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Conserved domains on  [gi|2528351387|ref|WP_289155256|]
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RNA polymerase-binding protein DksA [Porticoccus sp. W117]

Protein Classification

TraR/DksA C4-type zinc finger protein( domain architecture ID 3397)

TraR/DksA C4-type zinc finger protein may function as a transcriptional regulator

CATH:  1.10.287.3960
Gene Ontology:  GO:0008270
PubMed:  15294157
SCOP:  4003090

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
zf-dskA_traR super family cl00755
Prokaryotic dksA/traR C4-type zinc finger;
22-158 6.30e-64

Prokaryotic dksA/traR C4-type zinc finger;


The actual alignment was detected with superfamily member PRK10778:

Pssm-ID: 445081  Cd Length: 151  Bit Score: 192.66  E-value: 6.30e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2528351387  22 ISLHGFEPYKEKKGEEYMNEKQRDHFKGLLLAWKRELMEEVDRTVSHMKDEASNFPDPADRATQEEEFSLELRTRDRERK 101
Cdd:PRK10778   15 LAIAGVEPYQEKPGEEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERK 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2528351387 102 LIKKIDSTIERIDQDDYGFCDQCGIEIGIRRLEARPTANLCVDCKTLDEIKERQITG 158
Cdd:PRK10778   95 LIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMAG 151
 
Name Accession Description Interval E-value
dksA PRK10778
RNA polymerase-binding protein DksA;
22-158 6.30e-64

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 192.66  E-value: 6.30e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2528351387  22 ISLHGFEPYKEKKGEEYMNEKQRDHFKGLLLAWKRELMEEVDRTVSHMKDEASNFPDPADRATQEEEFSLELRTRDRERK 101
Cdd:PRK10778   15 LAIAGVEPYQEKPGEEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERK 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2528351387 102 LIKKIDSTIERIDQDDYGFCDQCGIEIGIRRLEARPTANLCVDCKTLDEIKERQITG 158
Cdd:PRK10778   95 LIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMAG 151
dksA TIGR02420
RNA polymerase-binding protein DksA; The model that is the basis for this family describes a ...
 39-148 1.12e-60

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: 182.83  E-value: 1.12e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2528351387  39 MNEKQRDHFKGLLLAWKRELMEEVDRTVSHMKDEASNFPDPADRATQEEEFSLELRTRDRERKLIKKIDSTIERIDQDDY 118
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2528351387 119 GFCDQCGIEIGIRRLEARPTANLCVDCKTL 148
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKTL 110
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
39-155 1.94e-47

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 149.67  E-value: 1.94e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2528351387  39 MNEKQRDHFKGLLLAWKRELMEEVDRTVSHMK--DEASNFPDPADRATQEEEFSLELRTRDRERKLIKKIDSTIERIDQD 116
Cdd:COG1734     1 MSDEQLEEFRERLLEEREELLEELEETEEELLsgDLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2528351387 117 DYGFCDQCGIEIGIRRLEARPTANLCVDCKTLDEIKERQ 155
Cdd:COG1734    81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRERR 119
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
117-150 8.33e-08

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 46.12  E-value: 8.33e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2528351387 117 DYGFCDQCGIEIGIRRLEARPTANLCVDCKTLDE 150
Cdd:pfam01258   2 SYGSCEDCGEPIPEARLRAVPGARLCIECQEKYE 35
 
Name Accession Description Interval E-value
dksA PRK10778
RNA polymerase-binding protein DksA;
22-158 6.30e-64

RNA polymerase-binding protein DksA;


Pssm-ID: 182722  Cd Length: 151  Bit Score: 192.66  E-value: 6.30e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2528351387  22 ISLHGFEPYKEKKGEEYMNEKQRDHFKGLLLAWKRELMEEVDRTVSHMKDEASNFPDPADRATQEEEFSLELRTRDRERK 101
Cdd:PRK10778   15 LAIAGVEPYQEKPGEEYMNEAQLAHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERK 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2528351387 102 LIKKIDSTIERIDQDDYGFCDQCGIEIGIRRLEARPTANLCVDCKTLDEIKERQITG 158
Cdd:PRK10778   95 LIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMAG 151
dksA TIGR02420
RNA polymerase-binding protein DksA; The model that is the basis for this family describes a ...
 39-148 1.12e-60

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: 182.83  E-value: 1.12e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2528351387  39 MNEKQRDHFKGLLLAWKRELMEEVDRTVSHMKDEASNFPDPADRATQEEEFSLELRTRDRERKLIKKIDSTIERIDQDDY 118
Cdd:TIGR02420   1 MSEAQLEHFRKILLRWKQELLEEADKTLEHLQEESENFPDPADRATQEEERALELRTRDRERKLIKKIDEALKRIEDGEY 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2528351387 119 GFCDQCGIEIGIRRLEARPTANLCVDCKTL 148
Cdd:TIGR02420  81 GYCEECGEEIGLRRLEARPTATLCIDCKTL 110
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
39-155 1.94e-47

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 149.67  E-value: 1.94e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2528351387  39 MNEKQRDHFKGLLLAWKRELMEEVDRTVSHMK--DEASNFPDPADRATQEEEFSLELRTRDRERKLIKKIDSTIERIDQD 116
Cdd:COG1734     1 MSDEQLEEFRERLLEEREELLEELEETEEELLsgDLSAYDPDPADRATEEEERELELALRDRERKLLRKIDAALERIEEG 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2528351387 117 DYGFCDQCGIEIGIRRLEARPTANLCVDCKTLDEIKERQ 155
Cdd:COG1734    81 TYGICEECGEPIPLERLEARPTATLCIECKERQERRERR 119
bacill_yteA TIGR02890
regulatory protein, yteA family; Members of this predicted regulatory protein are found only ...
 42-153 9.21e-15

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: 67.37  E-value: 9.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2528351387  42 KQRDHFKGLLLAWKRELMEEVDR-----TVSHMKD---EASNFPD-PADRATQEEEFSLELRTRDRERKLIKKIDSTIER 112
Cdd:TIGR02890   1 QQLAELKNMLLQEKKELEQRLKQmnkedGIASQREstgELSQYDNhPADLATELYEREKDIALREHEERELREIEHALQK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2528351387 113 IDQDDYGFCDQCGIEIGIRRLEARPTANLCVDCKTLDEIKE 153
Cdd:TIGR02890  81 IENGTYGICEVCGKPIPYERLEAIPTATTCVECQNRKEVKN 121
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
117-150 8.33e-08

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 46.12  E-value: 8.33e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2528351387 117 DYGFCDQCGIEIGIRRLEARPTANLCVDCKTLDE 150
Cdd:pfam01258   2 SYGSCEDCGEPIPEARLRAVPGARLCIECQEKYE 35
 
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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