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Conserved domains on  [gi|198279189|emb|CAP04628|]
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RNA polymerase beta subunit, partial (plastid) [Conostylis teretifolia subsp. planescens]

Protein Classification

DNA-directed RNA polymerase subunit beta'( domain architecture ID 1004693)

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

EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0006351|GO:0003677|GO:0046872|GO:0000428
PubMed:  24211837|18468900|12361249

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rpoC1 super family cl29902
RNA polymerase beta' subunit
 1-176 6.07e-154

RNA polymerase beta' subunit


The actual alignment was detected with superfamily member CHL00018:

Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 439.72  E-value: 6.07e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:CHL00018 362 GKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEIL 441

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:CHL00018 442 QEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLS 521

                        170
                 ....*....|....*.
gi 198279189 161 PAMGDPISVPTQDMLM 176
Cdd:CHL00018 522 PAIGDPISVPSQDMLL 537
 
Name Accession Description Interval E-value
rpoC1 CHL00018
RNA polymerase beta' subunit
 1-176 6.07e-154

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 439.72  E-value: 6.07e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:CHL00018 362 GKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEIL 441

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:CHL00018 442 QEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLS 521

                        170
                 ....*....|....*.
gi 198279189 161 PAMGDPISVPTQDMLM 176
Cdd:CHL00018 522 PAIGDPISVPSQDMLL 537
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 1-176 1.99e-130

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: 379.56  E-value: 1.99e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:cd01609  238 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDIL 317

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:cd01609  318 EEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILS 397

                        170
                 ....*....|....*.
gi 198279189 161 PAMGDPISVPTQDMLM 176
Cdd:cd01609  398 PASGKPIVTPSQDMVL 413
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-174 7.04e-109

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: 335.59  E-value: 7.04e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:COG0086   323 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDIL 402

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:COG0086   403 EEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILS 482

                         170
                  ....*....|....
gi 198279189  161 PAMGDPISVPTQDM 174
Cdd:COG0086   483 PANGKPIIVPSQDM 496
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 1-176 1.28e-104

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: 323.92  E-value: 1.28e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189     1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:TIGR02386  315 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVL 394

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:TIGR02386  395 EDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILN 474

                          170
                   ....*....|....*.
gi 198279189   161 PAMGDPISVPTQDMLM 176
Cdd:TIGR02386  475 PKDGKPIVTPSQDMVL 490
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
1-176 5.71e-101

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 292.50  E-value: 5.71e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189     1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHV------------------ASNI 62
Cdd:smart00663  98 GKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLrklvrngpngakyiirgkKTNL 177

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    63 GIAK-SKIREKESVVWEILREVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLS 141
Cdd:smart00663 178 KLAKkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQS 257

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 198279189   142 LEAQAEARLLMFSHINLLSPAMGDPISVPTQDMLM 176
Cdd:smart00663 258 LEARAEARELMLVPNNILSPKNGKPIIGPIQDMLL 292
RNA_pol_Rpb1_2 pfam00623
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 12-152 5.14e-49

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: 155.92  E-value: 5.14e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   12 GKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHV--ASNIG-----IAKSKIREKESVV-------- 76
Cdd:pfam00623   1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLrqLVENGpnvypGANYIIRINGARRdlryqkrr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   77 --------WEILREVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEA 148
Cdd:pfam00623  81 ldkeleigDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160


                  ....
gi 198279189  149 RLLM 152
Cdd:pfam00623 161 EELM 164
 
Name Accession Description Interval E-value
rpoC1 CHL00018
RNA polymerase beta' subunit
 1-176 6.07e-154

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 439.72  E-value: 6.07e-154
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:CHL00018 362 GKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEIL 441

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:CHL00018 442 QEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLS 521

                        170
                 ....*....|....*.
gi 198279189 161 PAMGDPISVPTQDMLM 176
Cdd:CHL00018 522 PAIGDPISVPSQDMLL 537
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 1-176 1.99e-130

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: 379.56  E-value: 1.99e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:cd01609  238 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDIL 317

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:cd01609  318 EEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILS 397

                        170
                 ....*....|....*.
gi 198279189 161 PAMGDPISVPTQDMLM 176
Cdd:cd01609  398 PASGKPIVTPSQDMVL 413
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 1-174 2.27e-120

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 365.93  E-value: 2.27e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:PRK00566  323 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVL 402

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:PRK00566  403 EEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILS 482

                         170
                  ....*....|....
gi 198279189  161 PAMGDPISVPTQDM 174
Cdd:PRK00566  483 PANGKPIIVPSQDM 496
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-174 7.04e-109

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: 335.59  E-value: 7.04e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:COG0086   323 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDIL 402

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:COG0086   403 EEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILS 482

                         170
                  ....*....|....
gi 198279189  161 PAMGDPISVPTQDM 174
Cdd:COG0086   483 PANGKPIIVPSQDM 496
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
 1-176 8.16e-106

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 315.53  E-value: 8.16e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:PRK02625 341 GKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADPEVWQVL 420

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:PRK02625 421 EEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILS 500

                        170
                 ....*....|....*.
gi 198279189 161 PAMGDPISVPTQDMLM 176
Cdd:PRK02625 501 PATGEPIVTPSQDMVL 516
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 1-176 1.28e-104

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: 323.92  E-value: 1.28e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189     1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:TIGR02386  315 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVL 394

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:TIGR02386  395 EDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILN 474

                          170
                   ....*....|....*.
gi 198279189   161 PAMGDPISVPTQDMLM 176
Cdd:TIGR02386  475 PKDGKPIVTPSQDMVL 490
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
1-176 5.71e-101

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 292.50  E-value: 5.71e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189     1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHV------------------ASNI 62
Cdd:smart00663  98 GKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLrklvrngpngakyiirgkKTNL 177

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    63 GIAK-SKIREKESVVWEILREVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLS 141
Cdd:smart00663 178 KLAKkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQS 257

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 198279189   142 LEAQAEARLLMFSHINLLSPAMGDPISVPTQDMLM 176
Cdd:smart00663 258 LEARAEARELMLVPNNILSPKNGKPIIGPIQDMLL 292
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
1-176 5.51e-92

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 292.16  E-value: 5.51e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:PRK14906  411 GKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGASYVWDVL 490

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:PRK14906  491 EEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKS 570

                         170
                  ....*....|....*.
gi 198279189  161 PAMGDPISVPTQDMLM 176
Cdd:PRK14906  571 PAHGRPLTVPTQDMII 586
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-176 6.42e-81

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 261.10  E-value: 6.42e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:PRK14844 1766 GKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDML 1845

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:PRK14844 1846 EEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLS 1925

                         170
                  ....*....|....*.
gi 198279189  161 PAMGDPISVPTQDMLM 176
Cdd:PRK14844 1926 PSNGRPIIVPSKDIVL 1941
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-176 1.71e-77

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 251.00  E-value: 1.71e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHVASNIGIAKSKIREKESVVWEIL 80
Cdd:PRK09603 1722 GKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKSNEVWECL 1801

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   81 REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:PRK09603 1802 QEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILL 1881

                         170
                  ....*....|....*.
gi 198279189  161 PAMGDPISVPTQDMLM 176
Cdd:PRK09603 1882 PASGKAVAIPSQDMVL 1897
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 1-175 2.69e-64

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: 205.74  E-value: 2.69e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELfqtfvirglirqhvasnigiakskirekesvvweil 80
Cdd:cd00399  146 GKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL------------------------------------ 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  81 revmQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLS 160
Cdd:cd00399  190 ----DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILS 265

                        170
                 ....*....|....*
gi 198279189 161 PAMGDPISVPTQDML 175
Cdd:cd00399  266 PQNGEPLIGLSQDTL 280
RNA_pol_Rpb1_2 pfam00623
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 12-152 5.14e-49

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: 155.92  E-value: 5.14e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   12 GKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQTFVIRGLIRQHV--ASNIG-----IAKSKIREKESVV-------- 76
Cdd:pfam00623   1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLrqLVENGpnvypGANYIIRINGARRdlryqkrr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   77 --------WEILREVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEA 148
Cdd:pfam00623  81 ldkeleigDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160


                  ....
gi 198279189  149 RLLM 152
Cdd:pfam00623 161 EELM 164
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 1-173 4.66e-47

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: 163.57  E-value: 4.66e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIA-------------IELFQTFVIRGlIRQHVASNIGIAK- 66
Cdd:cd02582  302 GKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAkeltvpervtewnIEKMRKLVLNG-PDKWPGANYVIRPd 380

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  67 -SKIR----EKESVV------WEILREVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMA 135
Cdd:cd02582  381 gRRIRlryvNREELAerlepgWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMN 460

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 198279189 136 VHVPLSLEAQAEARLLMFSHINLLSPAMGDPISVPTQD 173
Cdd:cd02582  461 LHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQD 498
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 1-173 4.70e-44

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 155.01  E-value: 4.70e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIA-------------IELFQTFVIRGLIRqHVASNIGIAK- 66
Cdd:PRK08566 306 GKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAkeltvpervtewnIEELREYVLNGPEK-HPGANYVIRPd 384

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  67 -SKIR----EKESVV------WEILREVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMA 135
Cdd:PRK08566 385 gRRIKltdkNKEELAeklepgWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMN 464

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 198279189 136 VHVPLSLEAQAEARLLMFSHINLLSPAMGDPISVPTQD 173
Cdd:PRK08566 465 LHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQD 502
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
 1-175 5.73e-40

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: 143.46  E-value: 5.73e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIA-------------IELFQTFVIRG---------LIRQHV 58
Cdd:cd02583  275 GKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAkiltypervtrynIEKLRKLVLNGpdvhpganfVIKRDG 354

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  59 --ASNIGIAKSKIREKESVVWEIL-REVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMA 135
Cdd:cd02583  355 gkKKFLKYGNRRKIARELKIGDIVeRHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMN 434

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 198279189 136 VHVPLSLEAQAEARLLMFSHINLLSPAMGDPISVPTQDML 175
Cdd:cd02583  435 LHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFL 474
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 1-175 8.26e-38

bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 137.46  E-value: 8.26e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189    1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIA-------------IELFQTFVIRG--------LIRQHVA 59
Cdd:PRK14977  316 GKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAmkltipeivnennIEKMKELVINGpdefpganAIRKGDG 395

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   60 SNIGI---------AKSKIREKESVVWEILREVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFD 130
Cdd:PRK14977  396 TKIRLdfledkgkdALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFD 475

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 198279189  131 GDQMAVHVPLSLEAQAEARLLMFSHINLLSPAMGDPISVPTQDML 175
Cdd:PRK14977  476 GDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFI 520
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 1-164 3.11e-30

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: 115.71  E-value: 3.11e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   1 GKEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIEL-FQTFV-------IRGLIRQHVASNIGiAKSKIRE- 71
Cdd:cd02733  225 GKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLtFPEIVtpfnidrLQELVRNGPNEYPG-AKYIIRDd 303

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  72 ----------KESVV-----WEILREVMQGHPVLLNRAPTLHRLGIQAFqpilvegRAICLHPL-------VCKGFNADF 129
Cdd:cd02733  304 geridlrylkKASDLhlqygYIVERHLQDGDVVLFNRQPSLHKMSMMGH-------RVKVLPYStfrlnlsVTTPYNADF 376

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 198279189 130 DGDQMAVHVPLSLEAQAEARLLMFSHINLLSPA-----MG 164
Cdd:cd02733  377 DGDEMNLHVPQSLETRAELKELMMVPRQIVSPQsnkpvMG 416
RNAP_I_RPA1_N cd01435
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
 2-173 6.42e-30

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: 114.59  E-value: 6.42e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   2 KEGRFRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELfqTF---------------VIRG--------LIRQHV 58
Cdd:cd01435  237 KEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKL--TFpepvtpfnveelrqaVINGpdvypganAIEDED 314

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  59 ASNIGIAKSKIREKES-------------------VVWeilREVMQGHPVLLNRAPTLHRLGIQAFQ-PILVEGRAICLH 118
Cdd:cd01435  315 GRLILLSALSEERRKAlaklllllssaklllngpkKVY---RHLLDGDVVLLNRQPTLHKPSIMAHKvRVLPGEKTLRLH 391

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 198279189 119 PLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHINLLSPAMGDPISVPTQD 173
Cdd:cd01435  392 YANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQD 446
RNAP_IV_RPD1_N cd10506
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
 6-175 3.21e-25

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: 101.33  E-value: 3.21e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189   6 FRETLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIEL-------------FQTFVIRGLI---RQHVASNIGIAKSKI 69
Cdd:cd10506  206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLtvservsswnrerLQEYCDLTLLlkgVIGVRRNGRLVGVRS 285

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 198279189  70 REKESVVWEILREVMQGHPVLLNRAPTLHRLGIQAFQ-PILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEA 148
Cdd:cd10506  286 HNTLQIGDVIHRPLVDGDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAEL 365

                        170       180
                 ....*....|....*....|....*..
gi 198279189 149 RLLMFSHINLLSPAMGDPISVPTQDML 175
Cdd:cd10506  366 EELVALPKQLISSQSGQNLLSLTQDSL 392
 
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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