cdd:TIGR03670 309 TERR---RDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 956 PDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIF 1035
Cdd:TIGR03670 386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF-EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIF 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1036 IGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLC 1115
Cdd:TIGR03670 465 IGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENC 544
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 740086795 1116 GIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRM 1164
Cdd:TIGR03670 545 GHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
558-1165 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 751.02 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 558 TKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIiVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLK 637
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEI-SEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLK 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 638 EREYnnySWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKevaycstYTHCEIHPSMILGVCASIIPFPDHNQSPRNTY 717
Cdd:PRK07225 84 NGEL---TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE-------HTHLEIDPSLILGIGAGMIPYPEHNASPRITM 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 718 QSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRG 797
Cdd:PRK07225 154 GAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERG 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 798 FFRSVFYRSYKEQESKKGFDQEEVFEKPTRETcQGMRHA-IYDKLDDDGLIAPGVRVSGDDVIIGKTVT---LPENEDEL 873
Cdd:PRK07225 234 LGRSHFFRTYEGEERRYPGGQEDRFEIPDKDV-RGYRGEeAYRHLDEDGLVNPETEVKEGDVLIGKTSPprfLEEPDDFG 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 874 ESTNRRytkRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG 953
Cdd:PRK07225 313 ISPEKR---RETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESG 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 954 ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDaVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQ 1033
Cdd:PRK07225 390 VVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSG-EDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAE 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1034 IFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCN 1113
Cdd:PRK07225 469 IFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCA 548
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 740086795 1114 LCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMM 1165
Cdd:PRK07225 549 KCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLE 600
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
23-1166 |
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: 701.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 23 ISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQaeaqhaSGEVEepprylLKFEQIYLSKPTHwerdgapspmM 102
Cdd:COG0085 7 IKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDF------TGNLS------LEFGDYRLGEPKY----------T 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 103 PNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMLRStycllngltdrdlcelnecpldpgGYFIING 182
Cdd:COG0085 65 PEECKERDLTYAAPLYVKVRLVNKETGEIKEQE----VFMGDFPLMTDS------------------------GTFIING 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 183 SEKVLIAQEKMATNTVYVFAK-KDSKYAYTGECRSclensSRPTstiWVSMLARggqgaKKSAIGQRIVAtlpyiKQEVP 261
Cdd:COG0085 117 TERVIVSQLVRSPGVYFVEEEdKSGKDLYSAKVIP-----SRGA---WLEFETD-----KDGTIYVRIDR-----KRKIP 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 262 IIIVFRALGFVSDRDILEHiiydFEDPEMMEMVKPSLDEAFVI-QEQnvALNFIGSRgAKPGvtKEKRIKYAKEVL---- 336
Cdd:COG0085 179 VTVLLRALGLETDEEILEA----FGDDPIQEYILATLEKDNTKtQEE--ALLEIYRK-LRPG--EPPTIERAEQLLdnlf 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 337 ---QKEMLPHVG-----------VSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFK 402
Cdd:COG0085 250 fdpKRYDLAHVGrykinkklgldVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLS 329
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 403 NLLKEVRiyaqkfiDR-----GKDFNLELAIKTRIISDGLKYSLATGnwgdqkkahqaraGVSQVLNRLTFASTLSHLRR 477
Cdd:COG0085 330 RMERVVR-------ERmttqdVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRR 389
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 478 LN----SPIGRDgklaKP----RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqpspilEFleewsmenleei 549
Cdd:COG0085 390 LSalgpGGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------EY------------ 444
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 550 spaaiadatkifvngcwvgihkdpeqlmntlrklrrqmdiivsevsmirdirereiriytdaGRICRPLLIVEKQKLLLK 629
Cdd:COG0085 445 --------------------------------------------------------------GFIETPYRKVENGKVTDE 462
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 630 krhidqlkereynnyswqdlvasgvVEYIDTLEEETVMLAMTPDDLQEK--------------EVAYCST--YTHCEIHP 693
Cdd:COG0085 463 -------------------------IEYLTADEEENYYIAQANAPLDEDgnfleervlvryrgEEVLVPPeeVDYMDVSP 517
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 694 SMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNfhvrmdtlAHVLYYP--------------QKPLVttRSMEY 759
Cdd:COG0085 518 KQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPIV--RVGDR 587
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 760 LR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSY--KEQESKKGfdQEEVfekp 825
Cdd:COG0085 588 VEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYeiEARDTKLG--PEEI---- 661
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 826 TREtcqgmrhaI-------YDKLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDELESTNR----------RYtKRDCSTF 888
Cdd:COG0085 662 TRD--------IpnvseeaLRNLDEDGIIRIGAEVKGGDILVGK-VT-PKGETELTPEERllraifgekaRE-VRDTSLR 730
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 889 LRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIIN 961
Cdd:COG0085 731 VPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLN 810
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 962 PHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYY 1041
Cdd:COG0085 811 PLGVPSRMNVGQVLETHLGWAAALLGRRVATPVF-DGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYY 889
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1042 QRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYqvhvcnlCGimaia 1121
Cdd:COG0085 890 LKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDV-------CG----- 957
|
1210 1220 1230 1240
....*....|....*....|....*....|....*....|....*
gi 740086795 1122 ntRTHTYECRgcRNKTQISLVRMPYACKLLFQELMSMSIAPRMMS 1166
Cdd:COG0085 958 --RVKVYEAI--VKGENIPEPGIPESFKVLLKELQSLGLDVEVLS 998
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
700-1073 |
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 740086795 700 CASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYT 779
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 780 GYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGfDQEEVFEKPTREtcqgmRHAIYDKLDDDGLIAPGVRVSGDDVI 859
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLG-PIEEITRDIPNV-----SEEALKKLDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 860 IGKTV-TLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV-TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGT 937
Cdd:pfam00562 155 VGKVGpTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 938 CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA-VNVQKISNLLSDYGYHLR 1016
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGAsTEVEDIGELLEKAGYNYY 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 740086795 1017 GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR 1073
Cdd:pfam00562 315 GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
31-434 |
3.96e-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: 528.10 E-value: 3.96e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 31 GLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEeppRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRN 110
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGD---KLSLKFGQIRLGKPMFDETDGSTREIYPQECRLRN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 111 LTYSAPLYVDITKTVIKEGEEQlqtqHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQ 190
Cdd:pfam04563 78 LTYSAPLYVDLELSVYNGEDIK----PIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQ 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 191 EKMATNTVYVFAKKD-SKYAYTGECRSCLENSSRPTSTIWVSMLARggqgakksAIGQRIVATLPYIKQEVPIIIVFRAL 269
Cdd:pfam04563 154 EHRSRNHPIVFKKADpKKRGSVASVRSSAEISVRPDSTSWVNVLEY--------LSNGTIYFKFPYIKKEIPIVIILRAL 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 270 GFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVI--QEQNVALNFIGSRGAKP---GVTKEKRIKYAKEVLQKEMLPHV 344
Cdd:pfam04563 226 GFTSDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQKEVLPHL 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 345 GVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNL 424
Cdd:pfam04563 306 GTYELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLML 385
|
410
....*....|
gi 740086795 425 ELAIKTRIIS 434
Cdd:pfam04563 386 QLLVNAKPIT 395
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
20-540 |
3.23e-138 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 427.83 E-value: 3.23e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 20 WIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaqhasgEVEEPPRYLLKFEQIYLSKPTHWERDGAPS 99
Cdd:PRK09606 6 RVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPI-----------ETEIEDGVYVELGKIRVGKPVVKEADGSER 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 100 PMMPNEARLRNLTYSAPLYVDITktVIKEGEEQlqtQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFI 179
Cdd:PRK09606 75 EIYPMEARLRNLTYSAPLYLEMS--PVEGGEEE---EPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFI 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 180 INGSEKVLIAQEKMATNTVYVfaKKDSKYAYTGECRSCLenSSRPTSTIWVSmLARGGQGakksaigqRIVATLPYIKQE 259
Cdd:PRK09606 150 VNGSERVLMTLEDLAPNKILV--EKDERYGDRIEVAKVF--SQRRGYRALVT-VERNRDG--------LLEVSFPSVPGS 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 260 VPIIIVFRALGFVSDRDILEHIiydFEDPEMMEMVKPSLDEAfVIQEQNVALNFIGSRGAkPGVTKEKRIKYAKEVLQKE 339
Cdd:PRK09606 217 IPFVILMRALGLETDEEIVEAV---SDDPEIVKFMLENLEEA-EVDTQEEALEYIGKRVA-PGQTKEYRIKRAEYVIDRY 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 340 MLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRG 419
Cdd:PRK09606 292 LLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRN 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 420 KDFNLELAIKTRIISDGLKYSLATGNW-GdqkkahqARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTL 498
Cdd:PRK09606 372 RELSIKTAVRSDVLTERLEHAMATGNWvG-------GRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQ 444
|
490 500 510 520
....*....|....*....|....*....|....*....|..
gi 740086795 499 WGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEE 540
Cdd:PRK09606 445 WGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKE 486
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
23-1105 |
5.53e-71 |
|
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: 258.05 E-value: 5.53e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 23 ISSYFDEKGLVRQQLDSFDEFIQMS----------VQRIVEDAPPIdlqaeaQHASGeveeppRYLLKFEQIYLSKPTHw 92
Cdd:TIGR02013 11 IPEVLEVPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPI------EDYTG------NIELEYLSYRLGEPKY- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 93 erdgapspmMPNEARLRNLTYSAPLYVDiTKTVIKEGEEQLQTQHQKTFIGKIPIMlrstycllnglTDRdlcelnecpl 172
Cdd:TIGR02013 78 ---------SVEECKERGLTYSAPLKVK-LRLINKEEDGTKEIKEQDVYMGDIPLM-----------TDR---------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 173 dpgGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKyaytgecRSCLENSSR--PTSTIWVSMlarggQGAKKSAIGQRIV 250
Cdd:TIGR02013 127 ---GTFIINGAERVVVSQLHRSPGVFFSSEKDTTK-------SGKVLFSARiiPYRGSWLEF-----ETDKKDVLYVRID 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 251 AtlpyiKQEVPIIIVFRALGFVSDRDILEHiiydFEDPEMME---MVKPSL--DEAFVIQeqnvalnfigSRGAKPG--V 323
Cdd:TIGR02013 192 R-----KRKLPATVLLRALGYTIDTLILNR----LGSGEYIRntlRKDPTNseEEALVEI----------YRKLRPGepP 252
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 324 TKEKrikyAKEVLQKEM-------LPHVG---VSDFCETKKAYFLGYMVHRLLLAAL--------GRRELDDRDHYGNKR 385
Cdd:TIGR02013 253 TVEA----ARSLLENLFfdpkrydLGRVGrykLNKKLGLDVPESIGVLTKEDIIATIkyliklrnGKGEIDDIDHLGNRR 328
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 386 LDLAGPLLAFLFRGMFKNLLKEVRiyaqkfiDRGKDFNLELA-----IKTRIISDGLKYSLATGNwgdqkkahqaragVS 460
Cdd:TIGR02013 329 IRSVGELLQNQFRVGLARMERIVR-------ERMSTQDTDTLtpqdlINAKPISAAIKEFFGSSQ-------------LS 388
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 461 QVLNRLTFASTLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVgsqpspiLE 536
Cdd:TIGR02013 389 QFMDQTNPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE-------YG 461
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 537 FLEewsmenleeiSPAAIADATKIFVNGCWVGIHKDPEQlmntlRKLRRQMDIIVSEVSMIRDirereiriytdagricr 616
Cdd:TIGR02013 462 FIE----------TPYRKVKDGKVVVTDEIDYLTADEED-----NYVIAQANAPLDENGRFVE----------------- 509
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 617 pllivekqklllkkrhidqlkereynnyswqDLVASGVVEYIDTLEEETVmlamtpddlqekevaycstyTHCEIHPSMI 696
Cdd:TIGR02013 510 -------------------------------DLVVARYRGEITLVSPDQV--------------------DYMDVSPKQV 538
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 697 LGVCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------GV---------YITNFHVR 736
Cdd:TIGR02013 539 VSVAASLIPFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVveyvdakriVIRYDEDE 618
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 737 MDTLAHVLYYP--------------QKPLVTT-------------RSMEylrFRELPAGINSIVAIASYTGYNQEDSVIM 789
Cdd:TIGR02013 619 EEPDGGIDIYRllkyqrsnqdtcinQRPIVSVgdrveagdvladgPSTD---LGELALGRNVLVAFMPWNGYNYEDAILI 695
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 790 NRSAVDRGFFRSVFYRSYK--EQESKKGfdQEEVfekpTRETCQGMRHAIyDKLDDDGLIAPGVRVSGDDVIIGKTVtlP 867
Cdd:TIGR02013 696 SERLVKDDVFTSIHIEEYEveARDTKLG--PEEI----TRDIPNVSEEAL-RNLDENGIVRIGAEVKAGDILVGKVT--P 766
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 868 ENEDELESTNRRYTK---------RDCSTFLRTSETGIVDQVMVTLNQEG-------YKFCKIRVRSVRIPQIGDKFASR 931
Cdd:TIGR02013 767 KGETELTPEEKLLRAifgekardvRDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGR 846
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 932 HGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGD--ATPFNDAVNVQKISNLLS 1009
Cdd:TIGR02013 847 HGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPVFDGASEEEIKEYLE 926
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1010 DYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIA 1089
Cdd:TIGR02013 927 KAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEA 1006
|
1210
....*....|....*.
gi 740086795 1090 HGAAQFLRERLFEASD 1105
Cdd:TIGR02013 1007 YGAAYTLQEMLTVKSD 1022
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
77-1109 |
3.01e-57 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 216.11 E-value: 3.01e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 77 YLLKFEQIYLSKPthwerdgapsPMMPNEARLRNLTYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMlrstycll 156
Cdd:CHL00207 45 LLLFGKNYKLKYP----------KYNLLSAKSYDSNYSIQIYLPLKFINLKTNK----IKFINYLIGNLPKM-------- 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 157 nglTDRdlcelnecpldpgGYFIINGSEKVLIAQeKMATNTVYVFAKKDSKYaytgecRSCLENSSRPTSTIWVSMLARg 236
Cdd:CHL00207 103 ---TQR-------------GTFIINGLERVIVSQ-IIRSPGIYFKKEIKKNS------NKIYSATLIPNRGSWIKFELD- 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 237 gqgaKKSAIGQRIVATLpyikqEVPIIIVFRALGfVSDRDILEHIIYDFEDP-------------------EMMEMVKPS 297
Cdd:CHL00207 159 ----KNKEIWIRIDKNR-----KKPLIIFLKALG-LTDQDIYSRLTKSEFLKklkpillnsnsytneeillEIYKNLSPI 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 298 LDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCEtkkayflgyMVHRLLLAALGRRELDD 377
Cdd:CHL00207 229 EPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILS---------IIDKLINLKINKGNFDD 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 378 RDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKF-IDRGKDFNLelaIKTRIISDGLKYSLATGNwgdqkkahqar 456
Cdd:CHL00207 300 IDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICdIDSLSKFNL---INPKPLIALIREFFGSSQ----------- 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 457 agVSQVLNRLTFASTLSHLRRLNS--PIGRDgKLAKP---RQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISvgsqp 531
Cdd:CHL00207 366 --LSQYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLATNARIN----- 437
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 532 spILEFLEE--WSMENLeeispaaiadatKIFVNGCWVGIHKDPEQLMNTLrklrrqmdiivsevsmIRDIREREIRiyt 609
Cdd:CHL00207 438 --KFGFIETpfYKVING------------KVKKFGNPIYLTADSEDLYRIA----------------PNDINLNKNN--- 484
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 610 dagricrpllivekqklLLKKRHIdqlkEREYNNyswqdlvasgvvEYIDTLEEETVMLAMTPDDlqekevaycstythc 689
Cdd:CHL00207 485 -----------------YFKKNII----PVRYKQ------------EFKTVNPSKVDFIAISPIQ--------------- 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 690 eihpsmILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG---------------------------------VYITNF--H 734
Cdd:CHL00207 517 ------VFSIAESLIPFLEHNDANRALMGSNMQRQAVPllypekpivgtgyekqialdsgmtiisltegivVSVSAYkiI 590
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 735 VRMDTLAHVLYYPQK-------------PLV----------TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNR 791
Cdd:CHL00207 591 IQDDNNRYIHYYLQKyqrsnqntcinyrPIVwvgekinigqILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINK 670
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 792 SAVDRGFFRSVFYRSYKEQESKKGFDQEEVfekpTRETCQGMRHAIYdKLDDDGLIAPGVRVSGDDVIIGKTVTLPENED 871
Cdd:CHL00207 671 RLVYEDLFTSIHIEKYEIELRQTKLGSEEI----TRNIPNVSEYSLK-NLDENGIISIGSKVLAGDILVGKITPKGESDQ 745
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 872 ELEST--------NRRYTKrDCSTFLRTSETGIVDQVMVTLNQEG--YKF-----CKIRVRSVRIPQIGDKFASRHGQKG 936
Cdd:CHL00207 746 LPEGKllraifgeKAKDVK-DTSLRMPNGGYGRVIKVEIFSRSKGdeLKFgyylkIRVFIAQIRKIQVGDKLAGRHGNKG 824
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 937 TCG-IQYRQeDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDA--------------VNV 1001
Cdd:CHL00207 825 IISrILPRQ-DMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMygseysrilinnklNQA 903
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1002 QKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGE 1081
Cdd:CHL00207 904 SIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGE 983
|
1130 1140
....*....|....*....|....*...
gi 740086795 1082 MERDCQIAHGAAQFLRERLFEASDPYQV 1109
Cdd:CHL00207 984 MEVWALEAFGAAYTLKELLTIKSDDMQG 1011
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
194-387 |
5.89e-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: 5.89e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 194 ATNTVYVFAKKDSKyaytgecrsclenssrPTSTIWVSMLARGGQGAKKSAIGQR-IVATLPYIKQEVPIIIVFRALGFV 272
Cdd:pfam04561 1 RSNGIYVEKELDKN----------------GIIATYTSSLISNRGSWLKLEIDGKtLIWSRPSKKRKIPIVIFLKALGLV 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 273 SDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSrGAKPGVTKEKRIKYAKEVLQK-----EMLPHVGVS 347
Cdd:pfam04561 65 SDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLN 143
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 740086795 348 DFCETK--KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLD 387
Cdd:pfam04561 144 EPFENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
36-1100 |
2.16e-47 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 185.30 E-value: 2.16e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 36 QLDSFDEFIQMSV-------QRIVEDAPPIdlqaeaQHASGeveeppRYLLKFEQIYLSKPTHWERdgapspmmpnEARL 108
Cdd:PRK00405 31 QLDSFDWFLQLDVppedeglEEVFRSIFPI------EDFNG------NLSLEFVSYELGEPKYDVE----------ECKE 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 109 RNLTYSAPLYVDITKTVIKEGEeqlqTQHQKTFIGKIPIMlrstycllnglTDRdlcelnecpldpgGYFIINGSEKVLI 188
Cdd:PRK00405 89 RGLTYSAPLRVKLRLINKETGE----IKEQEVYMGDIPLM-----------TEN-------------GTFIINGTERVIV 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 189 AQekmatnTVY---VFAKKDSKYAYTGEcrscLENSSR--PTstiwvsmlaRGG----QGAKKSAIGQRIVatlpyIKQE 259
Cdd:PRK00405 141 SQ------LHRspgVYFDHDKDKTSSGK----LLYSARiiPY---------RGSwlefEFDPKDILYVRID-----RRRK 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 260 VPIIIVFRALGFvSDRDILEhIIYDFED-PEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQK 338
Cdd:PRK00405 197 LPVTVLLRALGY-SDEEILD-LFYEKEEfGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEELDGPYIRNTLEK 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 339 E--------------ML-----PHVgvsdfcETKKAYF-----------LG----YMV-HRL---------------LLA 368
Cdd:PRK00405 275 DptssreealveiyrRLrpgepPTV------EAARSLLenlffdpkrydLSkvgrYKLnKKLgldededvrvltkedIIA 348
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 369 AL--------GRRELDDRDHYGNKRLDLAGPLLAFLFR-GMfknllkeVRIyaQKFI-DR--GKDFN----LELaIKTRI 432
Cdd:PRK00405 349 TIkylinlrnGKGEVDDIDHLGNRRVRSVGELLQNQFRiGL-------SRM--ERAVrERmsLQDLDtltpQDL-INAKP 418
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 433 ISDGLKYSLATgnwgdqkkaHQaragVSQVL---NRLtfaSTLSHLRRLNS--PIG----------RDgklakprqLHNT 497
Cdd:PRK00405 419 VVAAIKEFFGS---------SQ----LSQFMdqtNPL---SELTHKRRLSAlgPGGltreragfevRD--------VHPT 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 498 LWGMVCPAETPEGHAVGLVKNLALMAYI-SVGsqpspileFLEewsmenleeiSPaaiadaTKIFVNGcwvgihkdpeql 576
Cdd:PRK00405 475 HYGRICPIETPEGPNIGLINSLATYARVnEYG--------FIE----------TP------YRKVVDG------------ 518
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 577 mntlrklrrqmdIIVSEVSMIRDIREREIRI------YTDAGRICRPLLIVekqklllkkrhidqlkeREYNNYswqDLV 650
Cdd:PRK00405 519 ------------KVTDEIVYLTADEEDNYVIaqanapLDEDGRFVDELVTA-----------------RYKGEF---VLV 566
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 651 ASGVVEYIDtleeetvmlamtpddlqekevaycstythceIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQA----- 725
Cdd:PRK00405 567 PPEEVDYMD-------------------------------VSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAvpllr 615
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 726 ---------M-----------------GV---------YITNFHVRMDTLAHVLY-------------YPQKPLVTTR-- 755
Cdd:PRK00405 616 peaplvgtgMerrvardsgavvvakrdGVveyvdasriVVRVEELDPGEDGVDIYnlikfqrsnqntcINQRPIVKVGdr 695
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 756 -----------SMEYlrfRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVfyrSYKEQE-----SKKGfdQE 819
Cdd:PRK00405 696 vekgdvladgpSTDN---GELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSI---HIEEYEieardTKLG--PE 767
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 820 EVfekpTREtcqgmrhaIYD-------KLDDDGLIAPGVRVSGDDVIIGKtVTlPENEDEL------------Estnrry 880
Cdd:PRK00405 768 EI----TRD--------IPNvseealrNLDESGIVRIGAEVKPGDILVGK-VT-PKGETELtpeekllraifgE------ 827
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 881 tK----RDCStfLR--TSETGIVDQVMV-TLNQEGY-------KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQED 946
Cdd:PRK00405 828 -KardvKDTS--LRvpHGEEGTVIDVKVfTRIEQGDelppgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVED 904
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 947 MPFTCEGiTP-DIIINPHAIPSRMTIGHLIECLQGKVSANKGE-IgdATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNG 1024
Cdd:PRK00405 905 MPYLEDG-TPvDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIkF--ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDG 981
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1025 FTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMErdcqI----AHGAAQFLRERL 1100
Cdd:PRK00405 982 RTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEME----VwaleAYGAAYTLQEML 1057
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1075-1167 |
2.86e-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: 2.86e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1075 GGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANtrthtyECRGCRNKTQISLVRMPYACKLLFQE 1154
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYN------KCPICKGETDISPGYIPESFKLLFQE 74
|
90
....*....|...
gi 740086795 1155 LMSMSIAPRMMSV 1167
Cdd:pfam04560 75 LQSLGIDPRLLLE 87
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
31-1105 |
1.73e-38 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 156.60 E-value: 1.73e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 31 GLVRQQLDSFDEFIQMSVQRIVEDAPPIdlqaeaQHASGEVEepprYLLKFEQIYLSKPTHWERDgapspmmpneARLRN 110
Cdd:CHL00001 14 GFNQIQFEGFCRFIDQGLTEELSKFPKI------EDTDQEIE----FQLFVETYQLVEPLIKERD----------AVYES 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 111 LTYSAPLYVDITKTVIKEGEEQLQTqhqkTFIGKIPIMlrstycllngltdrdlcelnecplDPGGYFIINGSEKVLIAQ 190
Cdd:CHL00001 74 LTYSSELYVPAGLIWKKSRDMQEQT----VFIGNIPLM------------------------NSLGTFIINGIYRVVINQ 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 191 eKMATNTVYVFAKKDSK--YAYTG----ECRSCLENSSRPTSTIWVsmlarggqgakksaigqRIVAtlpyiKQEVPIII 264
Cdd:CHL00001 126 -ILRSPGIYYRSELDHNgiSVYTGtiisDWGGRLELEIDRKARIWA-----------------RVSR-----KQKISILV 182
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 265 VFRALGFvSDRDILEHIIYdfedPEMMemvkpsldeafviqeqnvaLNFIGSRGAKPGVTKEKRIkyakeVLQKEMLPHV 344
Cdd:CHL00001 183 LLSAMGL-NLREILDNVCY----PEIF-------------------LSFLNDKEKKKIGSKENAI-----LEFYQQFACV 233
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 345 GV------SDFCETKKAYF-----LGY-----MVHRL---------------LLAA--------LGRRELDDRDHYGNKR 385
Cdd:CHL00001 234 GGdpvfseSLCKELQKKFFqqrceLGRigrrnMNRKLnldipenntfllpqdVLAAadyligmkFGMGTLDDIDHLKNKR 313
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 386 LDLAGPLLaflfRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLkyslaTGNWGDQKKAHQaragVSQVLNR 465
Cdd:CHL00001 314 IRSVADLL----QDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPL-----TTTYESFFGSHP----LSQFLDQ 380
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 466 LTFASTLSHLRRLNS--PIGRDGKLA--KPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYI-SVGSQPSPILEFLEE 540
Cdd:CHL00001 381 TNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIgHWGSLESPFYEISER 460
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 541 WSMENLEEISPAaiadatkifvngcwvgihKDpEQLMntlrklrrqmdiIVSEVSMI--RDIREREIriyTDAgricrpl 618
Cdd:CHL00001 461 SKEERMVYLSPS------------------ED-EYYM------------IAAGNSLAlnQGIQEEQV---VPA------- 499
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 619 livekqklllkkRHidqlkEREYNNYSWQdlvasgvveyidtleeetvmlamtpddlqekEVAYCStythceIHPSMILG 698
Cdd:CHL00001 500 ------------RY-----RQEFLTIAWE-------------------------------QIHLRS------IFPFQYFS 525
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 699 VCASIIPFPDHNQSPRNTYQSAMGKQAM----------------------GV-----------YI-------------TN 732
Cdd:CHL00001 526 IGASLIPFLEHNDANRALMGSNMQRQAVplsrsekcivgtglerqvaldsGVvaiaehegkiiYTdtdkiilsgngdtLS 605
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 733 FHVRM------DTLAHvlyypQKPLVttRSMEYLRFRELPA------------GINSIVAIASYTGYNQEDSVIMNRSAV 794
Cdd:CHL00001 606 IPLVMyqrsnkNTCMH-----QKPQV--RRGKCVKKGQILAdgaatvggelalGKNVLVAYMPWEGYNFEDAVLISERLV 678
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 795 DRGFFRSVFYRSYKEQ--ESKKGFdqeevfEKPTRETCQ----GMRHaiydkLDDDGLIAPGVRVSGDDVIIGKtVTLPE 868
Cdd:CHL00001 679 YEDIYTSFHIRKYEIQthVTSQGP------ERITKEIPHleahLLRN-----LDKNGIVMLGSWVETGDILVGK-LTPQE 746
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 869 NEDELESTNRR----------YTKRDCSTFLRTSETGIVDQVMvTLNQEGYKFCKIRVRSVRIPQ-----IGDKFASRHG 933
Cdd:CHL00001 747 AEESSYAPEGRllraifgiqvSTSKETCLKLPIGGRGRVIDVR-WIQKKGGSSYNPETIHVYILQkreiqVGDKVAGRHG 825
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 934 QKGTCG-IQYRQeDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFnDAVNVQKIS-NLLSDY 1011
Cdd:CHL00001 826 NKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPF-DERYEQEASrKLVFSE 903
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1012 GYHLR--------------GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGL 1077
Cdd:CHL00001 904 LYEASkqtanpwvfepeypGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQ 983
|
1210 1220
....*....|....*....|....*...
gi 740086795 1078 RFGEMERDCQIAHGAAQFLRERLFEASD 1105
Cdd:CHL00001 984 RVGEMEVWALEGFGVAYILQEMLTYKSD 1011
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
371-1105 |
1.45e-34 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 144.68 E-value: 1.45e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 371 GRRELDDRDHYGNKRLDLAGPLLAflfrgmfkNLLKEVRIYAQKFIdRGKDFNLELAIKTRIISDGLKYSLATGNWGDQK 450
Cdd:PRK09603 450 NQGKIDDRDHLGNRRIRAVGELLA--------NELHSGLVKMQKTI-KDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFF 520
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 451 KAHQaragVSQVLNRLTFASTLSHLRRLnSPIGrDGKLAK------PRQLHNTLWGMVCPAETPEGHAVGLVKNLAlmAY 524
Cdd:PRK09603 521 MGGQ----LSQFMDQTNPLSEVTHKRRL-SALG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS--TF 592
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 525 ISVGSqpspiLEFLEewsmenleeispaaiADATKIfVNGcwvgihkdpeqlmntlrklrrqmdIIVSEVSMIRDIRERE 604
Cdd:PRK09603 593 TRVND-----LGFIE---------------APYKKV-VDG------------------------KVVGETIYLTAIQEDS 627
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 605 IRIYTDAGRIcrpllivekqklllkkrhidqlkerEYNNYSWQDLvasgvveyIDTLEEETVMLAmtpddlqEKevaycS 684
Cdd:PRK09603 628 HIIAPASTPI-------------------------DEEGNILGDL--------IETRVEGEIVLN-------EK-----S 662
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 685 TYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM-------------------------------------- 726
Cdd:PRK09603 663 KVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVpllrsdapivgtgiekiiardswgaikanragvvekid 742
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 727 ------------GVYITNFHVRMDTLAHV-LYYPQKPLVTT-------------RSMEYlrfRELPAGINSIVAIASYTG 780
Cdd:PRK09603 743 skniyilgegkeEAYIDAYSLQKNLRTNQnTSFNQVPIVKVgdkveagqiiadgPSMDR---GELALGKNVRVAFMPWNG 819
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 781 YNQEDSVIMNRSAVDRGFFRSV--FYRSYKEQESKKGFdqeevfEKPTRETcQGMRHAIYDKLDDDGLIAPGVRVSGDDV 858
Cdd:PRK09603 820 YNFEDAIVVSERITKDDIFTSThiYEKEVDARELKHGV------EEFTADI-PDVKEEALAHLDESGIVKVGTYVSAGMI 892
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 859 IIGKTV------TLPENE---------------------DELEST---------------------------------NR 878
Cdd:PRK09603 893 LVGKTSpkgeikSTPEERllraifgdkaghvvnkslycpPSLEGTvidvkvftkkgyekdarvlsayeeekakldmehFD 972
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 879 RYTKRDCSTFLRT----------SETGIVDQVM----------------VTLN----------QEGY------------- 909
Cdd:PRK09603 973 RLTMLNREELLRVssllsqaileEPFSHNGKDYkegdqipkeeiasinrFTLAslvkkyskevQNHYeitknnfleqkkv 1052
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 910 -----------------------KFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIP 966
Cdd:PRK09603 1053 lgeeheeklsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVP 1132
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 967 SRMTIGHLIECLQGKVSANKG-----------------------EIGD-------------------------------- 991
Cdd:PRK09603 1133 SRMNIGQILEMHLGLVGKEFGkqiasmledktkdfakelrakmlEIANainekdpltihalencsdeelleyakdwskgv 1212
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 992 --ATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPME 1069
Cdd:PRK09603 1213 kmAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVG 1292
|
970 980 990
....*....|....*....|....*....|....*.
gi 740086795 1070 GRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1105
Cdd:PRK09603 1293 GKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
560-622 |
3.80e-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: 3.80e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 740086795 560 IFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIvSEVSMIRDIREREIRIYTDAGRICRPLLIVE 622
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKIS-EEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
361-1105 |
2.59e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 124.35 E-value: 2.59e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 361 MVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFR-GMFKNLLKEVRIYAQKFIDR--GKDFnlelaIKTRIISDGL 437
Cdd:PRK14844 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRtGLLKLERAVVDSMSTSSLDKvsPSDF-----INPKVLTNVL 523
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 438 KyslatgnwgDQKKAHQaragVSQVLNRLTFASTLSHLRRLNS--PIG--RDGKLAKPRQLHNTLWGMVCPAETPEGHAV 513
Cdd:PRK14844 524 R---------DFFNSSQ----LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 514 GLVKNLALMAYIS-VGSQPSPILEFLEEWSMENLEEISPA-----AIADAT-KIFVNGCWVgihkdpeQLMNTLRKLRRQ 586
Cdd:PRK14844 591 GLINSLAIYARINkYGFIESPYRKVVNRVVTDQIEYLSAIdeglyYIADTSaKLDENNCFV-------DDMLYCRYAGSF 663
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 587 MDIIVSEVSMIrDIREREIrIYTDAGRIcrPLLivekqklllkkrhidqlkereYNNYSWQDLVASGVVEYIDTLEEETV 666
Cdd:PRK14844 664 VMVSSDQVSYI-DVSPKQV-ISVAASLI--PFL---------------------ENDDANRALMGSNMQRQAVPLLKPTA 718
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 667 MLAMTPddlQEKEVAYCSTythceihpSMILGVCASIIPFPDHNQSPRNTYQSAmGKQAMGVYItnFHVR-MDTLAHVLY 745
Cdd:PRK14844 719 PLVATG---MESFVASGSG--------AVVLAKRDGIVDSSDSNSIVIRAFDKE-RVNYLDVDI--YHLRkFQRSNHNTC 784
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 746 YPQKPLVttRSMEYLR------------FRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVfyrsYKEQESK 813
Cdd:PRK14844 785 INQKPLV--CVGDYVKegdviadgpainSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSI----HIEEFEC 858
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 814 KGFDQEEVFEKPTRETCQGMRHAIYdKLDDDGLIAPGVRVSGDDVIIGK-----TVTLP--------------------- 867
Cdd:PRK14844 859 VVHDTPLGSEKITRAIPGVNEENLY-HLDDSGIVKIGTRVGPGYILVGKvtpkpSLSLPpetkllmtifgeksfdcadss 937
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 868 -----------------------ENE-----------------------------DELE-------STNRR--------- 879
Cdd:PRK14844 938 lytspdvegtvidvqvftrrgveENErallikqkeindfekerdyiinvtseyfyDELKkllinsgSQDREkfdsiereq 1017
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 880 -----YTKRDCSTFLRTSETGIVDQVMVTLNQ---------EGYKFCKIRVRSVRI-------PQIGDKFASRHGQKGTC 938
Cdd:PRK14844 1018 wwgigLKNQSISEQVKSLKKDFDEKVSHAIAQfkrkveklhEGYDLPQGVSMSVKVfiavkhsLQPGDKMAGRHGNKGVI 1097
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 939 GIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQG--------KVS--------------------------- 983
Cdd:PRK14844 1098 SRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwackklgeKVGnildeinkiksafckgirslnddnftk 1177
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 984 -------------ANKGEIGDA---TPFNDAVN----------------------------------------VQKIS-N 1006
Cdd:PRK14844 1178 faaayldnkkienIDDDEITASvlnTPNKNALNdelnelvenylnscksaysnlrnflievyscgsnvsicnnIRDISdN 1257
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 740086795 1007 LLSDYGYHLR------------------------------GNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRA 1056
Cdd:PRK14844 1258 NLIEFARKLRdgipvaapvfegpkdeqiaklfelagldnsGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARS 1337
|
970 980 990 1000
....*....|....*....|....*....|....*....|....*....
gi 740086795 1057 RGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASD 1105
Cdd:PRK14844 1338 VGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
461-524 |
4.89e-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: 4.89e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 740086795 461 QVLNRLTFASTLSHLRRLNSPIG---RDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAY 524
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
646-693 |
3.48e-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: 93.37 E-value: 3.48e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 740086795 646 WQDLVASGVVEYIDTLEEETVMLAMTPDDL-----QEKEVAYCSTYTHCEIHP 693
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLeessrEEREGPYAHTYTHCEIHP 53
|
|
| |
