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Conserved domains on  [gi|541468514|gb|AGV23052|]
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DNA-dependent RNA polymerase, partial [Planktothrix rubescens CCAP 1459/30]

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
 1-148 4.07e-116

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: 341.73  E-value: 4.07e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514   1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:PRK02625  53 EMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMP 132

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 541468514  81 LRDVEQVVYFNAYVVLNPGNYEGLSYKQLLTEDTWLEIEDQIYSEDSTLTGIE-VGIGAEAISRLLEDI 148
Cdd:PRK02625 133 LRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSELEGEEvVGIGAEALKRLLEDL 201
 
Name Accession Description Interval E-value
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
 1-148 4.07e-116

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 341.73  E-value: 4.07e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514   1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:PRK02625  53 EMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMP 132

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 541468514  81 LRDVEQVVYFNAYVVLNPGNYEGLSYKQLLTEDTWLEIEDQIYSEDSTLTGIE-VGIGAEAISRLLEDI 148
Cdd:PRK02625 133 LRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSELEGEEvVGIGAEALKRLLEDL 201
rpoC1_cyan TIGR02387
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ...
 1-148 5.63e-107

DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.


Pssm-ID: 131440 [Multi-domain]  Cd Length: 619  Bit Score: 318.07  E-value: 5.63e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:TIGR02387  46 EMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMP 125

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 541468514   81 LRDVEQVVYFNAYVVLNPGNYEGLSYKQLLTEDTWLEIEDQIYSEDSTLTGIE-VGIGAEAISRLLEDI 148
Cdd:TIGR02387 126 LRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQWLEIEDQIYAEDSELENEEvVGIGAEALKQLLADL 194
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-148 5.73e-73

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: 236.98  E-value: 5.73e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:COG0086    42 ERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMS 121

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 541468514   81 LRDVEQVVYFNAYVVLNPGNyEGLSYKQLLTEDTWLEIEDQiYSEDstltgIEVGIGAEAISRLLEDI 148
Cdd:COG0086   122 LRDLERVLYFESYVVIDPGD-TPLEKGQLLTEDEYREILEE-YGDE-----FVAKMGAEAIKDLLGRI 182
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 1-90 1.38e-64

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: 208.53  E-value: 1.38e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514   1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:cd01609   38 EKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLS 117

                         90
                 ....*....|
gi 541468514  81 LRDVEQVVYF 90
Cdd:cd01609  118 PKDLERVIYF 127
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 4-148 2.04e-18

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: 80.03  E-value: 2.04e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    4 GLFCERIFGPAKDWECH-CGKYKRvrhrgivceRCGVevtesrvrrhRMGFIKLAAPVTHVWYLKGIpsymailldmpLR 82
Cdd:pfam04997  42 GLLDERMGTIDKDYECEtCGKKKK---------DCPG----------HFGHIELAKPVFHIGFFKKT-----------LK 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 541468514   83 DVEQVVYFNAYVVLNPGnyeglsykqlltedtwleiEDQIYSEDSTLTGIEV-GIGAEAISRLLEDI 148
Cdd:pfam04997  92 ILECVCKYCSKLLLDPG-------------------KPKLFNKDKKRLGLENlKMGAKAILELCKKK 139
 
Name Accession Description Interval E-value
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
 1-148 4.07e-116

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 341.73  E-value: 4.07e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514   1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:PRK02625  53 EMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMP 132

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 541468514  81 LRDVEQVVYFNAYVVLNPGNYEGLSYKQLLTEDTWLEIEDQIYSEDSTLTGIE-VGIGAEAISRLLEDI 148
Cdd:PRK02625 133 LRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSELEGEEvVGIGAEALKRLLEDL 201
rpoC1_cyan TIGR02387
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ...
 1-148 5.63e-107

DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.


Pssm-ID: 131440 [Multi-domain]  Cd Length: 619  Bit Score: 318.07  E-value: 5.63e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:TIGR02387  46 EMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMP 125

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 541468514   81 LRDVEQVVYFNAYVVLNPGNYEGLSYKQLLTEDTWLEIEDQIYSEDSTLTGIE-VGIGAEAISRLLEDI 148
Cdd:TIGR02387 126 LRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQWLEIEDQIYAEDSELENEEvVGIGAEALKQLLADL 194
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 1-148 5.56e-85

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 270.01  E-value: 5.56e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:PRK00566   42 ERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMS 121

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 541468514   81 LRDVEQVVYFNAYVVLNPGNyEGLSYKQLLTEDTWLEIEDQiYSEDstltgIEVGIGAEAISRLLEDI 148
Cdd:PRK00566  122 LKDLERVLYFESYVVIDPGD-TPLEKKQLLTEEEYREALEE-YGDE-----FVAKMGAEAIKELLKNI 182
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 1-149 2.70e-73

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: 237.64  E-value: 2.70e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514     1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:TIGR02386   34 EKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDIT 113

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 541468514    81 LRDVEQVVYFNAYVVLNPGNyEGLSYKQLLTEDTWLEiedqiySEDSTLTGIEVGIGAEAISRLLEDIP 149
Cdd:TIGR02386  114 AKELESVLYFENYVVLDPGD-TKLDKKEVLDETEYRE------VLKRYGDGFRAGMGAEAIKELLEKID 175
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 1-148 5.73e-73

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: 236.98  E-value: 5.73e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:COG0086    42 ERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMS 121

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 541468514   81 LRDVEQVVYFNAYVVLNPGNyEGLSYKQLLTEDTWLEIEDQiYSEDstltgIEVGIGAEAISRLLEDI 148
Cdd:COG0086   122 LRDLERVLYFESYVVIDPGD-TPLEKGQLLTEDEYREILEE-YGDE-----FVAKMGAEAIKDLLGRI 182
rpoC1 CHL00018
RNA polymerase beta' subunit
 1-148 3.17e-71

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 226.32  E-value: 3.17e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514   1 EMDGLFCERIFGPAKDWECHCGKYKRVRHR---GIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILL 77
Cdd:CHL00018  51 EKDGLFCERIFGPIKSGICACGNYRVIGDEkedPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLL 130

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 541468514  78 DMPLRDVEQVVYFN-AYVVLNPGNYEGLSYKQLLTED--TWLEIEDQIYS--EDSTLTGIEVGIGAEAISRLLEDI 148
Cdd:CHL00018 131 DKPLKELEGLVYCDfSFARPIAKKPTFLRLRGLFEYEiqSWKYSIPLFFStqGFDTFRNREISTGAGAIREQLADL 206
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 1-90 1.38e-64

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: 208.53  E-value: 1.38e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514   1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:cd01609   38 EKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTRSKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLS 117

                         90
                 ....*....|
gi 541468514  81 LRDVEQVVYF 90
Cdd:cd01609  118 PKDLERVIYF 127
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
1-95 3.03e-50

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 172.36  E-value: 3.03e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:PRK14906   44 EKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVTRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIK 123

                          90
                  ....*....|....*
gi 541468514   81 LRDVEQVVYFNAYVV 95
Cdd:PRK14906  124 PKDLEKVLYFASYII 138
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-148 1.18e-47

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 165.10  E-value: 1.18e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGI-VCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDM 79
Cdd:PRK09603 1431 ERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGV 1510

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 541468514   80 PLRDVEQVVYFNAYVVLNPGN--YEGLSYKQLLTEDTWLEIEDQIYSEDSTLTGIEVGIGAEAISRLLEDI 148
Cdd:PRK09603 1511 KMKDLERVLYYEAYIVKEPGEaaYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFVAQMGGEAIKDLLEEI 1581
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-145 2.02e-43

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 152.85  E-value: 2.02e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    1 EMDGLFCERIFGPAKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYMAILLDMP 80
Cdd:PRK14844 1483 EKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTSSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMS 1562

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 541468514   81 LRDVEQVVYFNAYVVLNPgNYEGLSYKQLLTEDTWLEIEDQiYSEDSTLTgievGIGAEAISRLL 145
Cdd:PRK14844 1563 LRDIENILYSDNYIVIDP-LVSPFEKGEIISEKAYNEAKDS-YGIDSFVA----MQGVEAIRELL 1621
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 4-148 2.04e-18

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: 80.03  E-value: 2.04e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 541468514    4 GLFCERIFGPAKDWECH-CGKYKRvrhrgivceRCGVevtesrvrrhRMGFIKLAAPVTHVWYLKGIpsymailldmpLR 82
Cdd:pfam04997  42 GLLDERMGTIDKDYECEtCGKKKK---------DCPG----------HFGHIELAKPVFHIGFFKKT-----------LK 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 541468514   83 DVEQVVYFNAYVVLNPGnyeglsykqlltedtwleiEDQIYSEDSTLTGIEV-GIGAEAISRLLEDI 148
Cdd:pfam04997  92 ILECVCKYCSKLLLDPG-------------------KPKLFNKDKKRLGLENlKMGAKAILELCKKK 139
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 22-71 1.14e-13

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: 67.46  E-value: 1.14e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 541468514  22 GKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPS 71
Cdd:cd00399   31 GKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKVPS 80
 
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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