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Conserved domains on  [gi|491010513|ref|WP_004872222|]
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MULTISPECIES: RNA polymerase-binding protein DksA [Acidithiobacillus]

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 ...
 33-142 7.18e-63

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: 188.22  E-value: 7.18e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491010513   33 MSPAQLAHFRKILEDWRDELMTEVERTVQNMQVENVNYSDPNDRASLETDMGLELRARDRERKLIRKINQALARIDAGEY 112
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 491010513  113 GYCESCGVEIGLRRLEARPTATLCIDCKTL 142
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 ...
 33-142 7.18e-63

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: 188.22  E-value: 7.18e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491010513   33 MSPAQLAHFRKILEDWRDELMTEVERTVQNMQVENVNYSDPNDRASLETDMGLELRARDRERKLIRKINQALARIDAGEY 112
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 491010513  113 GYCESCGVEIGLRRLEARPTATLCIDCKTL 142
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKTL 110
dksA PRK10778
RNA polymerase-binding protein DksA;
23-151 5.00e-53

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 164.92  E-value: 5.00e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491010513  23 PYQPAPNEPYMSPAQLAHFRKILEDWRDELMTEVERTVQNMQVENVNYSDPNDRASLETDMGLELRARDRERKLIRKINQ 102
Cdd:PRK10778  22 PYQEKPGEEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEK 101

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 491010513 103 ALARIDAGEYGYCESCGVEIGLRRLEARPTATLCIDCKTLEEKREKQMA 151
Cdd:PRK10778 102 TLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMA 150
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
33-149 1.10e-52

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 162.77  E-value: 1.10e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491010513  33 MSPAQLAHFRKILEDWRDELMTEVERTVQNMQV--ENVNYSDPNDRASLETDMGLELRARDRERKLIRKINQALARIDAG 110
Cdd:COG1734    1 MSDEQLEEFRERLLEEREELLEELEETEEELLSgdLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 491010513 111 EYGYCESCGVEIGLRRLEARPTATLCIDCKTLEEKREKQ 149
Cdd:COG1734   81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRERR 119
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
110-145 2.31e-11

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 54.98  E-value: 2.31e-11
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 491010513  110 GEYGYCESCGVEIGLRRLEARPTATLCIDCKTLEEK 145
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 ...
 33-142 7.18e-63

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: 188.22  E-value: 7.18e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491010513   33 MSPAQLAHFRKILEDWRDELMTEVERTVQNMQVENVNYSDPNDRASLETDMGLELRARDRERKLIRKINQALARIDAGEY 112
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 491010513  113 GYCESCGVEIGLRRLEARPTATLCIDCKTL 142
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKTL 110
dksA PRK10778
RNA polymerase-binding protein DksA;
23-151 5.00e-53

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 164.92  E-value: 5.00e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491010513  23 PYQPAPNEPYMSPAQLAHFRKILEDWRDELMTEVERTVQNMQVENVNYSDPNDRASLETDMGLELRARDRERKLIRKINQ 102
Cdd:PRK10778  22 PYQEKPGEEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEK 101

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 491010513 103 ALARIDAGEYGYCESCGVEIGLRRLEARPTATLCIDCKTLEEKREKQMA 151
Cdd:PRK10778 102 TLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMA 150
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
33-149 1.10e-52

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 162.77  E-value: 1.10e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491010513  33 MSPAQLAHFRKILEDWRDELMTEVERTVQNMQV--ENVNYSDPNDRASLETDMGLELRARDRERKLIRKINQALARIDAG 110
Cdd:COG1734    1 MSDEQLEEFRERLLEEREELLEELEETEEELLSgdLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 491010513 111 EYGYCESCGVEIGLRRLEARPTATLCIDCKTLEEKREKQ 149
Cdd:COG1734   81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRERR 119
bacill_yteA TIGR02890
regulatory protein, yteA family; Members of this predicted regulatory protein are found only ...
 37-146 1.42e-19

regulatory protein, yteA family; Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to Pfam family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. Smaller proteins from the proteobacteria with just the N-terminal domain, including DksA and DksA2 are RNA polymerase-binding regulatory proteins even if the Zn-binding site is not conserved. [Unknown function, General]


Pssm-ID: 274340  Cd Length: 159  Bit Score: 79.70  E-value: 1.42e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491010513   37 QLAHFRKILEDWRDELMTEVERTVQNMQV--------ENVNYSD-PNDRAS----LETDMGLelraRDRERKLIRKINQA 103
Cdd:TIGR02890   2 QLAELKNMLLQEKKELEQRLKQMNKEDGIasqrestgELSQYDNhPADLATelyeREKDIAL----REHEERELREIEHA 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 491010513  104 LARIDAGEYGYCESCGVEIGLRRLEARPTATLCIDC---KTLEEKR 146
Cdd:TIGR02890  78 LQKIENGTYGICEVCGKPIPYERLEAIPTATTCVECqnrKEVKNDR 123
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
110-145 2.31e-11

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 54.98  E-value: 2.31e-11
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 491010513  110 GEYGYCESCGVEIGLRRLEARPTATLCIDCKTLEEK 145
Cdd:pfam01258   1 GSYGSCEDCGEPIPEARLRAVPGARLCIECQEKYER 36
PRK11019 PRK11019
DksA/TraR family C4-type zinc finger protein;
100-148 2.91e-04

DksA/TraR family C4-type zinc finger protein;


Pssm-ID: 182903  Cd Length: 88  Bit Score: 37.54  E-value: 2.91e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 491010513 100 INQALARIDAGE-YGYCESCGVEIGLRRLEARPTATLCIDCKTLEEKREK 148
Cdd:PRK11019  23 IARARSELPRGEsLTECEECGEPIPEARRKAIPGVRLCVACQQEKDLQQA 72
PHA00080 PHA00080
DksA-like zinc finger domain containing protein
 71-152 4.86e-04

DksA-like zinc finger domain containing protein


Pssm-ID: 222775  Cd Length: 72  Bit Score: 36.65  E-value: 4.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491010513  71 SDPNDRASletdmglELRARDRERKLirkiNQALARIDAGEYGYCESCGVEIGLRRLEARPTATLCIDCKTLEEKREKQM 150
Cdd:PHA00080   1 ADIIDRAA-------EIEELQRERAL----ANRRNKYQAPSATHCEECGDPIPEARREAVPGCRTCVSCQEILELKSYQR 69


                 ..
gi 491010513 151 AQ 152
Cdd:PHA00080  70 GA 71
PRK13715 PRK13715
conjugal transfer protein TraR; Provisional
 115-151 7.88e-03

conjugal transfer protein TraR; Provisional


Pssm-ID: 184270  Cd Length: 73  Bit Score: 33.41  E-value: 7.88e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 491010513 115 CESCGVEIGLRRLEARPTATLCIDCKTLEEKREKQMA 151
Cdd:PRK13715  37 CEACGNPIPEARRKIFPGVTLCVECQAYQERQRKHYA 73
 
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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