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Conserved domains on  [gi|2541259027|ref|WP_297371509|]
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RNA polymerase-binding protein DksA [Acidocella sp.]

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 ...
 18-127 7.06e-52

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: 159.72  E-value: 7.06e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2541259027  18 MNPMQTEYFRQKLLRWRADLVKEANGTLASLGEGGILEPDITDRASVETDRALELRTRDRARKLIGKIDQALQRIENGSY 97
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2541259027  98 GFCEETGEPIGLKRLEARPIATLSIEAQER 127
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 ...
 18-127 7.06e-52

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: 159.72  E-value: 7.06e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2541259027  18 MNPMQTEYFRQKLLRWRADLVKEANGTLASLGEGGILEPDITDRASVETDRALELRTRDRARKLIGKIDQALQRIENGSY 97
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2541259027  98 GFCEETGEPIGLKRLEARPIATLSIEAQER 127
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKTL 110
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
18-133 8.47e-46

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 144.66  E-value: 8.47e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2541259027  18 MNPMQTEYFRQKLLRWRADLVKEANGTLASL--GEGGILEPDITDRASVETDRALELRTRDRARKLIGKIDQALQRIENG 95
Cdd:COG1734     1 MSDEQLEEFRERLLEEREELLEELEETEEELlsGDLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2541259027  96 SYGFCEETGEPIGLKRLEARPIATLSIEAQERHERMEK 133
Cdd:COG1734    81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRER 118
dksA PRK10778
RNA polymerase-binding protein DksA;
9-133 7.92e-26

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 95.20  E-value: 7.92e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2541259027   9 YRPSDDEEFMNPMQTEYFRQKLLRWRADLVKEANGTLASLGEGGILEPDITDRASVETDRALELRTRDRARKLIGKIDQA 88
Cdd:PRK10778   23 YQEKPGEEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEKT 102

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2541259027  89 LQRIENGSYGFCEETGEPIGLKRLEARPIATLSIEAQERHERMEK 133
Cdd:PRK10778  103 LKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREK 147
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
95-130 6.59e-12

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 56.14  E-value: 6.59e-12
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2541259027  95 GSYGFCEETGEPIGLKRLEARPIATLSIEAQERHER 130
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 ...
 18-127 7.06e-52

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: 159.72  E-value: 7.06e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2541259027  18 MNPMQTEYFRQKLLRWRADLVKEANGTLASLGEGGILEPDITDRASVETDRALELRTRDRARKLIGKIDQALQRIENGSY 97
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2541259027  98 GFCEETGEPIGLKRLEARPIATLSIEAQER 127
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKTL 110
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
18-133 8.47e-46

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 144.66  E-value: 8.47e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2541259027  18 MNPMQTEYFRQKLLRWRADLVKEANGTLASL--GEGGILEPDITDRASVETDRALELRTRDRARKLIGKIDQALQRIENG 95
Cdd:COG1734     1 MSDEQLEEFRERLLEEREELLEELEETEEELlsGDLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2541259027  96 SYGFCEETGEPIGLKRLEARPIATLSIEAQERHERMEK 133
Cdd:COG1734    81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRER 118
dksA PRK10778
RNA polymerase-binding protein DksA;
9-133 7.92e-26

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 95.20  E-value: 7.92e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2541259027   9 YRPSDDEEFMNPMQTEYFRQKLLRWRADLVKEANGTLASLGEGGILEPDITDRASVETDRALELRTRDRARKLIGKIDQA 88
Cdd:PRK10778   23 YQEKPGEEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEKT 102

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2541259027  89 LQRIENGSYGFCEETGEPIGLKRLEARPIATLSIEAQERHERMEK 133
Cdd:PRK10778  103 LKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREK 147
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
95-130 6.59e-12

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 56.14  E-value: 6.59e-12
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2541259027  95 GSYGFCEETGEPIGLKRLEARPIATLSIEAQERHER 130
Cdd:pfam01258   1 GSYGSCEDCGEPIPEARLRAVPGARLCIECQEKYER 36
C4_traR_proteo TIGR02419
phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Members of this family are ...
 65-126 2.17e-04

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: 37.37  E-value: 2.17e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2541259027  65 ETDRALELRTRDRARKLigkidqALQRI---ENGSYGFCEETGEPIGLKRLEARPIATLSIEAQE 126
Cdd:TIGR02419   2 EFDRAQELEEELLERAL------AAARAkkvIGPSLRECEDCGEPIPEARREALPGVTRCVSCQE 60
 
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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