|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-675 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 1414.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 1 MIDRYKHQQLRIGLVSPQQISAWATKIIPNGEIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80
Cdd:CHL00018 1 MIDRYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 81 NEDPKFCEQCGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPITKKPTFLRL 160
Cdd:CHL00018 81 KEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPIAKKPTFLRL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 161 RGSFEYEIQSWKYSIPLFFTTQGFDIFRNREISTGAGAIRDQLADLDLRIIIENSLVEWKQLGEEGPTGNEWEDRKIVRR 240
Cdd:CHL00018 161 RGLFEYEIQSWKYSIPLFFSTQGFDTFRNREISTGAGAIREQLADLDLRIIIDNSLVEWKELGEEGSTGNEWEDRKIGRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 241 KDFLVRRMELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSRSTPGEL 320
Cdd:CHL00018 241 KDFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGEL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 321 VMCQEKLVQEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPRE 400
Cdd:CHL00018 321 VMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPRE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 401 IAIELFQTFVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHP 480
Cdd:CHL00018 401 IAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 481 LVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTSGTRRGICANRYNPCNP 560
Cdd:CHL00018 481 LVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRRGIYANRYNPCNR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 561 KNykneriyetnykYTKEPFFCNSYDANGAYRQKRINLDSPLWLRWQLDQRVIASREVPIEVHYESFGNYHEIYAHYLIV 640
Cdd:CHL00018 561 KN------------STKEPYFSNSYDALGAYRQKRINLDSPLWLRWRLDQRIIASREVPIEVQYESLGTYHEIYEHYLIV 628
|
650 660 670
....*....|....*....|....*....|....*
gi 212288281 641 RSVKKETYCIYIRTTVGHISFYREIEEAIQGFSQA 675
Cdd:CHL00018 629 KSRKKEILSIYIRTTVGRILFNREIEEAIQGFSRA 663
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
10-553 |
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: 694.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 10 LRIGLVSPQQISAWatkiipngeIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDEnedPKFCEQ 89
Cdd:cd01609 6 IRISLASPEQIRSW---------SHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYK---GIICDR 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 90 CGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCdfsfarpitkkptflrlrgsfeyeiq 169
Cdd:cd01609 74 CGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF-------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 170 swkysiplffttqgfdifrnreistgagairdqladldlriiiensLVEWkqlgeegptgnewedrkivrrkdflvrrme 249
Cdd:cd01609 128 ----------------------------------------------VVES------------------------------ 131
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 250 lakhFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLVQ 329
Cdd:cd01609 132 ----FRKSGNRPEWMILTVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKKLLELG--APEIIVRNEKRMLQ 205
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 330 EAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTF 409
Cdd:cd01609 206 EAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPF 285
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 410 VIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPLVCKGFNAD 489
Cdd:cd01609 286 VIRELIERGLAPNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNAD 365
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 212288281 490 FDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTSGTRRGICAN 553
Cdd:cd01609 366 FDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTKERKGDKGEG 429
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-543 |
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: 607.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 1 MIDRYKHQQLRIGLVSPQQISAWAtkiipngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNY---RVI 77
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWS---------YGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYkrmVYK 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 78 GdenedpKFCEQCGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPITKKP-- 155
Cdd:COG0086 72 G------VVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLY----FESYVVIDPgd 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 156 TFLRlRGSF----EY-EIQSwKYSiplffttqgfDIFRnreISTGAGAIRDQLADLDLRIIIENSLVEWKQLGEEgptgn 230
Cdd:COG0086 142 TPLE-KGQLltedEYrEILE-EYG----------DEFV---AKMGAEAIKDLLGRIDLEKESEELREELKETTSE----- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 231 ewedrkivRRKDFLVRRMELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLL 310
Cdd:COG0086 202 --------QKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLL 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 311 ttSRSTPGELVMCQEKLVQEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSL 390
Cdd:COG0086 274 --ELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPEL 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 391 SLHRCGLPREIAIELFQTFVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPIL 470
Cdd:COG0086 352 KLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVL 431
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 212288281 471 VEGRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLT 543
Cdd:COG0086 432 IEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLT 504
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
10-544 |
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: 604.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 10 LRIGLVSPQQISAWATkiipngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIgdeNEDPKFCEQ 89
Cdd:TIGR02386 2 IKISIASPDTIRNWSY---------GEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKI---RYKGVVCER 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 90 CGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPITKKPTFLRLrgsFEYEIQ 169
Cdd:TIGR02386 70 CGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLY----FENYVVLDPGDTKL---DKKEVL 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 170 SWK-YSIPLFFTTQGFDIfrnreiSTGAGAIRDQLADLDLRIIIEnslvewkQLGEEGPTGNEweDRKIVRrkdfLVRRM 248
Cdd:TIGR02386 143 DETeYREVLKRYGDGFRA------GMGAEAIKELLEKIDLDKEIE-------ELKIQLRESKS--DQKRKK----LLKRL 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 249 ELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLV 328
Cdd:TIGR02386 204 EIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG--APEIIVRNEKRML 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 329 QEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQT 408
Cdd:TIGR02386 282 QEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKP 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 409 FVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPLVCKGFNA 488
Cdd:TIGR02386 362 FIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNA 441
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*.
gi 212288281 489 DFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTS 544
Cdd:TIGR02386 442 DFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTT 497
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
262-540 |
1.44e-138 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 407.29 E-value: 1.44e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 262 EWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLVQEAVDTLLDN-GI 340
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELG--APSIIIRNEKRLLQEAVDTLIDNeGL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 341 RGQPMRDGhnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHL- 419
Cdd:smart00663 79 PRANQKSG--RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLr 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 420 -----------------ASNIGVAK-SQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPL 481
Cdd:smart00663 157 klvrngpngakyiirgkKTNLKLAKkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPL 236
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 212288281 482 VCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLY 540
Cdd:smart00663 237 VCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
10-371 |
4.08e-47 |
|
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: 169.01 E-value: 4.08e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 10 LRIGLVSPQQISAWAtkiipngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICA-CGnyrvigdenedpKFCE 88
Cdd:pfam04997 7 IQFGIASPEEIRKWS---------VGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCG------------KKKK 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 89 QCGVEFvdsrirryqmGYIKLTCPVTHVWYLKrlpsYIANLLDKPLKeleglvYCdfsfarpitkkpTFLRLRGSFEYEI 168
Cdd:pfam04997 66 DCPGHF----------GHIELAKPVFHIGFFK----KTLKILECVCK------YC------------SKLLLDPGKPKLF 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 169 QSWKYsiplffttqgfdIFRNREISTGAGAIRDQLADLDLriiIENSLVEWKQLGEEGPTGNE--------WEDRKIVRR 240
Cdd:pfam04997 114 NKDKK------------RLGLENLKMGAKAILELCKKKDL---CEHCGGKNGVCGSQQPVSRKeglklkaaIKKSKEEEE 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 241 KDFLV--RRMELAKHFIRTNIE----------PEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTD 308
Cdd:pfam04997 179 KEILNpeKVLKIFKRISDEDVEilgfnpsgsrPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKK 258
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212288281 309 LLTTsrSTPGELVMCQEKLVQEAVDTLLDNGIRGQP---MRDghNKVYKSFSDVIEGKEGRFRETL 371
Cdd:pfam04997 259 LLEL--GAPSHIIREEWRLLQEHVATLFDNEIPGLPpalQKS--KRPLKSISQRLKGKEGRFRGNL 320
|
|
|
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-675 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 1414.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 1 MIDRYKHQQLRIGLVSPQQISAWATKIIPNGEIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80
Cdd:CHL00018 1 MIDRYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 81 NEDPKFCEQCGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPITKKPTFLRL 160
Cdd:CHL00018 81 KEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPIAKKPTFLRL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 161 RGSFEYEIQSWKYSIPLFFTTQGFDIFRNREISTGAGAIRDQLADLDLRIIIENSLVEWKQLGEEGPTGNEWEDRKIVRR 240
Cdd:CHL00018 161 RGLFEYEIQSWKYSIPLFFSTQGFDTFRNREISTGAGAIREQLADLDLRIIIDNSLVEWKELGEEGSTGNEWEDRKIGRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 241 KDFLVRRMELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSRSTPGEL 320
Cdd:CHL00018 241 KDFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGEL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 321 VMCQEKLVQEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPRE 400
Cdd:CHL00018 321 VMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPRE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 401 IAIELFQTFVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHP 480
Cdd:CHL00018 401 IAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 481 LVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTSGTRRGICANRYNPCNP 560
Cdd:CHL00018 481 LVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRRGIYANRYNPCNR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 561 KNykneriyetnykYTKEPFFCNSYDANGAYRQKRINLDSPLWLRWQLDQRVIASREVPIEVHYESFGNYHEIYAHYLIV 640
Cdd:CHL00018 561 KN------------STKEPYFSNSYDALGAYRQKRINLDSPLWLRWRLDQRIIASREVPIEVQYESLGTYHEIYEHYLIV 628
|
650 660 670
....*....|....*....|....*....|....*
gi 212288281 641 RSVKKETYCIYIRTTVGHISFYREIEEAIQGFSQA 675
Cdd:CHL00018 629 KSRKKEILSIYIRTTVGRILFNREIEEAIQGFSRA 663
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
10-553 |
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: 694.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 10 LRIGLVSPQQISAWatkiipngeIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDEnedPKFCEQ 89
Cdd:cd01609 6 IRISLASPEQIRSW---------SHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYK---GIICDR 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 90 CGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCdfsfarpitkkptflrlrgsfeyeiq 169
Cdd:cd01609 74 CGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF-------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 170 swkysiplffttqgfdifrnreistgagairdqladldlriiiensLVEWkqlgeegptgnewedrkivrrkdflvrrme 249
Cdd:cd01609 128 ----------------------------------------------VVES------------------------------ 131
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 250 lakhFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLVQ 329
Cdd:cd01609 132 ----FRKSGNRPEWMILTVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKKLLELG--APEIIVRNEKRMLQ 205
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 330 EAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTF 409
Cdd:cd01609 206 EAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPF 285
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 410 VIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPLVCKGFNAD 489
Cdd:cd01609 286 VIRELIERGLAPNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNAD 365
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 212288281 490 FDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTSGTRRGICAN 553
Cdd:cd01609 366 FDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTKERKGDKGEG 429
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1-543 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 657.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 1 MIDRYKHQQLRIGLVSPQQISAWATkiipngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80
Cdd:PRK00566 1 DVNKQDFDAIKIGLASPEKIRSWSY---------GEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYK 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 81 NedpKFCEQCGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPITKKP--TFL 158
Cdd:PRK00566 72 G---IICERCGVEVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLY----FESYVVIDPgdTPL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 159 RlRGSF----EY-EIQSwKYSiplffttqgfDIFrnrEISTGAGAIRDQLADLDLRIIIEnslvewkQLGEEGPTGNEwe 233
Cdd:PRK00566 145 E-KKQLlteeEYrEALE-EYG----------DEF---VAKMGAEAIKELLKNIDLEAEAE-------ELREELKETGS-- 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 234 DRKIVRrkdfLVRRMELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTS 313
Cdd:PRK00566 201 EQKRKK----ALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 314 rsTPgELVMCQEK-LVQEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSL 392
Cdd:PRK00566 277 --AP-EIIVRNEKrMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKL 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 393 HRCGLPREIAIELFQTFVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVE 472
Cdd:PRK00566 354 HQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIE 433
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 212288281 473 GRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLT 543
Cdd:PRK00566 434 GKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLT 504
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
10-669 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 640.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 10 LRIGLVSPQQISAWATKIIPNGEIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDENedpKFCEQ 89
Cdd:PRK02625 12 VKIGLASPERIRQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRG---IVCER 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 90 CGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPITKKP------TFLRLRGS 163
Cdd:PRK02625 89 CGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVY----FNCYVVLDPgnhknlKYKQLLTE 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 164 FEY-EIQSWKYSiplffttQGFDIFRNREISTGAGAIRDQLADLDLRIIIEnslvewkQLGEE--GPTGNEwedrkivRR 240
Cdd:PRK02625 165 DQWlEIEDQIYA-------EDSELEGEEVVGIGAEALKRLLEDLNLEEEAE-------QLREEiaNSKGQK-------RA 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 241 KdfLVRRMELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGEL 320
Cdd:PRK02625 224 K--LIKRLRVIDNFIATGSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEIL--APEII 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 321 VMCQEKLVQEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPRE 400
Cdd:PRK02625 300 VRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKE 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 401 IAIELFQTFVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHP 480
Cdd:PRK02625 380 MAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHP 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 481 LVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTSGtrrgicanrynpcNP 560
Cdd:PRK02625 460 LVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAE-------------NP 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 561 KNYKNERIYetnykytkepfFCNSYDANGAYRQKRINLDSPLWLRWQLDQRVIASREVPIEVHYESFGNYHEIYAHYLIV 640
Cdd:PRK02625 527 GAQKGAGRY-----------FASLEDVIMAFEQGRIDLHAWVWVRFNGEVEDDDEDTEPLKTETLEDGTRIEQYRYRRDR 595
|
650 660
....*....|....*....|....*....
gi 212288281 641 RSVKKETYCIYIRTTVGHISFYREIEEAI 669
Cdd:PRK02625 596 FDEDGNLISQYILTTVGRVIMNKTIQDAL 624
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-543 |
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: 607.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 1 MIDRYKHQQLRIGLVSPQQISAWAtkiipngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNY---RVI 77
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWS---------YGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYkrmVYK 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 78 GdenedpKFCEQCGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPITKKP-- 155
Cdd:COG0086 72 G------VVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLY----FESYVVIDPgd 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 156 TFLRlRGSF----EY-EIQSwKYSiplffttqgfDIFRnreISTGAGAIRDQLADLDLRIIIENSLVEWKQLGEEgptgn 230
Cdd:COG0086 142 TPLE-KGQLltedEYrEILE-EYG----------DEFV---AKMGAEAIKDLLGRIDLEKESEELREELKETTSE----- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 231 ewedrkivRRKDFLVRRMELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLL 310
Cdd:COG0086 202 --------QKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLL 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 311 ttSRSTPGELVMCQEKLVQEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSL 390
Cdd:COG0086 274 --ELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPEL 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 391 SLHRCGLPREIAIELFQTFVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPIL 470
Cdd:COG0086 352 KLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVL 431
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 212288281 471 VEGRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLT 543
Cdd:COG0086 432 IEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLT 504
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
10-544 |
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: 604.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 10 LRIGLVSPQQISAWATkiipngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIgdeNEDPKFCEQ 89
Cdd:TIGR02386 2 IKISIASPDTIRNWSY---------GEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKI---RYKGVVCER 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 90 CGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPITKKPTFLRLrgsFEYEIQ 169
Cdd:TIGR02386 70 CGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLY----FENYVVLDPGDTKL---DKKEVL 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 170 SWK-YSIPLFFTTQGFDIfrnreiSTGAGAIRDQLADLDLRIIIEnslvewkQLGEEGPTGNEweDRKIVRrkdfLVRRM 248
Cdd:TIGR02386 143 DETeYREVLKRYGDGFRA------GMGAEAIKELLEKIDLDKEIE-------ELKIQLRESKS--DQKRKK----LLKRL 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 249 ELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLV 328
Cdd:TIGR02386 204 EIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG--APEIIVRNEKRML 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 329 QEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQT 408
Cdd:TIGR02386 282 QEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKP 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 409 FVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPLVCKGFNA 488
Cdd:TIGR02386 362 FIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNA 441
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*.
gi 212288281 489 DFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTS 544
Cdd:TIGR02386 442 DFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTT 497
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
10-544 |
3.13e-166 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 514.81 E-value: 3.13e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 10 LRIGLVSPQQISAWATkiipngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIgdenedpKF--- 86
Cdd:PRK14906 12 LRISLASAEDIRSWSH---------GEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRI-------RFkgi 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 87 -CEQCGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARPITKKP---------- 155
Cdd:PRK14906 76 vCERCGVEVTRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITSVDKEAreedaddlrd 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 156 ------------------TFLRLRGSFEYEIQSWKYSIPLF------------------------FTTQGFDIFRN---- 189
Cdd:PRK14906 156 elaadleeldaerdrlieATRRLSVDYVPEDDEFVDDIGDDerltaeevraevadiyeeynerkaLRREAFDAFMQiepk 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 190 ---------REI----------STGAGAIRDQLADLDLRIIIEnslvEWKQLGEEGPTgnewedrkivRRKDFLVRRMEL 250
Cdd:PRK14906 236 qlisdealyREMrlnysiyfkgGMGAEAVRDLLDAIDLEKEAE----ELRAIIANGKG----------QKREKAVKRLKV 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 251 AKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLVQE 330
Cdd:PRK14906 302 VDAFLKSGNDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLG--APEIIVNNEKRMLQE 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 331 AVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFV 410
Cdd:PRK14906 380 AVDSLFDNGRRGRPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFV 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 411 IRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPLVCKGFNADF 490
Cdd:PRK14906 460 MKRLVELEYAANIKAAKRAVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADF 539
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....
gi 212288281 491 DGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTS 544
Cdd:PRK14906 540 DGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTT 593
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
14-543 |
1.82e-153 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 492.13 E-value: 1.82e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 14 LVSPQQISAWATkiipngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRvigdeneDPKF-----CE 88
Cdd:PRK09603 1403 LASPEKIHSWSY---------GEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYK-------KPRFkdigtCE 1466
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 89 QCGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYcdfsFARPITKKP--TFLRLRGS--- 163
Cdd:PRK09603 1467 KCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLY----YEAYIVKEPgeAAYDNEGTklv 1542
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 164 FEYEI--QSWKYSIPLFFTTQGFdifrnrEISTGAGAIRDQLADLDLrIIIENSLVEwkqlgeegptgnEWEDRKIVRRK 241
Cdd:PRK09603 1543 MKYDIlnEEQYQNISRRYEDRGF------VAQMGGEAIKDLLEEIDL-ITLLQSLKE------------EVKDTNSDAKK 1603
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 242 DFLVRRMELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGELV 321
Cdd:PRK09603 1604 KKLIKRLKVVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELG--APEIIV 1681
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 322 MCQEKLVQEAVDTLLDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREI 401
Cdd:PRK09603 1682 RNEKRMLQEAVDVLFDNGRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNM 1761
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 402 AIELFQTFVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPL 481
Cdd:PRK09603 1762 ALELFKPHLLSKLEERGYATTLKQAKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPL 1841
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 212288281 482 VCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLT 543
Cdd:PRK09603 1842 VCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLS 1903
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
9-543 |
2.48e-148 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 477.19 E-value: 2.48e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 9 QLRIGLVSPQQISAWAtkiipngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICACGNYRvigDENEDPKFCE 88
Cdd:PRK14844 1450 EVSISIASPESIKRMS---------YGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYK---KRRHRGRICE 1517
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 89 QCGVEFVDSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDfsfaRPITKKPtflrLRGSFEY-E 167
Cdd:PRK14844 1518 KCGVEVTSSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSD----NYIVIDP----LVSPFEKgE 1589
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 168 IQSWK--------YSIPLFFTTQGFDifrnreistgagAIRDQLADLDLRIIIENSLVEWKQLGEEgptgnewedrkiVR 239
Cdd:PRK14844 1590 IISEKayneakdsYGIDSFVAMQGVE------------AIRELLTRLDLHEIRKDLRLELESVASE------------IR 1645
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 240 RKDfLVRRMELAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrstPGE 319
Cdd:PRK14844 1646 RKK-IIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLN---PPE 1721
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 320 LVMCQEK-LVQEAVDTLLDNGIRGQPM-RDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGL 397
Cdd:PRK14844 1722 IMIRNEKrMLQEAVDSLFDNSRRNALVnKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGL 1801
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 398 PREIAIELFQTFVIRGLIRQHLASNIGVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTIC 477
Cdd:PRK14844 1802 PKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQ 1881
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212288281 478 LHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLT 543
Cdd:PRK14844 1882 LHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLT 1947
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
262-540 |
1.44e-138 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 407.29 E-value: 1.44e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 262 EWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLVQEAVDTLLDN-GI 340
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELG--APSIIIRNEKRLLQEAVDTLIDNeGL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 341 RGQPMRDGhnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHL- 419
Cdd:smart00663 79 PRANQKSG--RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLr 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 420 -----------------ASNIGVAK-SQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPL 481
Cdd:smart00663 157 klvrngpngakyiirgkKTNLKLAKkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPL 236
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 212288281 482 VCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLY 540
Cdd:smart00663 237 VCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
16-547 |
6.53e-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: 268.92 E-value: 6.53e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 16 SPQQISAWAtkiipngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFgpiksgicacgnyrvigdeneDPKFCEQCGVEFV 95
Cdd:cd00399 2 SPEEIRKWS---------VAKVIKPETIDNRTLKAERGGKYDPRLG---------------------SIDRCEKCGTCGT 51
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 96 DSRIRRYQMGYIKLTCPVTHVWYLKRLPSYIanlldkplkeleglvycdfsfarpitkkptflrlrgsfeyeiqswkysi 175
Cdd:cd00399 52 GLNDCPGHFGHIELAKPVFHVGFIKKVPSFL------------------------------------------------- 82
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 176 plffttqgfdifrnreistgagairdqladldlriiienslvewkqlgeegptgnewedrkivrrkdflvrrmelakhfi 255
Cdd:cd00399 --------------------------------------------------------------------------------
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 256 rtniEPEWMVLCLLPVLPPELRPIIQIEGgklmssdinelyrrviyrnntltdllttsrstpgelvmcQEKLVQEAVDTL 335
Cdd:cd00399 83 ----GPEWMILTCLPVPPPCLRPSVIIEE---------------------------------------RWRLLQEHVDTY 119
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 336 LDNGIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELfqtfvirgli 415
Cdd:cd00399 120 LDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL---------- 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 416 rqhlasnigvaksqirekkpivweilqevmQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPLVCKGFNADFDGDQM 495
Cdd:cd00399 190 ------------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEM 239
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|..
gi 212288281 496 ADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTSGTR 547
Cdd:cd00399 240 NLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTLGKQ 291
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
261-548 |
1.80e-54 |
|
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: 200.55 E-value: 1.80e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 261 PEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLVQEAVDTLLDNGI 340
Cdd:cd02582 202 PEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAG--APQLIIEDLWDLLQYHVTTYFDNEI 279
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 341 RGQP-MRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA-------------IELF 406
Cdd:cd02582 280 PGIPpARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAkeltvpervtewnIEKM 359
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 407 QTFVIRGLIRQHLASNI-----------GVAKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRT 475
Cdd:cd02582 360 RKLVLNGPDKWPGANYVirpdgrrirlrYVNREELAERLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKT 439
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 212288281 476 ICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTSGTRR 548
Cdd:cd02582 440 FRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTL 512
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
261-548 |
8.98e-50 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 186.99 E-value: 8.98e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 261 PEWMVLCLLPVLPPELRPIIQIEGG---------KLMssDInelyrrvIYRNNTLTDLLTTSrsTPGELVMCQEKLVQEA 331
Cdd:PRK08566 206 PEWMVLTVLPVPPVTVRPSITLETGqrseddlthKLV--DI-------IRINQRLKENIEAG--APQLIIEDLWELLQYH 274
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 332 VDTLLDNGIRGQPM---RDGhnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA------ 402
Cdd:PRK08566 275 VTTYFDNEIPGIPParhRSG--RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAkeltvp 352
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 403 -------IELFQTFVIRG---------LIRQHlASNIGVA---KSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGI 463
Cdd:PRK08566 353 ervtewnIEELREYVLNGpekhpganyVIRPD-GRRIKLTdknKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSI 431
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 464 QSFQPILVEGRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLT 543
Cdd:PRK08566 432 MAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLT 511
|
....*
gi 212288281 544 SGTRR 548
Cdd:PRK08566 512 RKSTL 516
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
261-543 |
4.95e-48 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 182.92 E-value: 4.95e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 261 PEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTDllTTSRSTPGELVMCQEKLVQEAVDTLLDNGI 340
Cdd:PRK14977 215 PEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKE--SKDAGAPPLIVEDEVDHLQYHTSTFFDNAT 292
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 341 RGQP--MRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA-------------IEL 405
Cdd:PRK14977 293 AGIPqaHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAmkltipeivnennIEK 372
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 406 FQTFVIRG--------LIRQHLASNIGV---------AKSQIREKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQP 468
Cdd:PRK14977 373 MKELVINGpdefpganAIRKGDGTKIRLdfledkgkdALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRV 452
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 212288281 469 ILVEGRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLT 543
Cdd:PRK14977 453 KVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLIT 527
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
10-371 |
4.08e-47 |
|
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: 169.01 E-value: 4.08e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 10 LRIGLVSPQQISAWAtkiipngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICA-CGnyrvigdenedpKFCE 88
Cdd:pfam04997 7 IQFGIASPEEIRKWS---------VGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCG------------KKKK 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 89 QCGVEFvdsrirryqmGYIKLTCPVTHVWYLKrlpsYIANLLDKPLKeleglvYCdfsfarpitkkpTFLRLRGSFEYEI 168
Cdd:pfam04997 66 DCPGHF----------GHIELAKPVFHIGFFK----KTLKILECVCK------YC------------SKLLLDPGKPKLF 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 169 QSWKYsiplffttqgfdIFRNREISTGAGAIRDQLADLDLriiIENSLVEWKQLGEEGPTGNE--------WEDRKIVRR 240
Cdd:pfam04997 114 NKDKK------------RLGLENLKMGAKAILELCKKKDL---CEHCGGKNGVCGSQQPVSRKeglklkaaIKKSKEEEE 178
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 241 KDFLV--RRMELAKHFIRTNIE----------PEWMVLCLLPVLPPELRPIIQIEGGKLMSSDINELYRRVIYRNNTLTD 308
Cdd:pfam04997 179 KEILNpeKVLKIFKRISDEDVEilgfnpsgsrPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKK 258
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212288281 309 LLTTsrSTPGELVMCQEKLVQEAVDTLLDNGIRGQP---MRDghNKVYKSFSDVIEGKEGRFRETL 371
Cdd:pfam04997 259 LLEL--GAPSHIIREEWRLLQEHVATLFDNEIPGLPpalQKS--KRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
373-513 |
7.35e-42 |
|
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: 149.37 E-value: 7.35e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 373 GKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELFQTFVIRGLIRQHL-------------ASNIGVAKSQIR-------- 431
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLrqlvengpnvypgANYIIRINGARRdlryqkrr 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 432 --EKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQPILVEGRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEA 509
Cdd:pfam00623 81 ldKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....
gi 212288281 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 |
3.59e-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: 160.39 E-value: 3.59e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 261 PEWMVLCLLPVLPPELRPIIQIEGGklMSS--DINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLVQEAVDTLLDN 338
Cdd:cd02733 125 PDWMILTVLPVPPPAVRPSVVMDGS--ARSedDLTHKLADIIKANNQLKRQEQNG--APAHIIEEDEQLLQFHVATYMDN 200
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 339 GIRGQPM---RDGhnKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIEL-FQTFV---- 410
Cdd:cd02733 201 EIPGLPQatqKSG--RPLKSIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLtFPEIVtpfn 278
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 411 ---IRGLIRQHLASNIGvAKSQIRE-----------KKPIVweILQE-------VMQGHPVLLNRAPTLHRLGIQSFQPI 469
Cdd:cd02733 279 idrLQELVRNGPNEYPG-AKYIIRDdgeridlrylkKASDL--HLQYgyiverhLQDGDVVLFNRQPSLHKMSMMGHRVK 355
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 212288281 470 LVEGRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLT 543
Cdd:cd02733 356 VLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLT 429
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
261-544 |
9.63e-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: 153.47 E-value: 9.63e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 261 PEWMVLCLLPVLPPELRPIIQIEGGKlMSS--DINELYRRVIYRNNTLTDLLTTSrsTPGELVMCQEKLVQEAVDTLLDN 338
Cdd:cd02583 175 PENLILTRIPVPPLCIRPSVVMDEKS-GTNedDLTVKLSEIIFLNDVIKKHLEKG--AKTQKIMEDWDFLQLQCALYINS 251
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 339 GIRGQPMRDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIA-------------IEL 405
Cdd:cd02583 252 ELPGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAkiltypervtrynIEK 331
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 406 FQTFVIRG---------LIRQHlasniGVAKSQIR--EKKPIVWE------ILQEVMQGHPVLLNRAPTLHRLGIQSFQP 468
Cdd:cd02583 332 LRKLVLNGpdvhpganfVIKRD-----GGKKKFLKygNRRKIARElkigdiVERHLEDGDIVLFNRQPSLHRLSIMAHRA 406
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 212288281 469 ILVEGRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTS 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 |
4.15e-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: 130.00 E-value: 4.15e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 269 LPVLPPELRPIIQIeGGKLMSSDINELYRRVIYRNNTLTDLLTTSRSTPGELVMC-------QEKLV------QEAVDTL 335
Cdd:cd01435 135 LLVPPNRFRPPSFL-GDKVFENPQNVLLSKILKDNQQIRDLLASMRQAESQSKLDlisgktnSEKLInawlqlQSAVNEL 213
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 336 LDNGIRGqpmrDGHNKVYKSFSDVIEGKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIELfqTF------ 409
Cdd:cd01435 214 FDSTKAP----KSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKL--TFpepvtp 287
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 410 ---------VIRG-------------------LIRQHLASNIGVAKSQIREKKP--------IVWEILQEvmqGHPVLLN 453
Cdd:cd01435 288 fnveelrqaVINGpdvypganaiededgrlilLSALSEERRKALAKLLLLLSSAklllngpkKVYRHLLD---GDVVLLN 364
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 454 RAPTLHRLGIQSFQ-PILVEGRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPT 532
Cdd:cd01435 365 RQPTLHKPSIMAHKvRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLI 444
|
330
....*....|..
gi 212288281 533 QDMLIGLYVLTS 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 ... |
367-544 |
6.79e-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: 97.48 E-value: 6.79e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 367 FRETLLGKRVDYSGRSVIVVGPSLSLHRCGLPREIAIEL-------------FQTFVIRGLI---RQHLASNIGVAKSQI 430
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLtvservsswnrerLQEYCDLTLLlkgVIGVRRNGRLVGVRS 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212288281 431 REKKPIVWEILQEVMQGHPVLLNRAPTLHRLGIQSFQ-PILVEGRTICLHPLVCKGFNADFDGDQMADHVPLSLEAQAEA 509
Cdd:cd10506 286 HNTLQIGDVIHRPLVDGDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAEL 365
|
170 180 190
....*....|....*....|....*....|....*
gi 212288281 510 RLLMFSHMNLLSPAIGDPISVPTQDMLIGLYVLTS 544
Cdd:cd10506 366 EELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTE 400
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
518-555 |
4.41e-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: 44.16 E-value: 4.41e-05
10 20 30
....*....|....*....|....*....|....*...
gi 212288281 518 NLLSPAIGDPISVPTQDMLIGLYVLtsgTRRGICANRY 555
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLL---TREDTFFDRE 35
|
|
|