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Conserved domains on  [gi|302858180|ref|XP_002960035|]
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uncharacterized protein VOLCADRAFT_72193, partial [Volvox carteri f. nagariensis]

Protein Classification

RNA polymerase alpha/RpoL/Rpb11 family protein( domain architecture ID 27744)

RNA polymerase alpha/RpoL/Rpb11 family protein such as DNA-directed RNA polymerase subunit L (RpoL) and DNA-directed RNA polymerase subunit alpha

EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0046983
PubMed:  19419240

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_RPB11_RPB3 super family cl11409
RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA ...
 13-136 1.91e-38

RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal 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, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts.


The actual alignment was detected with superfamily member cd06928:

Pssm-ID: 472176 [Multi-domain]  Cd Length: 215  Bit Score: 129.13  E-value: 1.91e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180  13 SRIENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICNLQSIVLKKQ 92
Cdd:cd06928    1 SKVENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFKSD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 302858180  93 eisftnitlrSTKKTYRGFLNVSGPRVIKAMDLKLPSGLQCVDP 136
Cdd:cd06928   81 ----------SEDEPQVLRLKVKGPGVVTAADIELPSGVEIVNP 114
 
Name Accession Description Interval E-value
RNAP_alpha_NTD cd06928
N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha ...
 13-136 1.91e-38

N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD.


Pssm-ID: 132904 [Multi-domain]  Cd Length: 215  Bit Score: 129.13  E-value: 1.91e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180  13 SRIENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICNLQSIVLKKQ 92
Cdd:cd06928    1 SKVENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFKSD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 302858180  93 eisftnitlrSTKKTYRGFLNVSGPRVIKAMDLKLPSGLQCVDP 136
Cdd:cd06928   81 ----------SEDEPQVLRLKVKGPGVVTAADIELPSGVEIVNP 114
rpoA CHL00013
RNA polymerase alpha subunit
 3-136 1.01e-30

RNA polymerase alpha subunit


Pssm-ID: 214333 [Multi-domain]  Cd Length: 327  Bit Score: 111.98  E-value: 1.01e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180   3 TTDFFIACKESRIENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLIC 82
Cdd:CHL00013   2 TQTLQWKCVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 302858180  83 NLQSIVLKKQeisftnitlrsTKKTYRGFLNVSGPRVIKAMDLKLPSGLQCVDP 136
Cdd:CHL00013  82 NLKEIVLKSN-----------LYGPQKASICVQGPKYVTAQDIILPPSVEIVDP 124
RpoA COG0202
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ...
 4-136 8.64e-27

DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA polymerase, alpha subunit/40 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439972 [Multi-domain]  Cd Length: 317  Bit Score: 101.29  E-value: 8.64e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180   4 TDFFIACKESRIENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICN 83
Cdd:COG0202    1 LEFEKPRKIEVEEEISDNYGKFVLEPLERGYGTTLGNALRRVLLSSLPGAAVTSVKIEGVLHEFSTIPGVKEDVTDIILN 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 302858180  84 LQSIVLKKQEISftNITLRstkktyrgfLNVSGPRVIKAMDLKLPSGLQCVDP 136
Cdd:COG0202   81 LKGLRLKLHSDE--PKTLR---------LEKKGPGEVTAGDIELPSDVEILNP 122
RNA_pol_L pfam01193
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ...
 37-104 4.67e-13

RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.


Pssm-ID: 460104 [Multi-domain]  Cd Length: 191  Bit Score: 62.81  E-value: 4.67e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 302858180   37 TIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICNLQSIVLKKQEISFTNITLRST 104
Cdd:pfam01193   9 TLGNALRRILLSEVPGVAIDAVKIEGNTSEFSDEPGAHRLGLIPLLNLKELFFKLSSDDDETLELDKE 76
RPOLD smart00662
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain
 37-129 4.97e-12

RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain


Pssm-ID: 214766 [Multi-domain]  Cd Length: 224  Bit Score: 60.70  E-value: 4.97e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180    37 TIANDIRRTLLSELTSLAITSIEIEGilhkysSLPGMKETVLDLICNLQSIVLK---KQEISFTNITLRSTKKTYRGFLN 113
Cdd:smart00662  11 TLANALRRVLLSSVPGMAVTSVYIEG------NTSGVQDEVLAHRLGLKPLASDpdgDEYQRDCECEEGCEKCSVTLTLD 84

                           90
                   ....*....|....*.
gi 302858180   114 VSGPRVIKAMDLKLPS 129
Cdd:smart00662  85 VKGPGEVTAGDLKSDS 100
 
Name Accession Description Interval E-value
RNAP_alpha_NTD cd06928
N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha ...
 13-136 1.91e-38

N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD.


Pssm-ID: 132904 [Multi-domain]  Cd Length: 215  Bit Score: 129.13  E-value: 1.91e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180  13 SRIENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICNLQSIVLKKQ 92
Cdd:cd06928    1 SKVENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFKSD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 302858180  93 eisftnitlrSTKKTYRGFLNVSGPRVIKAMDLKLPSGLQCVDP 136
Cdd:cd06928   81 ----------SEDEPQVLRLKVKGPGVVTAADIELPSGVEIVNP 114
rpoA CHL00013
RNA polymerase alpha subunit
 3-136 1.01e-30

RNA polymerase alpha subunit


Pssm-ID: 214333 [Multi-domain]  Cd Length: 327  Bit Score: 111.98  E-value: 1.01e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180   3 TTDFFIACKESRIENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLIC 82
Cdd:CHL00013   2 TQTLQWKCVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 302858180  83 NLQSIVLKKQeisftnitlrsTKKTYRGFLNVSGPRVIKAMDLKLPSGLQCVDP 136
Cdd:CHL00013  82 NLKEIVLKSN-----------LYGPQKASICVQGPKYVTAQDIILPPSVEIVDP 124
PRK05182 PRK05182
DNA-directed RNA polymerase subunit alpha; Provisional
 16-136 3.62e-28

DNA-directed RNA polymerase subunit alpha; Provisional


Pssm-ID: 235359 [Multi-domain]  Cd Length: 310  Bit Score: 104.79  E-value: 3.62e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180  16 ENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICNLQSIVLKKQEIS 95
Cdd:PRK05182  14 ESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDGVLHEFSTIPGVREDVTEIILNLKGLRLKLHGDE 93

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 302858180  96 ftNITLRstkktyrgfLNVSGPRVIKAMDLKLPSGLQCVDP 136
Cdd:PRK05182  94 --PVTLT---------LSKKGPGEVTAGDIETDGDVEIVNP 123
RpoA COG0202
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ...
 4-136 8.64e-27

DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA polymerase, alpha subunit/40 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439972 [Multi-domain]  Cd Length: 317  Bit Score: 101.29  E-value: 8.64e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180   4 TDFFIACKESRIENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICN 83
Cdd:COG0202    1 LEFEKPRKIEVEEEISDNYGKFVLEPLERGYGTTLGNALRRVLLSSLPGAAVTSVKIEGVLHEFSTIPGVKEDVTDIILN 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 302858180  84 LQSIVLKKQEISftNITLRstkktyrgfLNVSGPRVIKAMDLKLPSGLQCVDP 136
Cdd:COG0202   81 LKGLRLKLHSDE--PKTLR---------LEKKGPGEVTAGDIELPSDVEILNP 122
RNA_pol_L pfam01193
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ...
 37-104 4.67e-13

RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.


Pssm-ID: 460104 [Multi-domain]  Cd Length: 191  Bit Score: 62.81  E-value: 4.67e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 302858180   37 TIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICNLQSIVLKKQEISFTNITLRST 104
Cdd:pfam01193   9 TLGNALRRILLSEVPGVAIDAVKIEGNTSEFSDEPGAHRLGLIPLLNLKELFFKLSSDDDETLELDKE 76
RNA_pol_A_bac pfam01000
RNA polymerase Rpb3/RpoA insert domain; Members of this family include: alpha subunit from ...
 58-136 1.35e-12

RNA polymerase Rpb3/RpoA insert domain; Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal


Pssm-ID: 425983  Cd Length: 117  Bit Score: 59.96  E-value: 1.35e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 302858180   58 IEIEGILHKYSSLPGMKETVLDLICNLQSIVLKKQEISFTNITLRstkktyrgfLNVSGPRVIKAMDLKLPSGLQCVDP 136
Cdd:pfam01000   1 VYINGVAHEFGLIPGVSEDVLEIILNLKELVCKEEGCEECSVTLT---------LDVKGPGEVTAGDLESDPDVEIVNP 70
RPOLD smart00662
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain
 37-129 4.97e-12

RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain


Pssm-ID: 214766 [Multi-domain]  Cd Length: 224  Bit Score: 60.70  E-value: 4.97e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302858180    37 TIANDIRRTLLSELTSLAITSIEIEGilhkysSLPGMKETVLDLICNLQSIVLK---KQEISFTNITLRSTKKTYRGFLN 113
Cdd:smart00662  11 TLANALRRVLLSSVPGMAVTSVYIEG------NTSGVQDEVLAHRLGLKPLASDpdgDEYQRDCECEEGCEKCSVTLTLD 84

                           90
                   ....*....|....*.
gi 302858180   114 VSGPRVIKAMDLKLPS 129
Cdd:smart00662  85 VKGPGEVTAGDLKSDS 100
 
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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