|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
45-1125 |
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: 1149.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 45 LVKQHLDSFNYFVDVDLKKIIKANQ-LILSDVDPEFYLKYVDIRVGQ-RSGSPHKDQLVPPHECRLRDMTYSAPIYVDIE 122
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPpITDTDDDGRLKLKFGDIYLGKpKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 123 YTRGRNIIM-HKNVEIGRMPIMLRSNKCILHGADEKMMARLSECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEadEKK 201
Cdd:cd00653 81 LTVNDKGKIkEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 202 DIVQASVTS---------STHERKSKTYVVTKNGKIYLKHnsiaeevpivivlkaagiisdleimqlvcgndssyqdifs 272
Cdd:cd00653 159 GKRIYTKTSipsyspyrgSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 273 vnleeaaklnictQQQALEYIGAKVktmrrqkltilqegieaiattiiahltvealdfrekaLYIATMTRRVVMAMHNPK 352
Cdd:cd00653 199 -------------QEEALKYIGKRF-------------------------------------EDLIYMIRKLILLVLGKG 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 353 MVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMeydalLSINVHSNNITSGLNRAISTGNWSL 432
Cdd:cd00653 229 KLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIKEFLATGNWGS 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 433 KRFKMERAGVTHVLSRLSYISALGMMTRISS-QFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITtd 511
Cdd:cd00653 304 KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 512 deeepirklcyvlgvepislldsaslhlnygvylngtligttkfpsnfvsrfrflrrtgkvsefisiytndhhnavhiat 591
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 592 dgGRICRPLIIVKDgksmveaehlkrllsgelvfddflklglveyldvneendsyialyekdithDITHLEIEPFTVLGA 671
Cdd:cd00653 382 --GRIERPYRIVEK---------------------------------------------------EVTHIEISPSQILSV 408
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 672 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 751
Cdd:cd00653 409 AASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYS 488
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 752 GYDIEDALVLNKSSIDRGFGRCETRRKTTTVLKKYPNHTKDalcGMRVDENGEAIWQHESLGPDGLGEVGLKIRSGQIYI 831
Cdd:cd00653 489 GYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEE---ITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILV 565
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 832 NKSVPVQSSDAMAVNQAQ---YRETPVIYRAPELSIIDQVMMSTSDNDQD---LIKVLLRQNRRPELGDKFSSRHGQKGV 905
Cdd:cd00653 566 GKITPKGETESTPIFGEKardVRDTSLKYPGGEKGIVDDVKIFSRELNDGgnkLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 906 CGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVDQGFNYSGK 985
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGK 725
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 986 DMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLE 1065
Cdd:cd00653 726 EVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQE 805
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1066 RLMISSDAFEVDVCSNCGLMGYSGWCSTCKSAEHIIKMTIPYAAKLLFQELLAMNIAPRL 1125
Cdd:cd00653 806 RLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
189-366 |
7.14e-46 |
|
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: 163.29 E-value: 7.14e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 189 SKNRIIVEADEKKDIVQASVTSSTHERKSKTYVVTKNGKIYLKHN-SIAEEVPIVIVLKAAGIISDLEIMQLVCGNDSSY 267
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGSWLKLEIDGKTLIWSRpSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 268 QDIFSVNLEEAAKLNICTQQQALEYIGaKVKTMRRQKLTILQEGIEAIATT-----IIAHLTVEALDFRE--KALYIATM 340
Cdd:pfam04561 81 QMLELLKPELEEAENIYTQEEALDYIG-KGFALRRGEEPRLQRAREILYSRdpkynLNKHLGLNEPFENErlKAQDILYM 159
|
170 180
....*....|....*....|....*.
gi 2306256062 341 TRRVVMAMHNPKMVDDRDYVGNKRLE 366
Cdd:pfam04561 160 IDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
543-604 |
1.63e-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: 114.39 E-value: 1.63e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2306256062 543 VYLNGTLIGTTKFPSNFVSRFRFLRRTGKVSEFISIYTNDHHNAVHIATDGGRICRPLIIVK 604
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
625-665 |
1.34e-11 |
|
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: 60.25 E-value: 1.34e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 2306256062 625 FDDFLKLGLVEYLDVNEENDSYIALYEKDI------------THDITHLEIEP 665
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLeessreeregpyAHTYTHCEIHP 53
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
45-1125 |
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: 1149.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 45 LVKQHLDSFNYFVDVDLKKIIKANQ-LILSDVDPEFYLKYVDIRVGQ-RSGSPHKDQLVPPHECRLRDMTYSAPIYVDIE 122
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPpITDTDDDGRLKLKFGDIYLGKpKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 123 YTRGRNIIM-HKNVEIGRMPIMLRSNKCILHGADEKMMARLSECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEadEKK 201
Cdd:cd00653 81 LTVNDKGKIkEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 202 DIVQASVTS---------STHERKSKTYVVTKNGKIYLKHnsiaeevpivivlkaagiisdleimqlvcgndssyqdifs 272
Cdd:cd00653 159 GKRIYTKTSipsyspyrgSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 273 vnleeaaklnictQQQALEYIGAKVktmrrqkltilqegieaiattiiahltvealdfrekaLYIATMTRRVVMAMHNPK 352
Cdd:cd00653 199 -------------QEEALKYIGKRF-------------------------------------EDLIYMIRKLILLVLGKG 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 353 MVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMeydalLSINVHSNNITSGLNRAISTGNWSL 432
Cdd:cd00653 229 KLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIKEFLATGNWGS 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 433 KRFKMERAGVTHVLSRLSYISALGMMTRISS-QFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITtd 511
Cdd:cd00653 304 KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 512 deeepirklcyvlgvepislldsaslhlnygvylngtligttkfpsnfvsrfrflrrtgkvsefisiytndhhnavhiat 591
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 592 dgGRICRPLIIVKDgksmveaehlkrllsgelvfddflklglveyldvneendsyialyekdithDITHLEIEPFTVLGA 671
Cdd:cd00653 382 --GRIERPYRIVEK---------------------------------------------------EVTHIEISPSQILSV 408
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 672 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 751
Cdd:cd00653 409 AASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYS 488
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 752 GYDIEDALVLNKSSIDRGFGRCETRRKTTTVLKKYPNHTKDalcGMRVDENGEAIWQHESLGPDGLGEVGLKIRSGQIYI 831
Cdd:cd00653 489 GYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEE---ITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILV 565
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 832 NKSVPVQSSDAMAVNQAQ---YRETPVIYRAPELSIIDQVMMSTSDNDQD---LIKVLLRQNRRPELGDKFSSRHGQKGV 905
Cdd:cd00653 566 GKITPKGETESTPIFGEKardVRDTSLKYPGGEKGIVDDVKIFSRELNDGgnkLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 906 CGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVDQGFNYSGK 985
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGK 725
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 986 DMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLE 1065
Cdd:cd00653 726 EVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQE 805
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1066 RLMISSDAFEVDVCSNCGLMGYSGWCSTCKSAEHIIKMTIPYAAKLLFQELLAMNIAPRL 1125
Cdd:cd00653 806 RLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
32-1131 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1075.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 32 KWNLLPAFLKVKGLVKQHLDSFNYFVDVDLKKIIKANQLILSDVdPEFYLKYVDIRVGQ-----RSGSPHkdqLVPPHEC 106
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEpeikeADGSER---PITPMEA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 107 RLRDMTYSAPIYVDIEYTRGRNIIMHKNVEIGRMPIMLRSNKCILHGADEKMMARLSECPLDPGGYFIVNGTEKVILVQE 186
Cdd:PRK08565 77 RLRNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 187 QLSKNRIIVEADEKKDIVQ--ASVTSSTHERKSKTYVV-TKNGKIYLKHNSIAEEVPIVIVLKAAGIISDLEIMQLVcGN 263
Cdd:PRK08565 157 DLAPNRVLVDKGEAGSSIThtAKVISSRAGYRAQVTVErRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAV-SL 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 264 DSSYQDIFSVNLEEAAKLNIcTQQQALEYIGAKV-----KTMRRQKLTilqegiEAIATTIIAHLTVEALDFREKALYIA 338
Cdd:PRK08565 236 DPEIQQELLPSLEQASSIAA-TVEDALDYIGKRVaigqpREYRIERAE------QILDKYLLPHLGTSPEDRIKKAYFLG 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 339 TMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVLKKpnramEYDALLSINVHSNNIT 418
Cdd:PRK08565 309 QMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYAR-----GRKLDLRAIVRPDIIT 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 419 SGLNRAISTGNWSlkrfkMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGL 498
Cdd:PRK08565 384 ERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGL 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 499 VKNLALMTHITTDDEEEPIRKLCYVLGVEPI-SLLDSASLHLnYGVYLNGTLIGTTKFPSNFVSRFRFLRRTGKVSEFIS 577
Cdd:PRK08565 459 VKNLALMAQISVGVDEEEVEEILYELGVVPVeEAREEEYISW-SRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN 537
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 578 I--YTNDHHNAVHIATDGGRICRPLIIVKDGKSMVEAEHLKRLLSGELVFDDFLKLGLVEYLDVNEENDSYIALYEKDIT 655
Cdd:PRK08565 538 VayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLT 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 656 HDITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYD 735
Cdd:PRK08565 618 PEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYN 697
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 736 KLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCETRRKTTTVLKKYPNHTKDA-------LCGMRvdenGEAIWQ 808
Cdd:PRK08565 698 DRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKieipepnVRGYR----GEEYYR 773
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 809 HesLGPDGLGEVGLKIRSGQIYINKSVP---VQSSDAMAVNQAQYRETPVIYRAPELSIIDQVMMSTSDNDQDLIKVLLR 885
Cdd:PRK08565 774 K--LDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVR 851
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 886 QNRRPELGDKFSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGG 965
Cdd:PRK08565 852 DLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYG 931
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 966 SKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLR 1045
Cdd:PRK08565 932 EPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLR 1011
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1046 LGEMERDCVIAYGASQLLLERLMISSDAFEVDVCSNCGLMGYSG------WCSTCKSAEHIIKMTIPYAAKLLFQELLAM 1119
Cdd:PRK08565 1012 FGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSM 1091
|
1130
....*....|..
gi 2306256062 1120 NIAPRLRLEDIF 1131
Cdd:PRK08565 1092 GISPRLKLGDKV 1103
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
543-1129 |
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: 726.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 543 VYLNGTLIGTTKFPSNFVSRFRFLRRTGKVSEFISIYTNDHHNAVHIATDGGRICRPLIIVKDGKSMVEAEHLKRLLSGE 622
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 623 LVFDDFLKLGLVEYLDVNEENDSYIALYEKDITHDITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIA 702
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 703 YNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCETRRKTTTV 782
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 783 LKKYPNHTKDALC-------GMRvdenGEAIWQHesLGPDGLGEVGLKIRSGQIYINKSVP---VQSSDAMAVNQAQYRE 852
Cdd:TIGR03670 241 ERRYPGGQEDRFEipepdvrGYR----GEEAYKH--LDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLVTERRRD 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 853 TPVIYRAPELSIIDQVMMSTSDNDQDLIKVLLRQNRRPELGDKFSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHG 932
Cdd:TIGR03670 315 TSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHA 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 933 FPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLK 1012
Cdd:TIGR03670 395 IPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLH 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1013 HMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCSNCGLMGY----- 1087
Cdd:TIGR03670 475 HMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrk 554
|
570 580 590 600
....*....|....*....|....*....|....*....|...
gi 2306256062 1088 -SGWCSTCKSAEHIIKMTIPYAAKLLFQELLAMNIAPRLRLED 1129
Cdd:TIGR03670 555 gTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
37-1129 |
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: 612.11 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 37 PAFLKVKGLVKQHLDSFNYFVDVDLKKIIKANQLIlSDVDPEFYLKYVDIRVGQrsgsPhkdqLVPPHECRLRDMTYSAP 116
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPI-EDFTGNLSLEFGDYRLGE----P----KYTPEECKERDLTYAAP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 117 IYVDIEYT-RGRNIIMHKNVEIGRMPIMLRSnkcilhgadekmmarlsecpldpgGYFIVNGTEKVILVQEQLSKNRIIV 195
Cdd:COG0085 79 LYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVYFV 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 196 EADEK--KDIVQASVTSStheRKSKTYVVT-KNGKIYLKHNSiAEEVPIVIVLKAAGIISDLEIMQLVcgNDSSYQDIFS 272
Cdd:COG0085 135 EEEDKsgKDLYSAKVIPS---RGAWLEFETdKDGTIYVRIDR-KRKIPVTVLLRALGLETDEEILEAF--GDDPIQEYIL 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 273 VNLEeaaKLNICTQQQALEYIGAKV-----KTMRRQKlTILQEGIEAIATTIIAH-----------LTVEALDFREKALY 336
Cdd:COG0085 209 ATLE---KDNTKTQEEALLEIYRKLrpgepPTIERAE-QLLDNLFFDPKRYDLAHvgrykinkklgLDVPPEDRVLTAED 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 337 IATMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKlsiDKVLKKPNRAMEYDALLSINVhsnn 416
Cdd:COG0085 285 IVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVR---ERMTTQDVEAITPQSLINIRP---- 357
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 417 ITSGLNRAISTGNwsLKRFkMER----AGVTHvLSRLSyisALGM--MTRISSQFEksrkVsgpRALQPSQFGMLCTADT 490
Cdd:COG0085 358 VVAAIKEFFGSSQ--LSQF-MDQtnplSELTH-KRRLS---ALGPggLSRERAGFE----V---RDVHPSHYGRMCPIET 423
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 491 PEGEACGLVKNLALMthittddeeepirklcyvlgvepislldsaslhlnygvylngtligttkfpsnfvsrfrflrrtG 570
Cdd:COG0085 424 PEGPNIGLIGSLALY----------------------------------------------------------------A 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 571 KVSEFisiytndhhnavhiatdgGRICRPLIIVKDGKsmveaehlkrllsgelVFDDflklglVEYLDVNEENDSYIALY 650
Cdd:COG0085 440 RVNEY------------------GFIETPYRKVENGK----------------VTDE------IEYLTADEEENYYIAQA 479
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 651 EKDI-----------------------THDITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYN-QF 706
Cdd:COG0085 480 NAPLdedgnfleervlvryrgeevlvpPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEaPL 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 707 KRIDTLLYL-----MIYPQQPMVKT----KTIELI------DYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFG 771
Cdd:COG0085 560 LHYPLQKFQrsnqgTCINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVL 639
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 772 R--------CETRR-------KTTTVlkkyPNHTKDALcgmrvdengeaiwqhESLGPDGLGEVGLKIRSGQIYINKSVP 836
Cdd:COG0085 640 TsihieeyeIEARDtklgpeeITRDI----PNVSEEAL---------------RNLDEDGIIRIGAEVKGGDILVGKVTP 700
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 837 VQSSD---------AMAVNQAQY-RETPVIYRAPELSIIDQVMMSTSDNDQDL-------IKVLLRQNRRPELGDKFSSR 899
Cdd:COG0085 701 KGETEltpeerllrAIFGEKAREvRDTSLRVPHGEKGKVIDVKVFSREEGDELppgvnklVRVYVAQKRKIEVGDKLAGR 780
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 900 HGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVDQG 979
Cdd:COG0085 781 HGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAG 860
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 980 FNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGA 1059
Cdd:COG0085 861 LPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGA 940
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1060 SQLLLERLMISSDafevDVCsncglmGYSGWCSTCKSAEHIIKMTIPYAAKLLFQELLAMNIAPRLRLED 1129
Cdd:COG0085 941 AYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
672-1040 |
3.48e-175 |
|
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: 518.62 E-value: 3.48e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 672 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 751
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 752 GYDIEDALVLNKSSIDRGFGRCETRRktTTVLKKYPNHTKDALCgMRVDENGEAIWQHesLGPDGLGEVGLKIRSGQIYI 831
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEIT-RDIPNVSEEALKK--LDEDGIVRVGAEVKPGDILV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 832 NKSVPVQSSDAMAV----NQAQYRETPVIYRAPELSIIDQVMM-STSDNDQDLIKVLLRQNRRPELGDKFSSRHGQKGVC 906
Cdd:pfam00562 156 GKVGPTELTKLLRAifgeKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 907 GIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSK--LEDMSKILVDQGFNYSG 984
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYYG 315
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 2306256062 985 KDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1040
Cdd:pfam00562 316 KEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
189-366 |
7.14e-46 |
|
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: 163.29 E-value: 7.14e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 189 SKNRIIVEADEKKDIVQASVTSSTHERKSKTYVVTKNGKIYLKHN-SIAEEVPIVIVLKAAGIISDLEIMQLVCGNDSSY 267
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGSWLKLEIDGKTLIWSRpSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 268 QDIFSVNLEEAAKLNICTQQQALEYIGaKVKTMRRQKLTILQEGIEAIATT-----IIAHLTVEALDFRE--KALYIATM 340
Cdd:pfam04561 81 QMLELLKPELEEAENIYTQEEALDYIG-KGFALRRGEEPRLQRAREILYSRdpkynLNKHLGLNEPFENErlKAQDILYM 159
|
170 180
....*....|....*....|....*.
gi 2306256062 341 TRRVVMAMHNPKMVDDRDYVGNKRLE 366
Cdd:pfam04561 160 IDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
543-604 |
1.63e-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: 114.39 E-value: 1.63e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2306256062 543 VYLNGTLIGTTKFPSNFVSRFRFLRRTGKVSEFISIYTNDHHNAVHIATDGGRICRPLIIVK 604
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
625-665 |
1.34e-11 |
|
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: 60.25 E-value: 1.34e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 2306256062 625 FDDFLKLGLVEYLDVNEENDSYIALYEKDI------------THDITHLEIEP 665
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLeessreeregpyAHTYTHCEIHP 53
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
45-1125 |
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: 1149.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 45 LVKQHLDSFNYFVDVDLKKIIKANQ-LILSDVDPEFYLKYVDIRVGQ-RSGSPHKDQLVPPHECRLRDMTYSAPIYVDIE 122
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPpITDTDDDGRLKLKFGDIYLGKpKVEEGGVTRKLTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 123 YTRGRNIIM-HKNVEIGRMPIMLRSNKCILHGADEKMMARLSECPLDPGGYFIVNGTEKVILVQEQLSKNRIIVEadEKK 201
Cdd:cd00653 81 LTVNDKGKIkEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 202 DIVQASVTS---------STHERKSKTYVVTKNGKIYLKHnsiaeevpivivlkaagiisdleimqlvcgndssyqdifs 272
Cdd:cd00653 159 GKRIYTKTSipsyspyrgSWLEVKSDKKKDRIYVRIDLKR---------------------------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 273 vnleeaaklnictQQQALEYIGAKVktmrrqkltilqegieaiattiiahltvealdfrekaLYIATMTRRVVMAMHNPK 352
Cdd:cd00653 199 -------------QEEALKYIGKRF-------------------------------------EDLIYMIRKLILLVLGKG 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 353 MVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMeydalLSINVHSNNITSGLNRAISTGNWSL 432
Cdd:cd00653 229 KLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLT-----PQLLINSKPITSGIKEFLATGNWGS 303
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 433 KRFKMERAGVTHVLSRLSYISALGMMTRISS-QFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITtd 511
Cdd:cd00653 304 KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-- 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 512 deeepirklcyvlgvepislldsaslhlnygvylngtligttkfpsnfvsrfrflrrtgkvsefisiytndhhnavhiat 591
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 592 dgGRICRPLIIVKDgksmveaehlkrllsgelvfddflklglveyldvneendsyialyekdithDITHLEIEPFTVLGA 671
Cdd:cd00653 382 --GRIERPYRIVEK---------------------------------------------------EVTHIEISPSQILSV 408
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 672 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 751
Cdd:cd00653 409 AASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYS 488
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 752 GYDIEDALVLNKSSIDRGFGRCETRRKTTTVLKKYPNHTKDalcGMRVDENGEAIWQHESLGPDGLGEVGLKIRSGQIYI 831
Cdd:cd00653 489 GYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEE---ITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILV 565
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 832 NKSVPVQSSDAMAVNQAQ---YRETPVIYRAPELSIIDQVMMSTSDNDQD---LIKVLLRQNRRPELGDKFSSRHGQKGV 905
Cdd:cd00653 566 GKITPKGETESTPIFGEKardVRDTSLKYPGGEKGIVDDVKIFSRELNDGgnkLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 906 CGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVDQGFNYSGK 985
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGK 725
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 986 DMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLE 1065
Cdd:cd00653 726 EVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQE 805
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1066 RLMISSDAFEVDVCSNCGLMGYSGWCSTCKSAEHIIKMTIPYAAKLLFQELLAMNIAPRL 1125
Cdd:cd00653 806 RLTIKSDDVVARVCVKCGIILSANLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
32-1131 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 1075.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 32 KWNLLPAFLKVKGLVKQHLDSFNYFVDVDLKKIIKANQLILSDVdPEFYLKYVDIRVGQ-----RSGSPHkdqLVPPHEC 106
Cdd:PRK08565 1 RWTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKTEI-PGLKIVLGKIRVGEpeikeADGSER---PITPMEA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 107 RLRDMTYSAPIYVDIEYTRGRNIIMHKNVEIGRMPIMLRSNKCILHGADEKMMARLSECPLDPGGYFIVNGTEKVILVQE 186
Cdd:PRK08565 77 RLRNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 187 QLSKNRIIVEADEKKDIVQ--ASVTSSTHERKSKTYVV-TKNGKIYLKHNSIAEEVPIVIVLKAAGIISDLEIMQLVcGN 263
Cdd:PRK08565 157 DLAPNRVLVDKGEAGSSIThtAKVISSRAGYRAQVTVErRKDGTIYVSFPAVPGKIPFVILMRALGLETDRDIVYAV-SL 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 264 DSSYQDIFSVNLEEAAKLNIcTQQQALEYIGAKV-----KTMRRQKLTilqegiEAIATTIIAHLTVEALDFREKALYIA 338
Cdd:PRK08565 236 DPEIQQELLPSLEQASSIAA-TVEDALDYIGKRVaigqpREYRIERAE------QILDKYLLPHLGTSPEDRIKKAYFLG 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 339 TMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVLKKpnramEYDALLSINVHSNNIT 418
Cdd:PRK08565 309 QMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYAR-----GRKLDLRAIVRPDIIT 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 419 SGLNRAISTGNWSlkrfkMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGL 498
Cdd:PRK08565 384 ERIRHALATGNWV-----GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGL 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 499 VKNLALMTHITTDDEEEPIRKLCYVLGVEPI-SLLDSASLHLnYGVYLNGTLIGTTKFPSNFVSRFRFLRRTGKVSEFIS 577
Cdd:PRK08565 459 VKNLALMAQISVGVDEEEVEEILYELGVVPVeEAREEEYISW-SRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN 537
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 578 I--YTNDHHNAVHIATDGGRICRPLIIVKDGKSMVEAEHLKRLLSGELVFDDFLKLGLVEYLDVNEENDSYIALYEKDIT 655
Cdd:PRK08565 538 VayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLT 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 656 HDITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYD 735
Cdd:PRK08565 618 PEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYN 697
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 736 KLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCETRRKTTTVLKKYPNHTKDA-------LCGMRvdenGEAIWQ 808
Cdd:PRK08565 698 DRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKieipepnVRGYR----GEEYYR 773
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 809 HesLGPDGLGEVGLKIRSGQIYINKSVP---VQSSDAMAVNQAQYRETPVIYRAPELSIIDQVMMSTSDNDQDLIKVLLR 885
Cdd:PRK08565 774 K--LDEDGIVSPEVEVKGGDVLIGKTSPprfLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVR 851
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 886 QNRRPELGDKFSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGG 965
Cdd:PRK08565 852 DLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYG 931
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 966 SKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLR 1045
Cdd:PRK08565 932 EPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLR 1011
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1046 LGEMERDCVIAYGASQLLLERLMISSDAFEVDVCSNCGLMGYSG------WCSTCKSAEHIIKMTIPYAAKLLFQELLAM 1119
Cdd:PRK08565 1012 FGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIAWYDrrknkyVCPIHGDKGNISPVEVSYAFKLLLQELMSM 1091
|
1130
....*....|..
gi 2306256062 1120 NIAPRLRLEDIF 1131
Cdd:PRK08565 1092 GISPRLKLGDKV 1103
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
543-1129 |
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: 726.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 543 VYLNGTLIGTTKFPSNFVSRFRFLRRTGKVSEFISIYTNDHHNAVHIATDGGRICRPLIIVKDGKSMVEAEHLKRLLSGE 622
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGKPKLTREHVEKLKEGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 623 LVFDDFLKLGLVEYLDVNEENDSYIALYEKDITHDITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIA 702
Cdd:TIGR03670 81 LTWDDLVKQGVIEYLDAEEEENAYIALDPEELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 703 YNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCETRRKTTTV 782
Cdd:TIGR03670 161 ANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 783 LKKYPNHTKDALC-------GMRvdenGEAIWQHesLGPDGLGEVGLKIRSGQIYINKSVP---VQSSDAMAVNQAQYRE 852
Cdd:TIGR03670 241 ERRYPGGQEDRFEipepdvrGYR----GEEAYKH--LDEDGIVYPEVEVKGGDVLIGKTSPprfLEELREFGLVTERRRD 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 853 TPVIYRAPELSIIDQVMMSTSDNDQDLIKVLLRQNRRPELGDKFSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHG 932
Cdd:TIGR03670 315 TSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHA 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 933 FPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLK 1012
Cdd:TIGR03670 395 IPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLH 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1013 HMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCSNCGLMGY----- 1087
Cdd:TIGR03670 475 HMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIAWedkrk 554
|
570 580 590 600
....*....|....*....|....*....|....*....|...
gi 2306256062 1088 -SGWCSTCKSAEHIIKMTIPYAAKLLFQELLAMNIAPRLRLED 1129
Cdd:TIGR03670 555 gTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
543-1129 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 725.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 543 VYLNGTLIGTTKFPSNFVSRFRFLRRTGKVSEFISIYTNDHHNAVHIATDGGRICRPLIIVKDGKSMVEAEHLKRLLSGE 622
Cdd:PRK07225 7 VYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKNGE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 623 LVFDDFLKLGLVEYLDVNEENDSYIALYEKDITHDITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIA 702
Cdd:PRK07225 87 LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 703 YNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFGRCETRRKTTTV 782
Cdd:PRK07225 167 ANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 783 LKKYPNHTKDALC-------GMRvdenGEAIWQHesLGPDGLGEVGLKIRSGQIYINKSVP---VQSSDAMAVNQAQYRE 852
Cdd:PRK07225 247 ERRYPGGQEDRFEipdkdvrGYR----GEEAYRH--LDEDGLVNPETEVKEGDVLIGKTSPprfLEEPDDFGISPEKRRE 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 853 TPVIYRAPELSIIDQVMMSTSDNDQDLIKVLLRQNRRPELGDKFSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHG 932
Cdd:PRK07225 321 TSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHA 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 933 FPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLK 1012
Cdd:PRK07225 401 IPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLH 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1013 HMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCSNCGLMGY----- 1087
Cdd:PRK07225 481 HMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIydkkr 560
|
570 580 590 600
....*....|....*....|....*....|....*....|...
gi 2306256062 1088 -SGWCSTCKSAEHIIKMTIPYAAKLLFQELLAMNIAPRLRLED 1129
Cdd:PRK07225 561 nRKYCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELED 603
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
37-1129 |
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: 612.11 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 37 PAFLKVKGLVKQHLDSFNYFVDVDLKKIIKANQLIlSDVDPEFYLKYVDIRVGQrsgsPhkdqLVPPHECRLRDMTYSAP 116
Cdd:COG0085 8 KEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPI-EDFTGNLSLEFGDYRLGE----P----KYTPEECKERDLTYAAP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 117 IYVDIEYT-RGRNIIMHKNVEIGRMPIMLRSnkcilhgadekmmarlsecpldpgGYFIVNGTEKVILVQEQLSKNRIIV 195
Cdd:COG0085 79 LYVKVRLVnKETGEIKEQEVFMGDFPLMTDS------------------------GTFIINGTERVIVSQLVRSPGVYFV 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 196 EADEK--KDIVQASVTSStheRKSKTYVVT-KNGKIYLKHNSiAEEVPIVIVLKAAGIISDLEIMQLVcgNDSSYQDIFS 272
Cdd:COG0085 135 EEEDKsgKDLYSAKVIPS---RGAWLEFETdKDGTIYVRIDR-KRKIPVTVLLRALGLETDEEILEAF--GDDPIQEYIL 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 273 VNLEeaaKLNICTQQQALEYIGAKV-----KTMRRQKlTILQEGIEAIATTIIAH-----------LTVEALDFREKALY 336
Cdd:COG0085 209 ATLE---KDNTKTQEEALLEIYRKLrpgepPTIERAE-QLLDNLFFDPKRYDLAHvgrykinkklgLDVPPEDRVLTAED 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 337 IATMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKlsiDKVLKKPNRAMEYDALLSINVhsnn 416
Cdd:COG0085 285 IVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVR---ERMTTQDVEAITPQSLINIRP---- 357
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 417 ITSGLNRAISTGNwsLKRFkMER----AGVTHvLSRLSyisALGM--MTRISSQFEksrkVsgpRALQPSQFGMLCTADT 490
Cdd:COG0085 358 VVAAIKEFFGSSQ--LSQF-MDQtnplSELTH-KRRLS---ALGPggLSRERAGFE----V---RDVHPSHYGRMCPIET 423
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 491 PEGEACGLVKNLALMthittddeeepirklcyvlgvepislldsaslhlnygvylngtligttkfpsnfvsrfrflrrtG 570
Cdd:COG0085 424 PEGPNIGLIGSLALY----------------------------------------------------------------A 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 571 KVSEFisiytndhhnavhiatdgGRICRPLIIVKDGKsmveaehlkrllsgelVFDDflklglVEYLDVNEENDSYIALY 650
Cdd:COG0085 440 RVNEY------------------GFIETPYRKVENGK----------------VTDE------IEYLTADEEENYYIAQA 479
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 651 EKDI-----------------------THDITHLEIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYN-QF 706
Cdd:COG0085 480 NAPLdedgnfleervlvryrgeevlvpPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEaPL 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 707 KRIDTLLYL-----MIYPQQPMVKT----KTIELI------DYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDRGFG 771
Cdd:COG0085 560 LHYPLQKFQrsnqgTCINQRPIVRVgdrvEKGDVLadgpatDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVL 639
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 772 R--------CETRR-------KTTTVlkkyPNHTKDALcgmrvdengeaiwqhESLGPDGLGEVGLKIRSGQIYINKSVP 836
Cdd:COG0085 640 TsihieeyeIEARDtklgpeeITRDI----PNVSEEAL---------------RNLDEDGIIRIGAEVKGGDILVGKVTP 700
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 837 VQSSD---------AMAVNQAQY-RETPVIYRAPELSIIDQVMMSTSDNDQDL-------IKVLLRQNRRPELGDKFSSR 899
Cdd:COG0085 701 KGETEltpeerllrAIFGEKAREvRDTSLRVPHGEKGKVIDVKVFSREEGDELppgvnklVRVYVAQKRKIEVGDKLAGR 780
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 900 HGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSKLEDMSKILVDQG 979
Cdd:COG0085 781 HGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAG 860
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 980 FNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGA 1059
Cdd:COG0085 861 LPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGA 940
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1060 SQLLLERLMISSDafevDVCsncglmGYSGWCSTCKSAEHIIKMTIPYAAKLLFQELLAMNIAPRLRLED 1129
Cdd:COG0085 941 AYTLQERLTIKSD----DVC------GRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
672-1040 |
3.48e-175 |
|
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: 518.62 E-value: 3.48e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 672 VAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKRIDTLLYLMIYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYS 751
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 752 GYDIEDALVLNKSSIDRGFGRCETRRktTTVLKKYPNHTKDALCgMRVDENGEAIWQHesLGPDGLGEVGLKIRSGQIYI 831
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPIEEIT-RDIPNVSEEALKK--LDEDGIVRVGAEVKPGDILV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 832 NKSVPVQSSDAMAV----NQAQYRETPVIYRAPELSIIDQVMM-STSDNDQDLIKVLLRQNRRPELGDKFSSRHGQKGVC 906
Cdd:pfam00562 156 GKVGPTELTKLLRAifgeKARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 907 GIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGSLEYGTCFGGSK--LEDMSKILVDQGFNYSG 984
Cdd:pfam00562 236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYNYYG 315
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 2306256062 985 KDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSR 1040
Cdd:pfam00562 316 KEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
44-419 |
3.59e-148 |
|
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: 449.52 E-value: 3.59e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 44 GLVKQHLDSFNYFVDVDLKKIIKANQLILSDVDPE--------FYLKYVDIRVG-----QRSGSPHKdqlVPPHECRLRD 110
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQhpgengdkLSLKFGQIRLGkpmfdETDGSTRE---IYPQECRLRN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 111 MTYSAPIYVDIEYTR-GRNIIMHKNVEIGRMPIMLRSNKCILHGADEKMMARLSECPLDPGGYFIVNGTEKVILVQEQLS 189
Cdd:pfam04563 78 LTYSAPLYVDLELSVyNGEDIKPIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRS 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 190 KNRIIV--EADEKKDIVQASVTSSTHE--RKSKTYVV-----TKNGKIYLKHNSIAEEVPIVIVLKAAGIISDLEIMQLV 260
Cdd:pfam04563 158 RNHPIVfkKADPKKRGSVASVRSSAEIsvRPDSTSWVnvleyLSNGTIYFKFPYIKKEIPIVIILRALGFTSDREIFELI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 261 CG--NDSSYQDIFSVNLEEAAKLNICTQQQALEYIGAKVKT---MRRQKLTILQEGIEAIATTIIAHLTVEALDFREKAL 335
Cdd:pfam04563 238 CYdvNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEILQKEVLPHLGTYELDETKKAY 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 336 YIATMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMeydalLSINVHSN 415
Cdd:pfam04563 318 FIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLM-----LQLLVNAK 392
|
....
gi 2306256062 416 NITS 419
Cdd:pfam04563 393 PITS 396
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
30-529 |
1.15e-111 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 356.95 E-value: 1.15e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 30 DDKWNLLPAFLKVKGLVKQHLDSFNYFVDVDLKKIIKANQLILSDVDPEFYLKYVDIRVGQRS-----GSPHKdqlVPPH 104
Cdd:PRK09606 3 EDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVvkeadGSERE---IYPM 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 105 ECRLRDMTYSAPIYVDIEYTRGRNIIMHKNVEIGRMPIMLRSNKCILHGADEKMMARLSECPLDPGGYFIVNGTEKVILV 184
Cdd:PRK09606 80 EARLRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMT 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 185 QEQLSKNRIIVEADEK--KDIVQASVTSSTHERKSKTYV-VTKNGKIYLKHNSIAEEVPIVIVLKAAGIISDLEIMQLVc 261
Cdd:PRK09606 160 LEDLAPNKILVEKDERygDRIEVAKVFSQRRGYRALVTVeRNRDGLLEVSFPSVPGSIPFVILMRALGLETDEEIVEAV- 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 262 GNDSSYQDIFSVNLEEAaklNICTQQQALEYIGAKV-----KTMRRQKLTilqegiEAIATTIIAHLTVEALDFREKALY 336
Cdd:PRK09606 239 SDDPEIVKFMLENLEEA---EVDTQEEALEYIGKRVapgqtKEYRIKRAE------YVIDRYLLPHLGVEPEVRRAKAHY 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 337 IATMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVLKKpNRAmeydalLSIN--VHS 414
Cdd:PRK09606 310 LGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMR-NRE------LSIKtaVRS 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 415 NNITSGLNRAISTGNWslkrfKMERAGVTHVLSRLSYISALGMMTRISSQFEKSRKVSGPRALQPSQFGMLCTADTPEGE 494
Cdd:PRK09606 383 DVLTERLEHAMATGNW-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGP 457
|
490 500 510
....*....|....*....|....*....|....*
gi 2306256062 495 ACGLVKNLALMTHITTDDEEEPIRKLCYVLGVEPI 529
Cdd:PRK09606 458 NCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
37-1121 |
5.04e-68 |
|
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: 248.81 E-value: 5.04e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 37 PAFLKVKGLVKQHLDSFNYFVDVD----------LKKIIKANQLIlSDVDPEFYLKYVDIRVGQRSgsphkdqlVPPHEC 106
Cdd:TIGR02013 12 PEVLEVPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPI-EDYTGNIELEYLSYRLGEPK--------YSVEEC 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 107 RLRDMTYSAPIYVDIEYT----RGRNIIMHKNVEIGRMPIMLRSnkcilhgadekmmarlsecpldpgGYFIVNGTEKVI 182
Cdd:TIGR02013 83 KERGLTYSAPLKVKLRLInkeeDGTKEIKEQDVYMGDIPLMTDR------------------------GTFIINGAERVV 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 183 LVQEQLSKNRIIVEA----DEKKDIVQASVTSStheRKSKTYVVT-KNGKIYLKHNSiAEEVPIVIVLKAAGiisdLEIM 257
Cdd:TIGR02013 139 VSQLHRSPGVFFSSEkdttKSGKVLFSARIIPY---RGSWLEFETdKKDVLYVRIDR-KRKLPATVLLRALG----YTID 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 258 QLVCGNDSSYQDIFSVNLEEAAKlnicTQQQALEYIgakVKTMRRQkltilqegiEAiATTIIAHLTVEALDFREK---- 333
Cdd:TIGR02013 211 TLILNRLGSGEYIRNTLRKDPTN----SEEEALVEI---YRKLRPG---------EP-PTVEAARSLLENLFFDPKrydl 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 334 ----------------ALYIATMTRRVVMA-------MHNPKM-VDDRDYVGNKRLELAGQLISllfedlfkkfnNDFK- 388
Cdd:TIGR02013 274 grvgryklnkklgldvPESIGVLTKEDIIAtikylikLRNGKGeIDDIDHLGNRRIRSVGELLQ-----------NQFRv 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 389 --LSIDKVLKKPNRAMEYDALLSIN-VHSNNITSGLNRAISTGnwSLKRFkMER----AGVTHVlSRLSyisALGM--MT 459
Cdd:TIGR02013 343 glARMERIVRERMSTQDTDTLTPQDlINAKPISAAIKEFFGSS--QLSQF-MDQtnplAELTHK-RRLS---ALGPggLT 415
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 460 RISSQFEKsrkvsgpRALQPSQFGMLCTADTPEGEACGLVKNLAlmthittddeeepirklcyvlgvepislldsaslhl 539
Cdd:TIGR02013 416 RERAGFEV-------RDVHPTHYGRICPIETPEGPNIGLINSLS------------------------------------ 452
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 540 nygVYlngtligttkfpsnfvsrfrflrrtGKVSEFisiytndhhnavhiatdgGRICRPLIIVKDGKSMVEAEhlkrll 619
Cdd:TIGR02013 453 ---TY-------------------------ARVNEY------------------GFIETPYRKVKDGKVVVTDE------ 480
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 620 sgelvfddflklglVEYLDVNEENDSYIA-------------------LYEKDIT----HDITHLEIEPFTVLGAVAGLI 676
Cdd:TIGR02013 481 --------------IDYLTADEEDNYVIAqanapldengrfvedlvvaRYRGEITlvspDQVDYMDVSPKQVVSVAASLI 546
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 677 PYPHHNQSPRNTYQCAMGKQAI-------------------------------GAIAYNQFKRI---------DTLLYLM 716
Cdd:TIGR02013 547 PFLEHDDANRALMGSNMQRQAVpllrseaplvgtgmeakvardsgavivakrgGVVEYVDAKRIvirydedeeEPDGGID 626
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 717 IYP--------------QQPMV----KTKTIELI------DYDKLPAGQNATVAVMSYSGYDIEDALVLNK--------S 764
Cdd:TIGR02013 627 IYRllkyqrsnqdtcinQRPIVsvgdRVEAGDVLadgpstDLGELALGRNVLVAFMPWNGYNYEDAILISErlvkddvfT 706
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 765 SID--------RgfgrcETRRKTTTVLKKYPNHTKDALcgMRVDENGeaiwqheslgpdgLGEVGLKIRSGQIYINKSVP 836
Cdd:TIGR02013 707 SIHieeyeveaR-----DTKLGPEEITRDIPNVSEEAL--RNLDENG-------------IVRIGAEVKAGDILVGKVTP 766
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 837 VQSSD---------------AMAVNQAQYRETPviyrAPELSIIDQVMMSTSDNDQ------DLIKVLLRQNRRPELGDK 895
Cdd:TIGR02013 767 KGETEltpeekllraifgekARDVRDTSLRVPP----GVEGTVIDVKVFSREQGDElppgvnKLVKVYIAQKRKIQVGDK 842
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 896 FSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGslEYGTC-----FGGSKLED 970
Cdd:TIGR02013 843 MAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLG--RKGVPiatpvFDGASEEE 920
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 971 MSKILVDQGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEME 1050
Cdd:TIGR02013 921 IKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEME 1000
|
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2306256062 1051 RDCVIAYGASQLLLERLMISSDafevDVcsncglmgySGWCSTCKS---AEHIIKMTIPYAAKLLFQEL--LAMNI 1121
Cdd:TIGR02013 1001 VWALEAYGAAYTLQEMLTVKSD----DV---------VGRTKAYEAivkGENVPEPGIPESFNVLIKELqsLGLDI 1063
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
41-1121 |
1.59e-55 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 210.72 E-value: 1.59e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 41 KVKGLVKQHLDSFNYFVDVDLKKIIKANQLIlsdVDPEFYLKYVDIRVGQRSgsphKDQLVPPHECRLRDMTYSAPIYVD 120
Cdd:CHL00207 6 ALPDFLEIQRTSFCWFLNEGLNEELNIFSKI---FDYTGNLELLLFGKNYKL----KYPKYNLLSAKSYDSNYSIQIYLP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 121 IEYTRGR-NIIMHKNVEIGRMPIMLRSnkcilhgadekmmarlsecpldpgGYFIVNGTEKVILVQEQLSkNRIIVEADE 199
Cdd:CHL00207 79 LKFINLKtNKIKFINYLIGNLPKMTQR------------------------GTFIINGLERVIVSQIIRS-PGIYFKKEI 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 200 KKDIVQASVTSSTHERKS-KTYVVTKNGKIYLKHNSIaEEVPIVIVLKAAGIiSDLEIMQLVCGNDSSYQDIFSVNLE-- 276
Cdd:CHL00207 134 KKNSNKIYSATLIPNRGSwIKFELDKNKEIWIRIDKN-RKKPLIIFLKALGL-TDQDIYSRLTKSEFLKKLKPILLNSns 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 277 ---EAAKLNI---------CTQQQALEYIGAKVKTMRRQKLTILQEGIEAIATTIIAHLTVEALDFREkalyIATMTRRV 344
Cdd:CHL00207 212 ytnEEILLEIyknlspiepATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYED----ILSIIDKL 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 345 VMAMHNPKMVDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVlkkpnramEYDALLSINVHSNNITSGLNRA 424
Cdd:CHL00207 288 INLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTIC--------DIDSLSKFNLINPKPLIALIRE 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 425 ISTGNwSLKRFkMERagvTHVLSRLSY---ISALGmmtriSSQFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKN 501
Cdd:CHL00207 360 FFGSS-QLSQY-MDQ---TNPLSELTHkrrISILG-----PGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGS 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 502 LAlmTHITtddeeepIRKLCYVLgvepislldsaslhlnygVYLNGTLIGTTKFPSNFVsrfrFLrrTGKVSEFISIYTN 581
Cdd:CHL00207 430 LA--TNAR-------INKFGFIE------------------TPFYKVINGKVKKFGNPI----YL--TADSEDLYRIAPN 476
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 582 DhhnavhIATD-GGRICRPLIIVKDGKsmveaehlkrllsgelvfddflklglvEYLDVNEENDSYIAlyekdithdith 660
Cdd:CHL00207 477 D------INLNkNNYFKKNIIPVRYKQ---------------------------EFKTVNPSKVDFIA------------ 511
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 661 leIEPFTVLGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAI---------AYNQFKRIDTLL------------------ 713
Cdd:CHL00207 512 --ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLypekpivgtGYEKQIALDSGMtiisltegivvsvsayki 589
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 714 ------------YLMIYP---------QQPMV----KTKTIEL------IDYDKLPAGQNATVAVMSYSGYDIEDALVLN 762
Cdd:CHL00207 590 iiqddnnryihyYLQKYQrsnqntcinYRPIVwvgeKINIGQIladgsdIDNSELALGQNVLVAYMPWEGYNFEDAILIN 669
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 763 KS----------SIDR-GFGRCETRRKTTTVLKKYPNHtkdalcgmrvdenGEAIWQHesLGPDGLGEVGLKIRSGQIYI 831
Cdd:CHL00207 670 KRlvyedlftsiHIEKyEIELRQTKLGSEEITRNIPNV-------------SEYSLKN--LDENGIISIGSKVLAGDILV 734
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 832 NKSVPVQSSDAM---AVNQAQYRETPVI-----YRAPELS---IIDQVMMSTSDNDQ------DLIKVLLRQNRRPELGD 894
Cdd:CHL00207 735 GKITPKGESDQLpegKLLRAIFGEKAKDvkdtsLRMPNGGygrVIKVEIFSRSKGDElkfgyyLKIRVFIAQIRKIQVGD 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 895 KFSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAG--------VLNGSLEYGTcfggs 966
Cdd:CHL00207 815 KLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGdnlnkrfkILPFDEMYGS----- 889
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 967 kleDMSKILVDQGFN---------------YSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLT 1031
Cdd:CHL00207 890 ---EYSRILINNKLNqasiknneywlfnsyHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVT 966
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1032 RQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVdvcSNCGLMGYsgwcstcKSAEHIIKMTIPYAAKL 1111
Cdd:CHL00207 967 QQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQG---RNETLNAI-------VKGQPIPKPGTPESFKV 1036
|
1210
....*....|
gi 2306256062 1112 LFQELLAMNI 1121
Cdd:CHL00207 1037 LMRELQSLGL 1046
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
189-366 |
7.14e-46 |
|
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: 163.29 E-value: 7.14e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 189 SKNRIIVEADEKKDIVQASVTSSTHERKSKTYVVTKNGKIYLKHN-SIAEEVPIVIVLKAAGIISDLEIMQLVCGNDSSY 267
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGSWLKLEIDGKTLIWSRpSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 268 QDIFSVNLEEAAKLNICTQQQALEYIGaKVKTMRRQKLTILQEGIEAIATT-----IIAHLTVEALDFRE--KALYIATM 340
Cdd:pfam04561 81 QMLELLKPELEEAENIYTQEEALDYIG-KGFALRRGEEPRLQRAREILYSRdpkynLNKHLGLNEPFENErlKAQDILYM 159
|
170 180
....*....|....*....|....*.
gi 2306256062 341 TRRVVMAMHNPKMVDDRDYVGNKRLE 366
Cdd:pfam04561 160 IDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1042-1128 |
9.69e-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: 147.35 E-value: 9.69e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 1042 GGLRLGEMERDCVIAYGASQLLLERLMISSDAFEVDVCSNCGLMGYSGWCSTCKSAEHIIKMTIPYAAKLLFQELLAMNI 1121
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCGLYAAYNKCPICKGETDISPGYIPESFKLLFQELQSLGI 80
|
....*..
gi 2306256062 1122 APRLRLE 1128
Cdd:pfam04560 81 DPRLLLE 87
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
879-1072 |
2.63e-40 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 162.19 E-value: 2.63e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 879 LIKVLLRQNRRPELGDKFSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAGVLNGsLE 958
Cdd:PRK00405 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLG-IK 947
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 959 YGT-CFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEG 1037
Cdd:PRK00405 948 FATpVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
|
170 180 190
....*....|....*....|....*....|....*...
gi 2306256062 1038 RSRDGGLRLGEMErdcVIA---YGASQLLLERLMISSD 1072
Cdd:PRK00405 1028 KAQFGGQRFGEME---VWAleaYGAAYTLQEMLTVKSD 1062
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
872-1072 |
3.43e-31 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 132.72 E-value: 3.43e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 872 TSDNDQDLIKVLLRQNRRPELGDKFSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKAG 951
Cdd:CHL00001 796 GSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAG 875
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 952 vlnGSLE-----------YGtcfggsklEDMSKILVdqgF------------------NYSGKDMLYSGITGECLQAYIF 1002
Cdd:CHL00001 876 ---DLLNrhyriapfderYE--------QEASRKLV---FselyeaskqtanpwvfepEYPGKSRLFDGRTGDPFEQPVT 941
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2306256062 1003 FGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMErdcVIA---YGASQLLLERLMISSD 1072
Cdd:CHL00001 942 IGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEME---VWAlegFGVAYILQEMLTYKSD 1011
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
543-604 |
1.63e-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: 114.39 E-value: 1.63e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2306256062 543 VYLNGTLIGTTKFPSNFVSRFRFLRRTGKVSEFISIYTNDHHNAVHIATDGGRICRPLIIVK 604
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
879-1121 |
1.97e-28 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 124.65 E-value: 1.97e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 879 LIKVLLRQNRRPELGDKFSSRHGQKGVCGIIVQQEDMPFNDQGICPDIIMNPHGFPSRMTVGKMIEL---ISGK------ 949
Cdd:PRK09603 1077 KVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMhlgLVGKefgkqi 1156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 950 ----------------------AGVLNGS----------------LEYGT-----------CFGGSKLEDMSKILVDQGF 980
Cdd:PRK09603 1157 asmledktkdfakelrakmleiANAINEKdpltihalencsdeelLEYAKdwskgvkmaipVFEGISQEKFYKLFELAKI 1236
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 981 NYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGAS 1060
Cdd:PRK09603 1237 AMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAA 1316
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2306256062 1061 QLLLERLMISSDAFEvdvcsncglmGYSGWCSTCKSAEHIIKMTIPYAAKLLFQEL--LAMNI 1121
Cdd:PRK09603 1317 HTLKEMLTIKSDDIR----------GRENAYRAIAKGEQVGESEIPETFYVLTKELqsLALDI 1369
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
337-1072 |
2.57e-22 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 104.70 E-value: 2.57e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 337 IATMTRRVVMAMHNPKMVDDRDYVGNKRLELAGQLISllfedlfkkfnNDFKLSIDKVLKKPNRAMEYDALLSIN----V 412
Cdd:PRK14844 446 IIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIE-----------NQFRTGLLKLERAVVDSMSTSSLDKVSpsdfI 514
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 413 HSNNITSGLNRAISTGNwsLKRFkMERagvTHVLSRLSY---ISALGM--MTRISSQFEKsrkvsgpRALQPSQFGMLCT 487
Cdd:PRK14844 515 NPKVLTNVLRDFFNSSQ--LSQF-MDQ---TNPLSEITHkrrLSALGPggLTRERAGFEV-------RDVHPTHYGRICP 581
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 488 ADTPEGEACGLVKNLALMTHITTDDE-EEPIRKLCYVLG---VEPISLLDSASLHL--------NYGVYLNGTLIgtTKF 555
Cdd:PRK14844 582 IETPEGQNIGLINSLAIYARINKYGFiESPYRKVVNRVVtdqIEYLSAIDEGLYYIadtsakldENNCFVDDMLY--CRY 659
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 556 PSNFV----SRFRFLRRTGK-----VSEFISIYTNDHHNAVHIATDGGRICRPLIIVKDGKSMVEAEHLKRLLSGELVFD 626
Cdd:PRK14844 660 AGSFVmvssDQVSYIDVSPKqvisvAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLA 739
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 627 DflKLGLVeylDVNEENDSYIALYEKDithDITHLEIEPFtvlgavaglipypHHNQSPRNTYQCAMGKQAIGAIAyNQF 706
Cdd:PRK14844 740 K--RDGIV---DSSDSNSIVIRAFDKE---RVNYLDVDIY-------------HLRKFQRSNHNTCINQKPLVCVG-DYV 797
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 707 KRIDTLlylmiyPQQPMVKTKTIELidydklpaGQNATVAVMSYSGYDIEDALVLNKSSI------------------DR 768
Cdd:PRK14844 798 KEGDVI------ADGPAINSGELAL--------GQNLLVAFMSWQGYNFEDSIIISSEVVkkdlftsihieefecvvhDT 863
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 769 GFGRCETRRKTTTVLKKYPNHTKDA---LCGMRVDEN----GEAIWQHE-SLGPDG------LGEVGLKIRSGQIYINKS 834
Cdd:PRK14844 864 PLGSEKITRAIPGVNEENLYHLDDSgivKIGTRVGPGyilvGKVTPKPSlSLPPETkllmtiFGEKSFDCADSSLYTSPD 943
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 835 VP-----VQ---------SSDAMAVNQAQY----RETPVI------YRAPEL---------------------------- 862
Cdd:PRK14844 944 VEgtvidVQvftrrgveeNERALLIKQKEIndfeKERDYIinvtseYFYDELkkllinsgsqdrekfdsiereqwwgigl 1023
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 863 ---SIIDQVMMSTSDNDQ--------------------DL-------IKVLLRQNRRPELGDKFSSRHGQKGVCGIIVQQ 912
Cdd:PRK14844 1024 knqSISEQVKSLKKDFDEkvshaiaqfkrkveklhegyDLpqgvsmsVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPV 1103
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 913 EDMPFNDQGICPDIIMNPHGFPSRMTVGKMIELISGKA------------------------------------------ 950
Cdd:PRK14844 1104 EDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWAckklgekvgnildeinkiksafckgirslnddnftkfaaayl 1183
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 951 -----------------------GVLNGSLE------YGTC--------------------------------------- 962
Cdd:PRK14844 1184 dnkkienidddeitasvlntpnkNALNDELNelvenyLNSCksaysnlrnflievyscgsnvsicnnirdisdnnliefa 1263
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2306256062 963 -------------FGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFGPIYYQKLKHMVLDKMHARARGPRAV 1029
Cdd:PRK14844 1264 rklrdgipvaapvFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSL 1343
|
970 980 990 1000
....*....|....*....|....*....|....*....|...
gi 2306256062 1030 LTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLLERLMISSD 1072
Cdd:PRK14844 1344 VTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
445-507 |
1.36e-17 |
|
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: 77.95 E-value: 1.36e-17
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2306256062 445 VLSRLSYISALGMMTRISS---QFEKSRKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTH 507
Cdd:pfam04565 2 VLDRTNYLSTLSHLRRVNSprgGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
625-665 |
1.34e-11 |
|
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: 60.25 E-value: 1.34e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 2306256062 625 FDDFLKLGLVEYLDVNEENDSYIALYEKDI------------THDITHLEIEP 665
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLeessreeregpyAHTYTHCEIHP 53
|
|
| |
