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Conserved domains on  [gi|338855703|gb|AEJ32130|]
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DNA directed RNA polymerase beta subunit, partial [Synechococcus sp. A15-146]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rpoC1 super family cl29785
DNA-directed RNA polymerase subunit gamma; Provisional
 1-216 1.16e-139

DNA-directed RNA polymerase subunit gamma; Provisional


The actual alignment was detected with superfamily member PRK02625:

Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 404.13  E-value: 1.16e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:PRK02625 404 AAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLE 483

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASKpdfgDRSCTFAGLEDVIHAFEDNRIGLHDWVWV 160
Cdd:PRK02625 484 AQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQK----GAGRYFASLEDVIMAFEQGRIDLHAWVWV 559

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 338855703 161 RFNGEVQDDEELDAPSKSESLSDGTRIEEWSYRRDRFDEDGALISRYILTTVGRVV 216
Cdd:PRK02625 560 RFNGEVEDDDEDTEPLKTETLEDGTRIEQYRYRRDRFDEDGNLISQYILTTVGRVI 615
 
Name Accession Description Interval E-value
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
 1-216 1.16e-139

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 404.13  E-value: 1.16e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:PRK02625 404 AAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLE 483

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASKpdfgDRSCTFAGLEDVIHAFEDNRIGLHDWVWV 160
Cdd:PRK02625 484 AQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQK----GAGRYFASLEDVIMAFEQGRIDLHAWVWV 559

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 338855703 161 RFNGEVQDDEELDAPSKSESLSDGTRIEEWSYRRDRFDEDGALISRYILTTVGRVV 216
Cdd:PRK02625 560 RFNGEVEDDDEDTEPLKTETLEDGTRIEQYRYRRDRFDEDGNLISQYILTTVGRVI 615
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 1-127 4.28e-90

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: 277.86  E-value: 4.28e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:cd01609  301 SAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLE 380

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 338855703  81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASK 127
Cdd:cd01609  381 AQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTKERKGDKG 427
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-215 8.47e-89

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: 283.20  E-value: 8.47e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703    1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:COG0086   386 SAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLE 465

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASKPDFgdrscTFAGLEDVIHAFEDNRIGLHDWVWV 160
Cdd:COG0086   466 AQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGM-----IFADPEEVLRAYENGAVDLHARIKV 540

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 338855703  161 RFNgevqddeeldapskseslsdgtrieewsyrrdrfdEDGALISRYILTTVGRV 215
Cdd:COG0086   541 RIT-----------------------------------EDGEQVGKIVETTVGRY 560
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 1-166 1.82e-84

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: 271.15  E-value: 1.82e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703     1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:TIGR02386  378 SAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPE 457

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703    81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASKpdfgdRSCTFAGLEDVIHAFEDNRIGLHDWVWV 160
Cdd:TIGR02386  458 AQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKG-----EGKIFSNVDEAIRAYDNGKVHLHALIGV 532


                   ....*.
gi 338855703   161 RFNGEV 166
Cdd:TIGR02386  533 RTSGEI 538
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
3-116 5.43e-69

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 212.76  E-value: 5.43e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703     3 KKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQ 82
Cdd:smart00663 182 KSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEAR 261

                           90       100       110
                   ....*....|....*....|....*....|....
gi 338855703    83 TEARMLMLASNNILSPATGEPIITPSQDMVLGSY 116
Cdd:smart00663 262 AEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
RNA_pol_Rpb1_2 pfam00623
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 20-91 4.71e-34

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: 119.33  E-value: 4.71e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 338855703   20 VIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLA 91
Cdd:pfam00623  95 VIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEAEELMLV 166
 
Name Accession Description Interval E-value
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
 1-216 1.16e-139

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 404.13  E-value: 1.16e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:PRK02625 404 AAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLE 483

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASKpdfgDRSCTFAGLEDVIHAFEDNRIGLHDWVWV 160
Cdd:PRK02625 484 AQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQK----GAGRYFASLEDVIMAFEQGRIDLHAWVWV 559

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 338855703 161 RFNGEVQDDEELDAPSKSESLSDGTRIEEWSYRRDRFDEDGALISRYILTTVGRVV 216
Cdd:PRK02625 560 RFNGEVEDDDEDTEPLKTETLEDGTRIEQYRYRRDRFDEDGNLISQYILTTVGRVI 615
rpoC1 CHL00018
RNA polymerase beta' subunit
 1-215 6.44e-108

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 323.78  E-value: 6.44e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:CHL00018 425 AAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLE 504

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQP----GASKPDFGDRSCT----FAGLEDVIHAFEDNRI 152
Cdd:CHL00018 505 AQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRrgiyANRYNPCNRKNSTkepyFSNSYDALGAYRQKRI 584

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 338855703 153 GLHDWVWVRFNGEVQDDEELDAPSKSESLSDGTRIEEWSYRRDRFDEDGALISRYILTTVGRV 215
Cdd:CHL00018 585 NLDSPLWLRWRLDQRIIASREVPIEVQYESLGTYHEIYEHYLIVKSRKKEILSIYIRTTVGRI 647
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 1-165 7.95e-101

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 315.85  E-value: 7.95e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703    1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:PRK00566  386 SAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLE 465

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASkpdfGDRScTFAGLEDVIHAFEDNRIGLHDWVWV 160
Cdd:PRK00566  466 AQAEARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAK----GEGM-VFSSPEEALRAYENGEVDLHARIKV 540


                  ....*
gi 338855703  161 RFNGE 165
Cdd:PRK00566  541 RITSK 545
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 1-127 4.28e-90

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: 277.86  E-value: 4.28e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:cd01609  301 SAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLE 380

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 338855703  81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASK 127
Cdd:cd01609  381 AQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTKERKGDKG 427
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-215 8.47e-89

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: 283.20  E-value: 8.47e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703    1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:COG0086   386 SAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLE 465

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASKPDFgdrscTFAGLEDVIHAFEDNRIGLHDWVWV 160
Cdd:COG0086   466 AQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGM-----IFADPEEVLRAYENGAVDLHARIKV 540

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 338855703  161 RFNgevqddeeldapskseslsdgtrieewsyrrdrfdEDGALISRYILTTVGRV 215
Cdd:COG0086   541 RIT-----------------------------------EDGEQVGKIVETTVGRY 560
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 1-166 1.82e-84

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: 271.15  E-value: 1.82e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703     1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:TIGR02386  378 SAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPE 457

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703    81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASKpdfgdRSCTFAGLEDVIHAFEDNRIGLHDWVWV 160
Cdd:TIGR02386  458 AQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEKPGAKG-----EGKIFSNVDEAIRAYDNGKVHLHALIGV 532


                   ....*.
gi 338855703   161 RFNGEV 166
Cdd:TIGR02386  533 RTSGEI 538
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
3-116 5.43e-69

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 212.76  E-value: 5.43e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703     3 KKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQ 82
Cdd:smart00663 182 KSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEAR 261

                           90       100       110
                   ....*....|....*....|....*....|....
gi 338855703    83 TEARMLMLASNNILSPATGEPIITPSQDMVLGSY 116
Cdd:smart00663 262 AEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
1-180 7.40e-65

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 216.66  E-value: 7.40e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703    1 AAKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIE 80
Cdd:PRK14906  474 AAKRAVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQ 553

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   81 AQTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGaskpdFGDRSCTFAGLEDVIHAFEDNR-IGLHDWVW 159
Cdd:PRK14906  554 AQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDG-----FEGEGRTFADFDDALNAYDARAdLDLQAKIV 628

                         170       180
                  ....*....|....*....|....*..
gi 338855703  160 VRFN------GEVQDDEELDAPSKSES 180
Cdd:PRK14906  629 VRLSrdmtvrGSYGDLEETKAGERIET 655
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
2-155 1.06e-59

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 202.16  E-value: 1.06e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703    2 AKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEA 81
Cdd:PRK14844 1830 ASKLIRAEKPEVWDMLEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEA 1909

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 338855703   82 QTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPgasKPDFGDRSCTFAGLEdviHAFEDNRIGLH 155
Cdd:PRK14844 1910 QLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQEP---KEDDLPSFGAFCEVE---HSLSDGTLHIH 1977
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
2-155 3.55e-58

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 197.84  E-value: 3.55e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703    2 AKKLIQRADDEVMQVLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEA 81
Cdd:PRK09603 1786 AKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEA 1865

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 338855703   82 QTEARMLMLASNNILSPATGEPIITPSQDMVLGSYYLTALQPGASkpdfGDRScTFAGLEDVIHAFEDNRIGLH 155
Cdd:PRK09603 1866 IAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVK----GEHK-LFSSVNEIITAIDTKELDIH 1934
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 21-119 5.31e-52

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: 175.31  E-value: 5.31e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  21 IDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLASNNILSPAT 100
Cdd:cd00399  189 LDGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQN 268

                         90
                 ....*....|....*....
gi 338855703 101 GEPIITPSQDMVLGSYYLT 119
Cdd:cd00399  269 GEPLIGLSQDTLLGAYLLT 287
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 20-119 8.34e-36

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: 133.14  E-value: 8.34e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  20 VIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLASNNILSPA 99
Cdd:cd02582  408 LIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPR 487

                         90       100
                 ....*....|....*....|
gi 338855703 100 TGEPIITPSQDMVLGSYYLT 119
Cdd:cd02582  488 YGGPIIGGIQDYISGAYLLT 507
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 21-119 3.97e-35

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 131.13  E-value: 3.97e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  21 IDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLASNNILSPAT 100
Cdd:PRK08566 413 IDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRY 492

                         90
                 ....*....|....*....
gi 338855703 101 GEPIITPSQDMVLGSYYLT 119
Cdd:PRK08566 493 GGPIIGGIQDHISGAYLLT 511
RNA_pol_Rpb1_2 pfam00623
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 20-91 4.71e-34

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: 119.33  E-value: 4.71e-34
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 338855703   20 VIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLA 91
Cdd:pfam00623  95 VIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEAEELMLV 166
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
 16-152 6.92e-31

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: 119.19  E-value: 6.92e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  16 VLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLASNNI 95
Cdd:cd02583  378 VERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNL 457

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 338855703  96 LSPATGEPIITPSQDMVLGSYYLTalqpgaSKPDFGDRScTFAGLedvIHAFEDNRI 152
Cdd:cd02583  458 VTPRNGEPLIAATQDFLTASYLLT------SKDVFFDRA-QFCQL---CSYMLDGEI 504
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 16-119 1.56e-28

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


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 112.43  E-value: 1.56e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703   16 VLQEVIDGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLASNNI 95
Cdd:PRK14977  424 VERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNL 503

                          90       100
                  ....*....|....*....|....
gi 338855703   96 LSPATGEPIITPSQDMVLGSYYLT 119
Cdd:PRK14977  504 ISPRTGGPIIGALQDFITAAYLIT 527
RNAP_I_RPA1_N cd01435
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
 14-119 6.03e-22

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: 93.40  E-value: 6.03e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  14 MQVLQEVIDGHPILLNRAPTLHRLGIQAFEPK-LVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLAS 92
Cdd:cd01435  349 KKVYRHLLDGDVVLLNRQPTLHKPSIMAHKVRvLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTD 428

                         90       100       110
                 ....*....|....*....|....*....|
gi 338855703  93 NNILSPATGEPI---ItpsQDMVLGSYYLT 119
Cdd:cd01435  429 NQYLVPTDGKPLrglI---QDHVVSGVLLT 455
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 22-119 4.77e-18

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: 81.81  E-value: 4.77e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  22 DGHPILLNRAPTLHRLGIQAFEPKLVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLASNNILSPATG 101
Cdd:cd02733  332 DGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSN 411

                         90
                 ....*....|....*...
gi 338855703 102 EPIITPSQDMVLGSYYLT 119
Cdd:cd02733  412 KPVMGIVQDTLLGVRKLT 429
RNAP_IV_RPD1_N cd10506
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
 20-119 1.28e-16

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: 77.83  E-value: 1.28e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 338855703  20 VIDGHPILLNRAPTLHRLGIQAFEPKLV-DGRAIQLHPLVCPAFNADFDGDQMAVHVPLAIEAQTEARMLMLASNNILSP 98
Cdd:cd10506  299 LVDGDVVLVNRPPSIHQHSLIALSVKVLpTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISS 378

                         90       100
                 ....*....|....*....|.
gi 338855703  99 ATGEPIITPSQDMVLGSYYLT 119
Cdd:cd10506  379 QSGQNLLSLTQDSLLAAHLMT 399
RNA_pol_Rpb1_3 pfam04983
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 94-155 2.19e-12

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: 62.26  E-value: 2.19e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 338855703   94 NILSPATGEPIITPSQDMVLGSYYLTalqpgaskpdfgdRSCTFAGLEDVIHAFEDNRIGLH 155
Cdd:pfam04983   1 NILSPQNGKPIIGPSQDMVLGAYLLT-------------REDTFFDREEVMQLLMYGIVLPH 49
 
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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