NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|224612305|emb|CAP46486|]
View 

RNA polymerase beta subunit, partial (plastid) [Inga tenuistipula]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
rpoC1 super family cl29902
RNA polymerase beta' subunit
 1-151 9.20e-122

RNA polymerase beta' subunit


The actual alignment was detected with superfamily member CHL00018:

Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 356.52  E-value: 9.20e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305   1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:CHL00018 385 VVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQ 464

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305  81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:CHL00018 465 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDM 535
 
Name Accession Description Interval E-value
rpoC1 CHL00018
RNA polymerase beta' subunit
 1-151 9.20e-122

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 356.52  E-value: 9.20e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305   1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:CHL00018 385 VVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQ 464

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305  81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:CHL00018 465 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDM 535
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 1-151 1.50e-102

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: 307.14  E-value: 1.50e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305   1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:cd01609  261 VVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQ 340

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305  81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:cd01609  341 AFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDM 411
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-151 1.40e-86

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: 273.96  E-value: 1.40e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:COG0086   346 VVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQ 425

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305   81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:COG0086   426 AFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDM 496
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 1-151 9.12e-81

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: 258.06  E-value: 9.12e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305     1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:TIGR02386  338 VVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQ 417

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305    81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:TIGR02386  418 AFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDM 488
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
1-151 1.97e-73

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 221.24  E-value: 1.97e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305     1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGL------------------I*K*FASNIGVAK-SKIREKEPIVWQILQEVM 61
Cdd:smart00663 121 TPDPNLKLNEVGVPKEIALELTFPEIVTPLnidklrklvrngpngakyIIRGKKTNLKLAKkSKIANHLKIGDIVERHVI 200

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    62 QGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIG 141
Cdd:smart00663 201 DGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNG 280

                          170
                   ....*....|
gi 224612305   142 DPISVPTQDM 151
Cdd:smart00663 281 KPIIGPIQDM 290
RNA_pol_Rpb1_2 pfam00623
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-129 2.55e-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: 117.79  E-value: 2.55e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K----------------*FASNIGVAKSKIR-------EKEPIVWQIL 57
Cdd:pfam00623  13 SPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKrlrqlvengpnvypgaNYIIRINGARRDLRyqkrrldKELEIGDIVE 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 224612305   58 QEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 129
Cdd:pfam00623  93 RHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEAEELM 164
 
Name Accession Description Interval E-value
rpoC1 CHL00018
RNA polymerase beta' subunit
 1-151 9.20e-122

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 356.52  E-value: 9.20e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305   1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:CHL00018 385 VVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQ 464

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305  81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:CHL00018 465 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDM 535
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 1-151 1.50e-102

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: 307.14  E-value: 1.50e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305   1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:cd01609  261 VVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEVIKGHPVLLNRAPTLHRLGIQ 340

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305  81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:cd01609  341 AFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDM 411
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 1-151 1.65e-94

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 295.44  E-value: 1.65e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:PRK00566  346 VVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQ 425

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305   81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:PRK00566  426 AFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQDM 496
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-151 1.40e-86

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: 273.96  E-value: 1.40e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:COG0086   346 VVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILEEVIKEHPVLLNRAPTLHRLGIQ 425

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305   81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:COG0086   426 AFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDM 496
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 1-151 9.12e-81

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: 258.06  E-value: 9.12e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305     1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:TIGR02386  338 VVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQ 417

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305    81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:TIGR02386  418 AFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDM 488
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
 1-151 1.05e-80

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 249.67  E-value: 1.05e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305   1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:PRK02625 364 VVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQ 443

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305  81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:PRK02625 444 AFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDM 514
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
1-151 1.97e-73

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 221.24  E-value: 1.97e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305     1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGL------------------I*K*FASNIGVAK-SKIREKEPIVWQILQEVM 61
Cdd:smart00663 121 TPDPNLKLNEVGVPKEIALELTFPEIVTPLnidklrklvrngpngakyIIRGKKTNLKLAKkSKIANHLKIGDIVERHVI 200

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    62 QGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIG 141
Cdd:smart00663 201 DGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNG 280

                          170
                   ....*....|
gi 224612305   142 DPISVPTQDM 151
Cdd:smart00663 281 KPIIGPIQDM 290
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
1-151 1.02e-71

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 233.23  E-value: 1.02e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:PRK14906  434 VVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQ 513

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305   81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:PRK14906  514 AFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDM 584
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-151 1.28e-63

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 210.25  E-value: 1.28e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:PRK14844 1789 VVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEEVIKEHPVLLNRAPTLHRLGIQ 1868

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305   81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:PRK14844 1869 AFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDI 1939
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-151 1.90e-60

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 201.31  E-value: 1.90e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K*FASNIGVAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQ 80
Cdd:PRK09603 1745 VVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQ 1824

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 224612305   81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQDM 151
Cdd:PRK09603 1825 AFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDM 1895
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 1-150 6.45e-44

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: 151.05  E-value: 6.45e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305   1 VVGPSLSL*RCGLPR*IA**Lf*tfvirgli*k*fasnigvakskirekepivwqilqevmQGHPVLLNRAPTLHRLGIQ 80
Cdd:cd00399  169 SPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFNRQPSLHKLSIM 208

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305  81 AFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPTQD 150
Cdd:cd00399  209 AHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQD 278
RNA_pol_Rpb1_2 pfam00623
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-129 2.55e-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: 117.79  E-value: 2.55e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305    1 VVGPSLSL*RCGLPR*IA**LF*TFVIRGLI*K----------------*FASNIGVAKSKIR-------EKEPIVWQIL 57
Cdd:pfam00623  13 SPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKrlrqlvengpnvypgaNYIIRINGARRDLRyqkrrldKELEIGDIVE 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 224612305   58 QEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLM 129
Cdd:pfam00623  93 RHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEAEELM 164
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 41-150 1.32e-29

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: 112.73  E-value: 1.32e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305  41 VAKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLE 120
Cdd:cd02582  389 VNREELAERLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEE 468

                         90       100       110
                 ....*....|....*....|....*....|
gi 224612305 121 AQAEARLLMFSHMNLLSPAIGDPISVPTQD 150
Cdd:cd02582  469 ARAEARELMLVQEHILSPRYGGPIIGGIQD 498
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 43-150 1.94e-27

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 106.48  E-value: 1.94e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305  43 KSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQ 122
Cdd:PRK08566 395 KEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEAR 474

                         90       100
                 ....*....|....*....|....*...
gi 224612305 123 AEARLLMFSHMNLLSPAIGDPISVPTQD 150
Cdd:PRK08566 475 AEARILMLVQEHILSPRYGGPIIGGIQD 502
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 42-150 1.18e-23

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


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 95.86  E-value: 1.18e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305   42 AKSKIREKEPIVWQILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEA 121
Cdd:PRK14977  410 ALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDA 489

                          90       100
                  ....*....|....*....|....*....
gi 224612305  122 QAEARLLMFSHMNLLSPAIGDPISVPTQD 150
Cdd:PRK14977  490 RAEAIELMGVKDNLISPRTGGPIIGALQD 518
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
 66-150 1.21e-23

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: 95.69  E-value: 1.21e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305  66 VLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPIS 145
Cdd:cd02583  388 VLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLI 467


                 ....*
gi 224612305 146 VPTQD 150
Cdd:cd02583  468 AATQD 472
RNAP_I_RPA1_N cd01435
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
 66-150 1.52e-20

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: 86.85  E-value: 1.52e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305  66 VLLNRAPTLHRLGIQAFQ-PILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPI 144
Cdd:cd01435  361 VLLNRQPTLHKPSIMAHKvRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPL 440


                 ....*.
gi 224612305 145 SVPTQD 150
Cdd:cd01435  441 RGLIQD 446
RNAP_IV_RPD1_N cd10506
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
 1-150 7.01e-14

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: 67.81  E-value: 7.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305   1 VVG-PSLSL*RCGLPR*IA**L------------------F*TFVIRGLI*K*FASNIGVAKSKireKEPIVWQIL-QEV 60
Cdd:cd10506  223 VVGdPYLELNEIGIPCEIAERLtvservsswnrerlqeycDLTLLLKGVIGVRRNGRLVGVRSH---NTLQIGDVIhRPL 299

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305  61 MQGHPVLLNRAPTLHRLGIQAFQ-PILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPA 139
Cdd:cd10506  300 VDGDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQ 379

                        170
                 ....*....|.
gi 224612305 140 IGDPISVPTQD 150
Cdd:cd10506  380 SGQNLLSLTQD 390
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 66-138 1.64e-12

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: 63.71  E-value: 1.64e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 224612305  66 VLLNRAPTLHRLGIQAFqpilvegRAICLHPL-------VCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSP 138
Cdd:cd02733  336 VLFNRQPSLHKMSMMGH-------RVKVLPYStfrlnlsVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSP 408
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH