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Conserved domains on  [gi|1844850333|ref|WP_171558345|]
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MULTISPECIES: RNA polymerase-binding protein DksA [Rhodobacterales]

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 ...
 38-147 2.45e-49

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: 154.32  E-value: 2.45e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844850333  38 MNERQVEYFRRKLISWKEDLLAGSRDTVAGLQDGTRNIPDVADRASEETDRALELRTRDRQRKLIAKIDSALRRIEEGEY 117
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1844850333 118 GYCEDTGEPISLKRLDARPIATMSLEAQER 147
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKTL 110
 
Name Accession Description Interval E-value
dksA TIGR02420
RNA polymerase-binding protein DksA; The model that is the basis for this family describes a ...
 38-147 2.45e-49

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: 154.32  E-value: 2.45e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844850333  38 MNERQVEYFRRKLISWKEDLLAGSRDTVAGLQDGTRNIPDVADRASEETDRALELRTRDRQRKLIAKIDSALRRIEEGEY 117
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1844850333 118 GYCEDTGEPISLKRLDARPIATMSLEAQER 147
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKTL 110
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
38-153 2.46e-44

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 141.97  E-value: 2.46e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844850333  38 MNERQVEYFRRKLISWKEDLLAGSRDTVAGL--QDGTRNIPDVADRASEETDRALELRTRDRQRKLIAKIDSALRRIEEG 115
Cdd:COG1734     1 MSDEQLEEFRERLLEEREELLEELEETEEELlsGDLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1844850333 116 EYGYCEDTGEPISLKRLDARPIATMSLEAQERHERREK 153
Cdd:COG1734    81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRER 118
dksA PRK10778
RNA polymerase-binding protein DksA;
27-153 1.16e-26

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 97.90  E-value: 1.16e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844850333  27 EDYRPAEDEPFMNERQVEYFRRKLISWKEDLLAGSRDTVAGLQDGTRNIPDVADRASEETDRALELRTRDRQRKLIAKID 106
Cdd:PRK10778   21 EPYQEKPGEEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIE 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1844850333 107 SALRRIEEGEYGYCEDTGEPISLKRLDARPIATMSLEAQERHERREK 153
Cdd:PRK10778  101 KTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREK 147
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
115-150 1.31e-09

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 50.75  E-value: 1.31e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1844850333 115 GEYGYCEDTGEPISLKRLDARPIATMSLEAQERHER 150
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 ...
 38-147 2.45e-49

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: 154.32  E-value: 2.45e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844850333  38 MNERQVEYFRRKLISWKEDLLAGSRDTVAGLQDGTRNIPDVADRASEETDRALELRTRDRQRKLIAKIDSALRRIEEGEY 117
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1844850333 118 GYCEDTGEPISLKRLDARPIATMSLEAQER 147
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKTL 110
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
38-153 2.46e-44

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 141.97  E-value: 2.46e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844850333  38 MNERQVEYFRRKLISWKEDLLAGSRDTVAGL--QDGTRNIPDVADRASEETDRALELRTRDRQRKLIAKIDSALRRIEEG 115
Cdd:COG1734     1 MSDEQLEEFRERLLEEREELLEELEETEEELlsGDLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1844850333 116 EYGYCEDTGEPISLKRLDARPIATMSLEAQERHERREK 153
Cdd:COG1734    81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRER 118
dksA PRK10778
RNA polymerase-binding protein DksA;
27-153 1.16e-26

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 97.90  E-value: 1.16e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1844850333  27 EDYRPAEDEPFMNERQVEYFRRKLISWKEDLLAGSRDTVAGLQDGTRNIPDVADRASEETDRALELRTRDRQRKLIAKID 106
Cdd:PRK10778   21 EPYQEKPGEEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIE 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1844850333 107 SALRRIEEGEYGYCEDTGEPISLKRLDARPIATMSLEAQERHERREK 153
Cdd:PRK10778  101 KTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREK 147
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
115-150 1.31e-09

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 50.75  E-value: 1.31e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1844850333 115 GEYGYCEDTGEPISLKRLDARPIATMSLEAQERHER 150
Cdd:pfam01258   1 GSYGSCEDCGEPIPEARLRAVPGARLCIECQEKYER 36
 
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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