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Conserved domains on  [gi|499661806|ref|WP_011342540|]
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RNA polymerase-binding protein DksA [Syntrophotalea carbinolica]

Protein Classification

RNA polymerase-binding protein DksA( domain architecture ID 10020749)

RNA polymerase-binding protein DksA is required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters

Gene Ontology:  GO:0006355|GO:0019899
PubMed:  15294157
SCOP:  4003090

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
dksA TIGR02420
RNA polymerase-binding protein DksA; The model that is the basis for this family describes a ...
 1-109 9.17e-45

RNA polymerase-binding protein DksA; The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage. [Transcription, Transcription factors, Regulatory functions, Small molecule interactions]


:

Pssm-ID: 274124  Cd Length: 110  Bit Score: 140.84  E-value: 9.17e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499661806    1 MDQEALKEFKAILESQLEALLRDAGKTVSEMTDDQSNFPDPTDRASLESDRNFELRIRDRERKLIMKIRQALERIEQGTF 80
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100
                  ....*....|....*....|....*....
gi 499661806   81 GECECCEEPIGAERLRARPVTTLCIDCKT 109
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKT 109
 
Name Accession Description Interval E-value
dksA TIGR02420
RNA polymerase-binding protein DksA; The model that is the basis for this family describes a ...
 1-109 9.17e-45

RNA polymerase-binding protein DksA; The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage. [Transcription, Transcription factors, Regulatory functions, Small molecule interactions]


Pssm-ID: 274124  Cd Length: 110  Bit Score: 140.84  E-value: 9.17e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499661806    1 MDQEALKEFKAILESQLEALLRDAGKTVSEMTDDQSNFPDPTDRASLESDRNFELRIRDRERKLIMKIRQALERIEQGTF 80
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100
                  ....*....|....*....|....*....
gi 499661806   81 GECECCEEPIGAERLRARPVTTLCIDCKT 109
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKT 109
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
1-116 1.24e-39

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 128.10  E-value: 1.24e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499661806   1 MDQEALKEFKAILESQLEALLRDAGKTVSEM--TDDQSNFPDPTDRASLESDRNFELRIRDRERKLIMKIRQALERIEQG 78
Cdd:COG1734    1 MSDEQLEEFRERLLEEREELLEELEETEEELlsGDLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 499661806  79 TFGECECCEEPIGAERLRARPVTTLCIDCKTEQERKEK 116
Cdd:COG1734   81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRER 118
dksA PRK10778
RNA polymerase-binding protein DksA;
1-116 1.20e-27

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 99.05  E-value: 1.20e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499661806   1 MDQEALKEFKAILESQLEALLRDAGKTVSEMTDDQSNFPDPTDRASLESDRNFELRIRDRERKLIMKIRQALERIEQGTF 80
Cdd:PRK10778  32 MNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEKTLKKVEDEDF 111

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 499661806  81 GECECCEEPIGAERLRARPVTTLCIDCKTEQERKEK 116
Cdd:PRK10778 112 GYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREK 147
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
78-113 2.68e-10

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 51.52  E-value: 2.68e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 499661806   78 GTFGECECCEEPIGAERLRARPVTTLCIDCKTEQER 113
Cdd:pfam01258   1 GSYGSCEDCGEPIPEARLRAVPGARLCIECQEKYER 36
 
Name Accession Description Interval E-value
dksA TIGR02420
RNA polymerase-binding protein DksA; The model that is the basis for this family describes a ...
 1-109 9.17e-45

RNA polymerase-binding protein DksA; The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage. [Transcription, Transcription factors, Regulatory functions, Small molecule interactions]


Pssm-ID: 274124  Cd Length: 110  Bit Score: 140.84  E-value: 9.17e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499661806    1 MDQEALKEFKAILESQLEALLRDAGKTVSEMTDDQSNFPDPTDRASLESDRNFELRIRDRERKLIMKIRQALERIEQGTF 80
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100
                  ....*....|....*....|....*....
gi 499661806   81 GECECCEEPIGAERLRARPVTTLCIDCKT 109
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKT 109
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
1-116 1.24e-39

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 128.10  E-value: 1.24e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499661806   1 MDQEALKEFKAILESQLEALLRDAGKTVSEM--TDDQSNFPDPTDRASLESDRNFELRIRDRERKLIMKIRQALERIEQG 78
Cdd:COG1734    1 MSDEQLEEFRERLLEEREELLEELEETEEELlsGDLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 499661806  79 TFGECECCEEPIGAERLRARPVTTLCIDCKTEQERKEK 116
Cdd:COG1734   81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRER 118
dksA PRK10778
RNA polymerase-binding protein DksA;
1-116 1.20e-27

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 99.05  E-value: 1.20e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499661806   1 MDQEALKEFKAILESQLEALLRDAGKTVSEMTDDQSNFPDPTDRASLESDRNFELRIRDRERKLIMKIRQALERIEQGTF 80
Cdd:PRK10778  32 MNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEKTLKKVEDEDF 111

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 499661806  81 GECECCEEPIGAERLRARPVTTLCIDCKTEQERKEK 116
Cdd:PRK10778 112 GYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREK 147
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
78-113 2.68e-10

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 51.52  E-value: 2.68e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 499661806   78 GTFGECECCEEPIGAERLRARPVTTLCIDCKTEQER 113
Cdd:pfam01258   1 GSYGSCEDCGEPIPEARLRAVPGARLCIECQEKYER 36
PRK13715 PRK13715
conjugal transfer protein TraR; Provisional
 83-116 9.04e-04

conjugal transfer protein TraR; Provisional


Pssm-ID: 184270  Cd Length: 73  Bit Score: 35.34  E-value: 9.04e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 499661806  83 CECCEEPIGAERLRARPVTTLCIDCKTEQERKEK 116
Cdd:PRK13715  37 CEACGNPIPEARRKIFPGVTLCVECQAYQERQRK 70
PRK11019 PRK11019
DksA/TraR family C4-type zinc finger protein;
82-116 1.43e-03

DksA/TraR family C4-type zinc finger protein;


Pssm-ID: 182903  Cd Length: 88  Bit Score: 35.23  E-value: 1.43e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 499661806  82 ECECCEEPIGAERLRARPVTTLCIDCKTEQERKEK 116
Cdd:PRK11019  38 ECEECGEPIPEARRKAIPGVRLCVACQQEKDLQQA 72
C4_traR_proteo TIGR02419
phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Members of this family are ...
 48-112 2.59e-03

phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA. [Mobile and extrachromosomal element functions, Prophage functions]


Pssm-ID: 274123  Cd Length: 63  Bit Score: 33.91  E-value: 2.59e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499661806   48 ESDRNFELRIRDRERKLImkiRQALERIEQGTFGECECCEEPIGAERLRARPVTTLCIDCKTEQE 112
Cdd:TIGR02419   2 EFDRAQELEEELLERALA---AARAKKVIGPSLRECEDCGEPIPEARREALPGVTRCVSCQEILE 63
 
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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