|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-674 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 1397.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 1 MIDRYKHQQLRIGSVSPQQISTWANKILPNGEIVGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIGDK 80
Cdd:CHL00018 1 MIDRYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 81 KEDPNFCEQCGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPVAKKPTFLRL 160
Cdd:CHL00018 81 KEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPIAKKPTFLRL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 161 RGLFEYEIQSWKYSIPLFFTTQGFDTFRNREISTGAGAIREQLAGLDLRVIIDYSLVEWKELGEERSTGNEWEDRKIGRR 240
Cdd:CHL00018 161 RGLFEYEIQSWKYSIPLFFSTQGFDTFRNREISTGAGAIREQLADLDLRIIIDNSLVEWKELGEEGSTGNEWEDRKIGRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 241 KQFLVRRVELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSRSTPGDL 320
Cdd:CHL00018 241 KDFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGEL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 321 VMGQEKLVQEAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPRE 400
Cdd:CHL00018 321 VMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPRE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 401 IAIELFQTFLIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
Cdd:CHL00018 401 IAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 481 LVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGNPRGICTNRYNPWNR 560
Cdd:CHL00018 481 LVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRRGIYANRYNPCNR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 561 SNyqnerisdnnwKKKEPFFCNSYDAIGAYRQKRIHLDSPLWLRWRLDQRVIASREVPIEVQYESLGTYHEIYGHYIIVR 640
Cdd:CHL00018 561 KN-----------STKEPYFSNSYDALGAYRQKRINLDSPLWLRWRLDQRIIASREVPIEVQYESLGTYHEIYEHYLIVK 629
|
650 660 670
....*....|....*....|....*....|....
gi 1090892093 641 SVKTEILWMYIRTTVGHISLFREMEEAIQGFCRA 674
Cdd:CHL00018 630 SRKKEILSIYIRTTVGRILFNREIEEAIQGFSRA 663
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
10-551 |
0e+00 |
|
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain] Cd Length: 659 Bit Score: 684.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 10 LRIGSVSPQQISTWankilpngeIVGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIGDKkedPNFCEQ 89
Cdd:cd01609 6 IRISLASPEQIRSW---------SHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYK---GIICDR 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 90 CGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEglvycdfsfarpvakkptflrlrglfeyeiq 169
Cdd:cd01609 74 CGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLE------------------------------- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 170 swkysiplffttqgfdtfrnreistgagaireqlagldlRVIidYSLVEWkelgeerstgnewedrkigrrkqflvrrve 249
Cdd:cd01609 123 ---------------------------------------RVI--YFVVES------------------------------ 131
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 250 lakhFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSrsTPGDLVMGQEKLVQ 329
Cdd:cd01609 132 ----FRKSGNRPEWMILTVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKKLLELG--APEIIVRNEKRMLQ 205
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 330 EAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELFQTF 409
Cdd:cd01609 206 EAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPF 285
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 410 LIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNAD 489
Cdd:cd01609 286 VIRELIERGLAPNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNAD 365
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1090892093 490 FDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGNPRGIC 551
Cdd:cd01609 366 FDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTKERKGDKG 427
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-623 |
0e+00 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 615.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 1 MIDRYKHQQLRIGSVSPQQISTWANkilpngeivGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIGDK 80
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWSY---------GEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYK 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 81 KedpNFCEQCGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPVAKKP--TFL 158
Cdd:COG0086 72 G---VVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLY----FESYVVIDPgdTPL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 159 RLRGLF---EY-EIQSwKYSiplffttqgfDTFRnreISTGAGAIREQLAGLDLRVIIdyslvewKELGEE-RSTGNEwe 233
Cdd:COG0086 145 EKGQLLtedEYrEILE-EYG----------DEFV---AKMGAEAIKDLLGRIDLEKES-------EELREElKETTSE-- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 234 drkigRRKQFLVRRVELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLttS 313
Cdd:COG0086 202 -----QKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLL--E 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 314 RSTPGDLVMGQEKLVQEAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLH 393
Cdd:COG0086 275 LKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLH 354
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 394 RCGLPREIAIELFQTFLIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEG 473
Cdd:COG0086 355 QCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEG 434
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 474 RAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTsgnprgictn 553
Cdd:COG0086 435 KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLT---------- 504
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 554 rynpwnrsnyqnerISDNNWKKKEPFFCNSYDAIGAYRQKRIHLDSPLWLRWRLDQ------------RVIASREVPIEV 621
Cdd:COG0086 505 --------------REREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITEDGeqvgkivettvgRYLVNEILPQEV 570
|
..
gi 1090892093 622 QY 623
Cdd:COG0086 571 PF 572
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
10-604 |
0e+00 |
|
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 612.44 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 10 LRIGSVSPQQISTWANkilpngeivGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIGDKKEdpnFCEQ 89
Cdd:TIGR02386 2 IKISIASPDTIRNWSY---------GEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGV---VCER 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 90 CGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPVAKKP-----TFLRLRGLF 164
Cdd:TIGR02386 70 CGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLY----FENYVVLDPgdtklDKKEVLDET 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 165 EYEIQSWKYSiplffttqgfDTFRnreISTGAGAIREQLAGLDLRVIIDyslvewkELGEERSTGNEWEDRKIgrrkqfL 244
Cdd:TIGR02386 146 EYREVLKRYG----------DGFR---AGMGAEAIKELLEKIDLDKEIE-------ELKIQLRESKSDQKRKK------L 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 245 VRRVELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSrsTPGDLVMGQ 324
Cdd:TIGR02386 200 LKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG--APEIIVRNE 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 325 EKLVQEAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIE 404
Cdd:TIGR02386 278 KRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALE 357
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 405 LFQTFLIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCK 484
Cdd:TIGR02386 358 LFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCT 437
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 485 GFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGNPrgictnrynpwnrsnyq 564
Cdd:TIGR02386 438 AFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKP----------------- 500
|
570 580 590 600
....*....|....*....|....*....|....*....|
gi 1090892093 565 nerisdnNWKKKEPFFCNSYDAIGAYRQKRIHLDSPLWLR 604
Cdd:TIGR02386 501 -------GAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVR 533
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
262-540 |
9.42e-138 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 405.36 E-value: 9.42e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 262 EWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSrsTPGDLVMGQEKLVQEAVDTLLDNG-- 339
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELG--APSIIIRNEKRLLQEAVDTLIDNEgl 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 340 IRSRPVRdgqNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELFQTFLIRGLIRQHL 419
Cdd:smart00663 79 PRANQKS---GRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 420 ASDIV----GAK---------------SQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
Cdd:smart00663 156 RKLVRngpnGAKyiirgkktnlklakkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNP 235
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 481 LVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLY 540
Cdd:smart00663 236 LVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
10-371 |
2.49e-46 |
|
RNA polymerase Rpb1, domain 1; 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, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595 Cd Length: 320 Bit Score: 167.08 E-value: 2.49e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 10 LRIGSVSPQQISTWAnkilpngeiVGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICA-CGtyrviGDKKEdpnfce 88
Cdd:pfam04997 7 IQFGIASPEEIRKWS---------VGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCG-----KKKKD------ 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 89 qCGVEFvdsrirryqmGYIKLACPATHVWYLKrlpsYIANLLDKPLKeleglvYC--------DFSFARPVAKKPTFLRL 160
Cdd:pfam04997 67 -CPGHF----------GHIELAKPVFHIGFFK----KTLKILECVCK------YCskllldpgKPKLFNKDKKRLGLENL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 161 RGLFEyeiQSWKYSiplffttqgfdtfRNREISTGAGAIReqlaGLDLRVIIDYSLVEWKELGEERSTGNEWEDRKIG-- 238
Cdd:pfam04997 126 KMGAK---AILELC-------------KKKDLCEHCGGKN----GVCGSQQPVSRKEGLKLKAAIKKSKEEEEKEILNpe 185
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 239 RRKQFLVRRVELAKHFIRTNIE---PEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTsrS 315
Cdd:pfam04997 186 KVLKIFKRISDEDVEILGFNPSgsrPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLEL--G 263
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 1090892093 316 TPGDLVMGQEKLVQEAVDTLLDNGIRS-RPVRDGQNKVYKSFSDVIEGKEGRFRETL 371
Cdd:pfam04997 264 APSHIIREEWRLLQEHVATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-674 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 1397.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 1 MIDRYKHQQLRIGSVSPQQISTWANKILPNGEIVGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIGDK 80
Cdd:CHL00018 1 MIDRYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 81 KEDPNFCEQCGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPVAKKPTFLRL 160
Cdd:CHL00018 81 KEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPIAKKPTFLRL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 161 RGLFEYEIQSWKYSIPLFFTTQGFDTFRNREISTGAGAIREQLAGLDLRVIIDYSLVEWKELGEERSTGNEWEDRKIGRR 240
Cdd:CHL00018 161 RGLFEYEIQSWKYSIPLFFSTQGFDTFRNREISTGAGAIREQLADLDLRIIIDNSLVEWKELGEEGSTGNEWEDRKIGRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 241 KQFLVRRVELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSRSTPGDL 320
Cdd:CHL00018 241 KDFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGEL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 321 VMGQEKLVQEAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPRE 400
Cdd:CHL00018 321 VMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPRE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 401 IAIELFQTFLIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
Cdd:CHL00018 401 IAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 481 LVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGNPRGICTNRYNPWNR 560
Cdd:CHL00018 481 LVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRRGIYANRYNPCNR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 561 SNyqnerisdnnwKKKEPFFCNSYDAIGAYRQKRIHLDSPLWLRWRLDQRVIASREVPIEVQYESLGTYHEIYGHYIIVR 640
Cdd:CHL00018 561 KN-----------STKEPYFSNSYDALGAYRQKRINLDSPLWLRWRLDQRIIASREVPIEVQYESLGTYHEIYEHYLIVK 629
|
650 660 670
....*....|....*....|....*....|....
gi 1090892093 641 SVKTEILWMYIRTTVGHISLFREMEEAIQGFCRA 674
Cdd:CHL00018 630 SRKKEILSIYIRTTVGRILFNREIEEAIQGFSRA 663
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
10-551 |
0e+00 |
|
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain] Cd Length: 659 Bit Score: 684.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 10 LRIGSVSPQQISTWankilpngeIVGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIGDKkedPNFCEQ 89
Cdd:cd01609 6 IRISLASPEQIRSW---------SHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYK---GIICDR 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 90 CGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEglvycdfsfarpvakkptflrlrglfeyeiq 169
Cdd:cd01609 74 CGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLE------------------------------- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 170 swkysiplffttqgfdtfrnreistgagaireqlagldlRVIidYSLVEWkelgeerstgnewedrkigrrkqflvrrve 249
Cdd:cd01609 123 ---------------------------------------RVI--YFVVES------------------------------ 131
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 250 lakhFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSrsTPGDLVMGQEKLVQ 329
Cdd:cd01609 132 ----FRKSGNRPEWMILTVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKKLLELG--APEIIVRNEKRMLQ 205
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 330 EAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELFQTF 409
Cdd:cd01609 206 EAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPF 285
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 410 LIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNAD 489
Cdd:cd01609 286 VIRELIERGLAPNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNAD 365
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1090892093 490 FDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGNPRGIC 551
Cdd:cd01609 366 FDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTKERKGDKG 427
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1-624 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 666.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 1 MIDRYKHQQLRIGSVSPQQISTWANkilpngeivGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYR----- 75
Cdd:PRK00566 1 DVNKQDFDAIKIGLASPEKIRSWSY---------GEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKrvryk 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 76 -VIgdkkedpnfCEQCGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPVAKK 154
Cdd:PRK00566 72 gII---------CERCGVEVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLY----FESYVVID 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 155 P--TFLRLRGLF---EY-EIQSwKYSiplffttqgfDTFrnrEISTGAGAIREQLAGLDLRVIIdyslvewKELGEE-RS 227
Cdd:PRK00566 139 PgdTPLEKKQLLteeEYrEALE-EYG----------DEF---VAKMGAEAIKELLKNIDLEAEA-------EELREElKE 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 228 TGNEwedrkiGRRKQfLVRRVELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILA 307
Cdd:PRK00566 198 TGSE------QKRKK-ALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNNRLK 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 308 DLLTTSrsTPgDLVMGQEK-LVQEAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVV 386
Cdd:PRK00566 271 RLLELG--AP-EIIVRNEKrMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVV 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 387 GPTLPLHRCGLPREIAIELFQTFLIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAF 466
Cdd:PRK00566 348 GPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAF 427
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 467 QPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSgn 546
Cdd:PRK00566 428 EPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTR-- 505
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 547 prgictnrynpwnrsnyqnERIsdnNWKKKEPFFCNSYDAIGAYRQKRIHLDSPLWLRWRLDQ-------RVIASREVPI 619
Cdd:PRK00566 506 -------------------ERE---GAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITSKKlvettvgRVIFNEILPE 563
|
....*
gi 1090892093 620 EVQYE 624
Cdd:PRK00566 564 GLPFI 568
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
10-668 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 645.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 10 LRIGSVSPQQISTWANKILPNGEIVGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIgdkKEDPNFCEQ 89
Cdd:PRK02625 12 VKIGLASPERIRQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRV---RHRGIVCER 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 90 CGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVY--CDFSFARPVAKKPTFLRLRGLFEY- 166
Cdd:PRK02625 89 CGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYfnCYVVLDPGNHKNLKYKQLLTEDQWl 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 167 EIQSWKYSiplffttQGFDTFRNREISTGAGAIREQLAGLDLRVIIDyslvewkELGEERSTGNewedrkiGRRKQFLVR 246
Cdd:PRK02625 169 EIEDQIYA-------EDSELEGEEVVGIGAEALKRLLEDLNLEEEAE-------QLREEIANSK-------GQKRAKLIK 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 247 RVELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSrsTPGDLVMGQEK 326
Cdd:PRK02625 228 RLRVIDNFIATGSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEIL--APEIIVRNEKR 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 327 LVQEAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELF 406
Cdd:PRK02625 306 MLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELF 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 407 QTFLIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGF 486
Cdd:PRK02625 386 QPFVIHRLIRQGIVNNIKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAF 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 487 NADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGNPrgictnrynpwnrsnyqne 566
Cdd:PRK02625 466 NADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENP------------------- 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 567 risdNNWKKKEPFFCNSYDAIGAYRQKRIHLDSPLWLRWRLDQRVIASREVPIEVQYESLGTYHEIYGHYIIVRSVKTEI 646
Cdd:PRK02625 527 ----GAQKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRFNGEVEDDDEDTEPLKTETLEDGTRIEQYRYRRDRFDEDGNL 602
|
650 660
....*....|....*....|..
gi 1090892093 647 LWMYIRTTVGHISLFREMEEAI 668
Cdd:PRK02625 603 ISQYILTTVGRVIMNKTIQDAL 624
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-623 |
0e+00 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 615.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 1 MIDRYKHQQLRIGSVSPQQISTWANkilpngeivGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIGDK 80
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWSY---------GEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYK 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 81 KedpNFCEQCGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPVAKKP--TFL 158
Cdd:COG0086 72 G---VVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLY----FESYVVIDPgdTPL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 159 RLRGLF---EY-EIQSwKYSiplffttqgfDTFRnreISTGAGAIREQLAGLDLRVIIdyslvewKELGEE-RSTGNEwe 233
Cdd:COG0086 145 EKGQLLtedEYrEILE-EYG----------DEFV---AKMGAEAIKDLLGRIDLEKES-------EELREElKETTSE-- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 234 drkigRRKQFLVRRVELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLttS 313
Cdd:COG0086 202 -----QKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLL--E 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 314 RSTPGDLVMGQEKLVQEAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLH 393
Cdd:COG0086 275 LKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLH 354
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 394 RCGLPREIAIELFQTFLIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEG 473
Cdd:COG0086 355 QCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEG 434
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 474 RAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTsgnprgictn 553
Cdd:COG0086 435 KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLT---------- 504
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 554 rynpwnrsnyqnerISDNNWKKKEPFFCNSYDAIGAYRQKRIHLDSPLWLRWRLDQ------------RVIASREVPIEV 621
Cdd:COG0086 505 --------------REREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITEDGeqvgkivettvgRYLVNEILPQEV 570
|
..
gi 1090892093 622 QY 623
Cdd:COG0086 571 PF 572
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
10-604 |
0e+00 |
|
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 612.44 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 10 LRIGSVSPQQISTWANkilpngeivGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIGDKKEdpnFCEQ 89
Cdd:TIGR02386 2 IKISIASPDTIRNWSY---------GEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGV---VCER 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 90 CGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPVAKKP-----TFLRLRGLF 164
Cdd:TIGR02386 70 CGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLY----FENYVVLDPgdtklDKKEVLDET 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 165 EYEIQSWKYSiplffttqgfDTFRnreISTGAGAIREQLAGLDLRVIIDyslvewkELGEERSTGNEWEDRKIgrrkqfL 244
Cdd:TIGR02386 146 EYREVLKRYG----------DGFR---AGMGAEAIKELLEKIDLDKEIE-------ELKIQLRESKSDQKRKK------L 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 245 VRRVELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSrsTPGDLVMGQ 324
Cdd:TIGR02386 200 LKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG--APEIIVRNE 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 325 EKLVQEAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIE 404
Cdd:TIGR02386 278 KRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALE 357
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 405 LFQTFLIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCK 484
Cdd:TIGR02386 358 LFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCT 437
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 485 GFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGNPrgictnrynpwnrsnyq 564
Cdd:TIGR02386 438 AFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKP----------------- 500
|
570 580 590 600
....*....|....*....|....*....|....*....|
gi 1090892093 565 nerisdnNWKKKEPFFCNSYDAIGAYRQKRIHLDSPLWLR 604
Cdd:TIGR02386 501 -------GAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVR 533
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
10-544 |
1.39e-168 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 520.97 E-value: 1.39e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 10 LRIGSVSPQQISTWANkilpngeivGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIGDKKEdpnFCEQ 89
Cdd:PRK14906 12 LRISLASAEDIRSWSH---------GEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGI---VCER 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 90 CGVEFVDSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPVAKKP-------------- 155
Cdd:PRK14906 80 CGVEVTRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITSVDKEAreedaddlrdelaa 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 156 --------------TFLRLRGLFEYEIQSWKYSIPLF------------------------FTTQGFDTFRN-------- 189
Cdd:PRK14906 160 dleeldaerdrlieATRRLSVDYVPEDDEFVDDIGDDerltaeevraevadiyeeynerkaLRREAFDAFMQiepkqlis 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 190 -----REI----------STGAGAIREQLAGLDLRViidyslvEWKELGEERSTGNewedrkiGRRKQFLVRRVELAKHF 254
Cdd:PRK14906 240 dealyREMrlnysiyfkgGMGAEAVRDLLDAIDLEK-------EAEELRAIIANGK-------GQKREKAVKRLKVVDAF 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 255 IRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSrsTPGDLVMGQEKLVQEAVDT 334
Cdd:PRK14906 306 LKSGNDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLG--APEIIVNNEKRMLQEAVDS 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 335 LLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELFQTFLIRGL 414
Cdd:PRK14906 384 LFDNGRRGRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRL 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 415 IRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQ 494
Cdd:PRK14906 464 VELEYAANIKAAKRAVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQ 543
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 1090892093 495 MAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTS 544
Cdd:PRK14906 544 MAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTT 593
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
16-543 |
3.48e-157 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 502.92 E-value: 3.48e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 16 SPQQISTWANkilpngeivGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRVIgdKKEDPNFCEQCGVEFV 95
Cdd:PRK09603 1405 SPEKIHSWSY---------GEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKP--RFKDIGTCEKCGVAIT 1473
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 96 DSRIRRYQMGYIKLACPATHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPVAKKP--TFLRLRG---LFEYEI-- 168
Cdd:PRK09603 1474 HSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLY----YEAYIVKEPgeAAYDNEGtklVMKYDIln 1549
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 169 QSWKYSIPLFFTTQGFDTfrnreiSTGAGAIREQLAGLDLRVIIdyslvewKELGEE-RSTGNEwedrkigRRKQFLVRR 247
Cdd:PRK09603 1550 EEQYQNISRRYEDRGFVA------QMGGEAIKDLLEEIDLITLL-------QSLKEEvKDTNSD-------AKKKKLIKR 1609
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 248 VELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSrsTPGDLVMGQEKL 327
Cdd:PRK09603 1610 LKVVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELG--APEIIVRNEKRM 1687
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 328 VQEAVDTLLDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELFQ 407
Cdd:PRK09603 1688 LQEAVDVLFDNGRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFK 1767
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 408 TFLIRGLIRQHLASDIVGAKSQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFN 487
Cdd:PRK09603 1768 PHLLSKLEERGYATTLKQAKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFN 1847
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*.
gi 1090892093 488 ADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILT 543
Cdd:PRK09603 1848 ADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLS 1903
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
35-548 |
1.53e-146 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 472.18 E-value: 1.53e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 35 GEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICACGTYRvigDKKEDPNFCEQCGVEFVDSRIRRYQMGYIKLACPAT 114
Cdd:PRK14844 1467 GEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYK---KRRHRGRICEKCGVEVTSSKVRRERMGHIELASPVA 1543
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 115 HVWYLKRLPSYIANLLDKPLKELEGLVYCD-FSFARPVAKkpTFLRLRGLFE--YEIQSWKYSIPLFFTTQGFDtfrnre 191
Cdd:PRK14844 1544 HIWFLKSLPSRIGALLDMSLRDIENILYSDnYIVIDPLVS--PFEKGEIISEkaYNEAKDSYGIDSFVAMQGVE------ 1615
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 192 istgagAIREQLAGLDLRVIIDYSLVEWKELGEERstgnewedrkigRRKQfLVRRVELAKHFIRTNIEPEWMVLCLLPV 271
Cdd:PRK14844 1616 ------AIRELLTRLDLHEIRKDLRLELESVASEI------------RRKK-IIKRLRIVENFIKSGNRPEWMILTTIPI 1676
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 272 LPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLttSRSTPGDLVMGQEKLVQEAVDTLLDNGIRSRPV-RDGQN 350
Cdd:PRK14844 1677 LPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLL--SLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVnKAGAV 1754
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 351 KVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELFQTFLIRGLIRQHLASDIVGAKSQI 430
Cdd:PRK14844 1755 GYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLI 1834
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 431 REKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQTEAR 510
Cdd:PRK14844 1835 RAEKPEVWDMLEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEAR 1914
|
490 500 510
....*....|....*....|....*....|....*...
gi 1090892093 511 LLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGNPR 548
Cdd:PRK14844 1915 VLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEPK 1952
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
262-540 |
9.42e-138 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 405.36 E-value: 9.42e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 262 EWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTSrsTPGDLVMGQEKLVQEAVDTLLDNG-- 339
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELG--APSIIIRNEKRLLQEAVDTLIDNEgl 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 340 IRSRPVRdgqNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELFQTFLIRGLIRQHL 419
Cdd:smart00663 79 PRANQKS---GRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 420 ASDIV----GAK---------------SQIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
Cdd:smart00663 156 RKLVRngpnGAKyiirgkktnlklakkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNP 235
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 481 LVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLY 540
Cdd:smart00663 236 LVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
16-545 |
1.30e-82 |
|
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain] Cd Length: 528 Bit Score: 270.84 E-value: 1.30e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 16 SPQQISTWAnkilpngeiVGEVTKPYTFHYKTNKPERDGLFCERIFgpiksgicacgtyrvigdkkeDPNFCEQCGVEFV 95
Cdd:cd00399 2 SPEEIRKWS---------VAKVIKPETIDNRTLKAERGGKYDPRLG---------------------SIDRCEKCGTCGT 51
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 96 DSRIRRYQMGYIKLACPATHVWYLKRLPSYIanlldkplkeleglvycdfsfarpvakkptflrlrglfeyeiqswkysi 175
Cdd:cd00399 52 GLNDCPGHFGHIELAKPVFHVGFIKKVPSFL------------------------------------------------- 82
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 176 plffttqgfdtfrnreistgagaireqlagldlrviidyslvewkelgeerstgnewedrkigrrkqflvrrvelakhfi 255
Cdd:cd00399 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 256 rtniEPEWMVLCLLPVLPPELRPIIqmdggklmssdinelyrrviyrnniladllttsrstpgdLVMGQEKLVQEAVDTL 335
Cdd:cd00399 83 ----GPEWMILTCLPVPPPCLRPSV---------------------------------------IIEERWRLLQEHVDTY 119
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 336 LDNGIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELfqtflirgli 415
Cdd:cd00399 120 LDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL---------- 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 416 rqhlasdivgaksqirekepivweilqqvmQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQM 495
Cdd:cd00399 190 ------------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEM 239
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|
gi 1090892093 496 AVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSG 545
Cdd:cd00399 240 NLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTLG 289
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
261-548 |
8.84e-53 |
|
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain] Cd Length: 861 Bit Score: 195.54 E-value: 8.84e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 261 PEWMVLCLLPVLPPELRPIIQMDGG---------KLMssDINELYRRViyRNNILAdllttsrSTPGDLVMGQEKLVQEA 331
Cdd:cd02582 202 PEWMVLTVLPVPPVTVRPSITLETGerseddlthKLV--DIIRINQRL--KENIEA-------GAPQLIIEDLWDLLQYH 270
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 332 VDTLLDNGIRSRPV-RDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIA-------- 402
Cdd:cd02582 271 VTTYFDNEIPGIPPaRHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAkeltvper 350
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 403 -----IELFQTFLIRGLIRQHLASDIV---GAKSQIRE--KEPIV------WEILQQVMQGHPVLLNRAPTLHRLGIQAF 466
Cdd:cd02582 351 vtewnIEKMRKLVLNGPDKWPGANYVIrpdGRRIRLRYvnREELAerlepgWIVERHLIDGDIVLFNRQPSLHRMSIMAH 430
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 467 QPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGN 546
Cdd:cd02582 431 RVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKT 510
|
..
gi 1090892093 547 PR 548
Cdd:cd02582 511 TL 512
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
261-548 |
2.31e-48 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 182.75 E-value: 2.31e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 261 PEWMVLCLLPVLPPELRPIIQMDGG---------KLMssDI---NELYRRVIYR---NNILADLLTtsrstpgdlvmgqe 325
Cdd:PRK08566 206 PEWMVLTVLPVPPVTVRPSITLETGqrseddlthKLV--DIiriNQRLKENIEAgapQLIIEDLWE-------------- 269
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 326 kLVQEAVDTLLDNGIRSRPV---RDGqnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIA 402
Cdd:PRK08566 270 -LLQYHVTTYFDNEIPGIPParhRSG--RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIA 346
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 403 -------------IELFQTFLIRG---------LIRQhlasD------IVGAKSQIREKEPIVWEILQQVMQGHPVLLNR 454
Cdd:PRK08566 347 keltvpervtewnIEELREYVLNGpekhpganyVIRP----DgrriklTDKNKEELAEKLEPGWIVERHLIDGDIVLFNR 422
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 455 APTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQD 534
Cdd:PRK08566 423 QPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQD 502
|
330
....*....|....
gi 1090892093 535 MLIGLYILTSGNPR 548
Cdd:PRK08566 503 HISGAYLLTRKSTL 516
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
214-543 |
2.31e-46 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 177.91 E-value: 2.31e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 214 YSLVEWKELGEERSTGNEWEDR--KIGRRKQFLVrrvelakHFIRTNIEPEWMVLCLLPVLPPELRPIIQMDGGKLMSSD 291
Cdd:PRK14977 173 TIFIEKTEIEEHRLLPIEIRDIfeKIIDDDLELI-------GFDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDD 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 292 INELYRRVIYRNNILADllTTSRSTPGDLVMGQEKLVQEAVDTLLDNGIRSRPV--RDGQNKVYKSFSDVIEGKEGRFRE 369
Cdd:PRK14977 246 LTHILVDIIKANQKLKE--SKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQahHKGSGRPLKSLFQRLKGKEGRFRG 323
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 370 TLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIA-------------IELFQTFLIRG--------LIRQ----HLASDIV 424
Cdd:PRK14977 324 NLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAmkltipeivnennIEKMKELVINGpdefpganAIRKgdgtKIRLDFL 403
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 425 GAKS-----QIREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHV 499
Cdd:PRK14977 404 EDKGkdalrEAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHV 483
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 1090892093 500 PLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILT 543
Cdd:PRK14977 484 PQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLIT 527
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
10-371 |
2.49e-46 |
|
RNA polymerase Rpb1, domain 1; 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, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595 Cd Length: 320 Bit Score: 167.08 E-value: 2.49e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 10 LRIGSVSPQQISTWAnkilpngeiVGEVTKPYTFHYKTNKPERDGLFCERIFGPIKSGICA-CGtyrviGDKKEdpnfce 88
Cdd:pfam04997 7 IQFGIASPEEIRKWS---------VGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCG-----KKKKD------ 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 89 qCGVEFvdsrirryqmGYIKLACPATHVWYLKrlpsYIANLLDKPLKeleglvYC--------DFSFARPVAKKPTFLRL 160
Cdd:pfam04997 67 -CPGHF----------GHIELAKPVFHIGFFK----KTLKILECVCK------YCskllldpgKPKLFNKDKKRLGLENL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 161 RGLFEyeiQSWKYSiplffttqgfdtfRNREISTGAGAIReqlaGLDLRVIIDYSLVEWKELGEERSTGNEWEDRKIG-- 238
Cdd:pfam04997 126 KMGAK---AILELC-------------KKKDLCEHCGGKN----GVCGSQQPVSRKEGLKLKAAIKKSKEEEEKEILNpe 185
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 239 RRKQFLVRRVELAKHFIRTNIE---PEWMVLCLLPVLPPELRPIIQMDGGKLMSSDINELYRRVIYRNNILADLLTTsrS 315
Cdd:pfam04997 186 KVLKIFKRISDEDVEILGFNPSgsrPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLEL--G 263
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*..
gi 1090892093 316 TPGDLVMGQEKLVQEAVDTLLDNGIRS-RPVRDGQNKVYKSFSDVIEGKEGRFRETL 371
Cdd:pfam04997 264 APSHIIREEWRLLQEHVATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
373-513 |
1.27e-43 |
|
RNA polymerase Rpb1, 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). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498 Cd Length: 166 Bit Score: 154.38 E-value: 1.27e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 373 GKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELFQTFLIRGLIRQHL-------------AS----------DIVGAKSQ 429
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLrqlvengpnvypgANyiiringarrDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 430 IREKEPIVWEILQQVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQTEA 509
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....
gi 1090892093 510 RLLM 513
Cdd:pfam00623 161 EELM 164
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
261-543 |
5.24e-41 |
|
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain] Cd Length: 751 Bit Score: 160.01 E-value: 5.24e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 261 PEWMVLCLLPVLPPELRPIIQMDGGklMSS--DINELYRRVIYRNNILADLLTTSrsTPGDLVMGQEKLVQEAVDTLLDN 338
Cdd:cd02733 125 PDWMILTVLPVPPPAVRPSVVMDGS--ARSedDLTHKLADIIKANNQLKRQEQNG--APAHIIEEDEQLLQFHVATYMDN 200
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 339 GIRSRP-VRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELfqTF-------- 409
Cdd:cd02733 201 EIPGLPqATQKSGRPLKSIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNL--TFpeivtpfn 278
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 410 --LIRGLIR----QHLasdivGAKSQIRE-----------KEPIV-----WEILQQVMQGHPVLLNRAPTLHRLGIQAFq 467
Cdd:cd02733 279 idRLQELVRngpnEYP-----GAKYIIRDdgeridlrylkKASDLhlqygYIVERHLQDGDVVLFNRQPSLHKMSMMGH- 352
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 468 pilvegRAICLHPL-------VCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLY 540
Cdd:cd02733 353 ------RVKVLPYStfrlnlsVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVR 426
|
...
gi 1090892093 541 ILT 543
Cdd:cd02733 427 KLT 429
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
261-544 |
3.20e-39 |
|
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain] Cd Length: 816 Bit Score: 155.01 E-value: 3.20e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 261 PEWMVLCLLPVLPPELRPIIQMDGGKlMSS--DINELYRRVIYRNNILADLLTTSrsTPGDLVMGQEKLVQEAVDTLLDN 338
Cdd:cd02583 175 PENLILTRIPVPPLCIRPSVVMDEKS-GTNedDLTVKLSEIIFLNDVIKKHLEKG--AKTQKIMEDWDFLQLQCALYINS 251
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 339 GIRSRPVRDGQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIA-------------IEL 405
Cdd:cd02583 252 ELPGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAkiltypervtrynIEK 331
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 406 FQTFLIRG---------LIRQHlasdiVGAKSQIR--EKEPIVWE------ILQQVMQGHPVLLNRAPTLHRLGIQAFQP 468
Cdd:cd02583 332 LRKLVLNGpdvhpganfVIKRD-----GGKKKFLKygNRRKIARElkigdiVERHLEDGDIVLFNRQPSLHRLSIMAHRA 406
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1090892093 469 ILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTS 544
Cdd:cd02583 407 KVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTS 482
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
269-544 |
2.12e-31 |
|
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain] Cd Length: 779 Bit Score: 130.77 E-value: 2.12e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 269 LPVLPPELRPIIQMdGGKLMSSDINELYRRVIYRNNILADLLTTSRSTPGDLV-------MGQEKLV------QEAVDTL 335
Cdd:cd01435 135 LLVPPNRFRPPSFL-GDKVFENPQNVLLSKILKDNQQIRDLLASMRQAESQSKldlisgkTNSEKLInawlqlQSAVNEL 213
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 336 LDNGIRSRPvrdgQNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIELfqTF------ 409
Cdd:cd01435 214 FDSTKAPKS----GKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKL--TFpepvtp 287
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 410 ---------LIRG----------------LI---------RQHLASDIVGAKSQIREKEP--IVWEILQQvmqGHPVLLN 453
Cdd:cd01435 288 fnveelrqaVINGpdvypganaiededgrLIllsalseerRKALAKLLLLLSSAKLLLNGpkKVYRHLLD---GDVVLLN 364
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 454 RAPTLHRLGIQAFQ-PILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQTEARLLMFSHMNLLSPAMGDPISVPT 532
Cdd:cd01435 365 RQPTLHKPSIMAHKvRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLI 444
|
330
....*....|..
gi 1090892093 533 QDMLIGLYILTS 544
Cdd:cd01435 445 QDHVVSGVLLTS 456
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
367-546 |
8.56e-21 |
|
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain] Cd Length: 744 Bit Score: 97.09 E-value: 8.56e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 367 FRETLLGKRVDYSGRSVIVVGPTLPLHRCGLPREIAIEL------------------FQTFLIRGLIRQHLASDIVGAKS 428
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLtvservsswnrerlqeycDLTLLLKGVIGVRRNGRLVGVRS 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1090892093 429 ----QIREKepivweILQQVMQGHPVLLNRAPTLHRLGIQAFQ-PILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSL 503
Cdd:cd10506 286 hntlQIGDV------IHRPLVDGDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSL 359
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1090892093 504 EAQTEARLLMFSHMNLLSPAMGDPISVPTQDMLIGLYILTSGN 546
Cdd:cd10506 360 QARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERG 402
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
518-555 |
2.42e-05 |
|
RNA polymerase Rpb1, 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). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 44.93 E-value: 2.42e-05
10 20 30
....*....|....*....|....*....|....*...
gi 1090892093 518 NLLSPAMGDPISVPTQDMLIGLYILTSgnpRGICTNRY 555
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTR---EDTFFDRE 35
|
|
| |
