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Conserved domains on  [gi|1387714141|gb|PWA13880|]
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hypothetical protein CCH79_00019189 [Gambusia affinis]

Protein Classification

DNA-directed RNA polymerase II subunit RPB11( domain architecture ID 10161225)

DNA-directed RNA polymerase II subunit RPB11 is a component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs

CATH:  3.30.1360.10
Gene Ontology:  GO:0005665|GO:0001055|GO:0006366
PubMed:  8508029
SCOP:  4003562

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_II_RPB11 cd06926
RPB11 subunit of Eukaryotic RNA polymerase II; The eukaryotic RPB11 subunit of RNA polymerase ...
 124-215 2.72e-61

RPB11 subunit of Eukaryotic RNA polymerase II; The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.


:

Pssm-ID: 132902  Cd Length: 93  Bit Score: 186.64  E-value: 2.72e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387714141 124 EGEKKISISKDTKVPNACLFTLNKEDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITD 203
Cdd:cd06926     2 EGEKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAITD 81

                          90
                  ....*....|..
gi 1387714141 204 LISELSLLEERF 215
Cdd:cd06926    82 LISELSLLKEEF 93
 
Name Accession Description Interval E-value
RNAP_II_RPB11 cd06926
RPB11 subunit of Eukaryotic RNA polymerase II; The eukaryotic RPB11 subunit of RNA polymerase ...
 124-215 2.72e-61

RPB11 subunit of Eukaryotic RNA polymerase II; The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.


Pssm-ID: 132902  Cd Length: 93  Bit Score: 186.64  E-value: 2.72e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387714141 124 EGEKKISISKDTKVPNACLFTLNKEDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITD 203
Cdd:cd06926     2 EGEKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAITD 81

                          90
                  ....*....|..
gi 1387714141 204 LISELSLLEERF 215
Cdd:cd06926    82 LISELSLLKEEF 93
RNA_pol_L_2 pfam13656
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ...
 140-213 6.99e-38

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. Many of the members of this family carry only the N-terminal region of Rpb11.


Pssm-ID: 463947  Cd Length: 75  Bit Score: 126.48  E-value: 6.99e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1387714141 140 ACLFTLNKEDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITDLISELSLLEE 213
Cdd:pfam13656   1 AATFEINGEDHTLGNLLREELLKDPDVEFAGYKVPHPLEPKIELRIQTDGSITPLEALKKALEDLIDECEELEE 74
RPB11 COG1761
DNA-directed RNA polymerase, subunit L/RPAC2 [Transcription]; DNA-directed RNA polymerase, ...
 148-215 1.05e-18

DNA-directed RNA polymerase, subunit L/RPAC2 [Transcription]; DNA-directed RNA polymerase, subunit L/RPAC2 is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441367  Cd Length: 88  Bit Score: 77.55  E-value: 1.05e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1387714141 148 EDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITDLISELSLLEERF 215
Cdd:COG1761    20 EDHTLLNLLKEELLKDPGVDFATYDIKHPLISEPVLRIKTDGGIDPLEALKEAAKRIIEECDEFKKEF 87
PRK01146 PRK01146
DNA-directed RNA polymerase subunit L; Provisional
 148-213 1.12e-16

DNA-directed RNA polymerase subunit L; Provisional


Pssm-ID: 234909  Cd Length: 85  Bit Score: 72.20  E-value: 1.12e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1387714141 148 EDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITDLISELSLLEE 213
Cdd:PRK01146   20 EDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFLD 85
 
Name Accession Description Interval E-value
RNAP_II_RPB11 cd06926
RPB11 subunit of Eukaryotic RNA polymerase II; The eukaryotic RPB11 subunit of RNA polymerase ...
 124-215 2.72e-61

RPB11 subunit of Eukaryotic RNA polymerase II; The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is 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. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.


Pssm-ID: 132902  Cd Length: 93  Bit Score: 186.64  E-value: 2.72e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387714141 124 EGEKKISISKDTKVPNACLFTLNKEDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITD 203
Cdd:cd06926     2 EGEKKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNAITD 81

                          90
                  ....*....|..
gi 1387714141 204 LISELSLLEERF 215
Cdd:cd06926    82 LISELSLLKEEF 93
RNA_pol_L_2 pfam13656
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ...
 140-213 6.99e-38

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. Many of the members of this family carry only the N-terminal region of Rpb11.


Pssm-ID: 463947  Cd Length: 75  Bit Score: 126.48  E-value: 6.99e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1387714141 140 ACLFTLNKEDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITDLISELSLLEE 213
Cdd:pfam13656   1 AATFEINGEDHTLGNLLREELLKDPDVEFAGYKVPHPLEPKIELRIQTDGSITPLEALKKALEDLIDECEELEE 74
RNAP_RPB11_like cd07027
RPB11 subunit of RNA polymerase; The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as ...
 131-209 1.71e-25

RPB11 subunit of RNA polymerase; The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is 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.


Pssm-ID: 132905  Cd Length: 83  Bit Score: 94.88  E-value: 1.71e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1387714141 131 ISKDTkvpNACLFTLNKEDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITDLISELS 209
Cdd:cd07027     4 ISKEK---NSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKDALKRAVNKLSKLYE 79
RNAP_I_III_AC19 cd07029
AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III; The eukaryotic AC19 subunit ...
 133-206 3.09e-23

AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III; The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is 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. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to associate with the RPB3 counterpart, AC40, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III.


Pssm-ID: 132907  Cd Length: 85  Bit Score: 89.21  E-value: 3.09e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1387714141 133 KDTKVPNACLFTLNKEDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITDLIS 206
Cdd:cd07029     3 GEGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLKKGLEDLEQ 76
RPB11 COG1761
DNA-directed RNA polymerase, subunit L/RPAC2 [Transcription]; DNA-directed RNA polymerase, ...
 148-215 1.05e-18

DNA-directed RNA polymerase, subunit L/RPAC2 [Transcription]; DNA-directed RNA polymerase, subunit L/RPAC2 is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441367  Cd Length: 88  Bit Score: 77.55  E-value: 1.05e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1387714141 148 EDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITDLISELSLLEERF 215
Cdd:COG1761    20 EDHTLLNLLKEELLKDPGVDFATYDIKHPLISEPVLRIKTDGGIDPLEALKEAAKRIIEECDEFKKEF 87
PRK01146 PRK01146
DNA-directed RNA polymerase subunit L; Provisional
 148-213 1.12e-16

DNA-directed RNA polymerase subunit L; Provisional


Pssm-ID: 234909  Cd Length: 85  Bit Score: 72.20  E-value: 1.12e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1387714141 148 EDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITDLISELSLLEE 213
Cdd:PRK01146   20 EDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFLD 85
RNAP_L cd06927
L subunit of Archaeal RNA polymerase; The archaeal L subunit of RNA polymerase (RNAP) is ...
 148-213 2.41e-16

L subunit of Archaeal RNA polymerase; The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is 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. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.


Pssm-ID: 132903  Cd Length: 83  Bit Score: 71.08  E-value: 2.41e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1387714141 148 EDHTLGNIIRAQLLKDPQVLFAGYKVPHPLEHKIVIRVQTTPDYSPQEAFTNAITDLISELSLLEE 213
Cdd:cd06927    18 EDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFLD 83
RNAP_RPB11_RPB3 cd00460
RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA ...
 136-209 3.63e-16

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.


Pssm-ID: 132901  Cd Length: 86  Bit Score: 70.91  E-value: 3.63e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1387714141 136 KVPNACLFTLNKEDHTLGNIIRAQLLKDPqVLFAGYKVPHPLEH------KIVIRVQTTPDYSPQEAFTNAITDLISELS 209
Cdd:cd00460     6 KEKNYVDFVLENEDHTLGNSLRRILLKSP-VEFAAYYVEHPVKLqrtdedKFILRIETVGSIPPEEALRRAVEILRKKLE 84
 
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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