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Conserved domains on  [gi|170665713|gb|ACB29396|]
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RNA polymerase beta' subunit, partial (chloroplast) [Stokesia laevis]

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
 1-144 2.73e-108

RNA polymerase beta' subunit


The actual alignment was detected with superfamily member CHL00018:

Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 321.47  E-value: 2.73e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713   1 MIDRYTHQQLRIGLVSPQQISTWSKKILPNGEIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIGDD 80
Cdd:CHL00018   1 MIDRYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 170665713  81 KENPQFCEQCGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVYCG 144
Cdd:CHL00018  81 KEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCD 144
 
Name Accession Description Interval E-value
rpoC1 CHL00018
RNA polymerase beta' subunit
 1-144 2.73e-108

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 321.47  E-value: 2.73e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713   1 MIDRYTHQQLRIGLVSPQQISTWSKKILPNGEIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIGDD 80
Cdd:CHL00018   1 MIDRYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 170665713  81 KENPQFCEQCGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVYCG 144
Cdd:CHL00018  81 KEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCD 144
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 10-143 3.82e-59

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: 193.50  E-value: 3.82e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713  10 LRIGLVSPQQISTWSkkilpngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIgddKENPQFCEQ 89
Cdd:cd01609    6 IRISLASPEQIRSWS---------HGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRI---RYKGIICDR 73

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 170665713  90 CGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVYC 143
Cdd:cd01609   74 CGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF 127
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 10-142 4.43e-47

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: 162.53  E-value: 4.43e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713    10 LRIGLVSPQQISTWSKkilpngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIgddKENPQFCEQ 89
Cdd:TIGR02386    2 IKISIASPDTIRNWSY---------GEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKI---RYKGVVCER 69

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 170665713    90 CGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVY 142
Cdd:TIGR02386   70 CGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLY 122
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-143 1.68e-45

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: 158.01  E-value: 1.68e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713    1 MIDRYTHQQLRIGLVSPQQISTWSKkilpngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIgdd 80
Cdd:COG0086     1 MAFVEDFDAIKIGLASPEKIRSWSY---------GEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRM--- 68

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 170665713   81 KENPQFCEQCGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVYC 143
Cdd:COG0086    69 VYKGVVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYF 131
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 10-130 5.03e-19

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 80.80  E-value: 5.03e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713   10 LRIGLVSPQQISTWSkkilpngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICG-CGNYRvigddkenpqfcE 88
Cdd:pfam04997   7 IQFGIASPEEIRKWS---------VGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCGKKK------------K 65

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 170665713   89 QCGVEFvdsrirryqmGYIKLAYPVMHVWYLKrlpsYIVNLL 130
Cdd:pfam04997  66 DCPGHF----------GHIELAKPVFHIGFFK----KTLKIL 93
 
Name Accession Description Interval E-value
rpoC1 CHL00018
RNA polymerase beta' subunit
 1-144 2.73e-108

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 321.47  E-value: 2.73e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713   1 MIDRYTHQQLRIGLVSPQQISTWSKKILPNGEIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIGDD 80
Cdd:CHL00018   1 MIDRYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 170665713  81 KENPQFCEQCGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVYCG 144
Cdd:CHL00018  81 KEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCD 144
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 10-143 3.82e-59

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: 193.50  E-value: 3.82e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713  10 LRIGLVSPQQISTWSkkilpngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIgddKENPQFCEQ 89
Cdd:cd01609    6 IRISLASPEQIRSWS---------HGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRI---RYKGIICDR 73

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 170665713  90 CGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVYC 143
Cdd:cd01609   74 CGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF 127
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
 10-142 3.98e-56

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 184.95  E-value: 3.98e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713  10 LRIGLVSPQQISTWSKKILPNGEIVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIgddKENPQFCEQ 89
Cdd:PRK02625  12 VKIGLASPERIRQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRV---RHRGIVCER 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 170665713  90 CGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVY 142
Cdd:PRK02625  89 CGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVY 141
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 9-142 1.56e-47

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 163.70  E-value: 1.56e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713    9 QLRIGLVSPQQISTWSKkilpngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYR------VIgddke 82
Cdd:PRK00566    9 AIKIGLASPEKIRSWSY---------GEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKrvrykgII----- 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713   83 npqfCEQCGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVY 142
Cdd:PRK00566   75 ----CERCGVEVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLY 130
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 10-142 4.43e-47

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: 162.53  E-value: 4.43e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713    10 LRIGLVSPQQISTWSKkilpngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIgddKENPQFCEQ 89
Cdd:TIGR02386    2 IKISIASPDTIRNWSY---------GEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKI---RYKGVVCER 69

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 170665713    90 CGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVY 142
Cdd:TIGR02386   70 CGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLY 122
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-143 1.68e-45

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: 158.01  E-value: 1.68e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713    1 MIDRYTHQQLRIGLVSPQQISTWSKkilpngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIgdd 80
Cdd:COG0086     1 MAFVEDFDAIKIGLASPEKIRSWSY---------GEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRM--- 68

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 170665713   81 KENPQFCEQCGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVYC 143
Cdd:COG0086    69 VYKGVVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYF 131
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
10-142 3.20e-39

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 140.01  E-value: 3.20e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713   10 LRIGLVSPQQISTWSKkilpngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRVIgddKENPQFCEQ 89
Cdd:PRK14906   12 LRISLASAEDIRSWSH---------GEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRI---RFKGIVCER 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 170665713   90 CGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVY 142
Cdd:PRK14906   80 CGVEVTRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLY 132
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
14-142 3.33e-37

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 134.28  E-value: 3.33e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713   14 LVSPQQISTWSKkilpngeivGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRvigddkeNPQF-----CE 88
Cdd:PRK09603 1403 LASPEKIHSWSY---------GEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYK-------KPRFkdigtCE 1466

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 170665713   89 QCGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVY 142
Cdd:PRK09603 1467 KCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLY 1520
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
9-142 1.02e-31

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 118.57  E-value: 1.02e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713    9 QLRIGLVSPQQISTWSkkilpngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICGCGNYRvigDDKENPQFCE 88
Cdd:PRK14844 1450 EVSISIASPESIKRMS---------YGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYK---KRRHRGRICE 1517

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 170665713   89 QCGVEFVDSRIRRYQMGYIKLAYPVMHVWYLKRLPSYIVNLLDKPLNELEDLVY 142
Cdd:PRK14844 1518 KCGVEVTSSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILY 1571
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 10-130 5.03e-19

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 80.80  E-value: 5.03e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713   10 LRIGLVSPQQISTWSkkilpngeiVGEVTKPYTFHYKTNKPEKDGLFCERIFGPIKSGICG-CGNYRvigddkenpqfcE 88
Cdd:pfam04997   7 IQFGIASPEEIRKWS---------VGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCGKKK------------K 65

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 170665713   89 QCGVEFvdsrirryqmGYIKLAYPVMHVWYLKrlpsYIVNLL 130
Cdd:pfam04997  66 DCPGHF----------GHIELAKPVFHIGFFK----KTLKIL 93
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 16-126 7.96e-14

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: 67.07  E-value: 7.96e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170665713  16 SPQQISTWSkkilpngeiVGEVTKPYTFHYKTNKPEKDGLFcERIFGPIKSgicgcgnyrvigddkenpqfCEQCGVEFV 95
Cdd:cd00399    2 SPEEIRKWS---------VAKVIKPETIDNRTLKAERGGKY-DPRLGSIDR--------------------CEKCGTCGT 51

                         90       100       110
                 ....*....|....*....|....*....|.
gi 170665713  96 DSRIRRYQMGYIKLAYPVMHVWYLKRLPSYI 126
Cdd:cd00399   52 GLNDCPGHFGHIELAKPVFHVGFIKKVPSFL 82
 
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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