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Conserved domains on  [gi|212288281|sp|A4QKS2|]
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RecName: Full=DNA-directed RNA polymerase subunit beta'; AltName: Full=PEP; AltName: Full=Plastid-encoded RNA polymerase subunit beta'; Short=RNA polymerase subunit beta'

Protein Classification

DNA-directed RNA polymerase subunit beta'( domain architecture ID 11413999)

chloroplast DNA-directed RNA polymerase (RNAP) subunit beta' (rpoC1) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Graphical summary

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List of domain hits

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
 
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
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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