NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1585564935|gb|QBI84148|]
View 

putative transcriptional regulator [Pseudomonas phage vB_Pae_BR319a]

Protein Classification

TraR/DksA family transcriptional regulator( domain architecture ID 10009661)

TraR/DksA family transcriptional regulator similar to Escherichia virus uncharacterized 8.5 kDa protein in gpA 5'region

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PHA00080 PHA00080
DksA-like zinc finger domain containing protein
 1-63 8.94e-23

DksA-like zinc finger domain containing protein


:

Pssm-ID: 222775  Cd Length: 72  Bit Score: 82.11  E-value: 8.94e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1585564935  1 MDVIDQANERAENMVQAALAQRTNTRLAPSALWCEDCGEQIPEARRQAAPGCECCISCQELRE 63
Cdd:PHA00080   1 ADIIDRAAEIEELQRERALANRRNKYQAPSATHCEECGDPIPEARREAVPGCRTCVSCQEILE 63
 
Name Accession Description Interval E-value
PHA00080 PHA00080
DksA-like zinc finger domain containing protein
 1-63 8.94e-23

DksA-like zinc finger domain containing protein


Pssm-ID: 222775  Cd Length: 72  Bit Score: 82.11  E-value: 8.94e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1585564935  1 MDVIDQANERAENMVQAALAQRTNTRLAPSALWCEDCGEQIPEARRQAAPGCECCISCQELRE 63
Cdd:PHA00080   1 ADIIDRAAEIEELQRERALANRRNKYQAPSATHCEECGDPIPEARREAVPGCRTCVSCQEILE 63
C4_traR_proteo TIGR02419
phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Members of this family are ...
 2-63 3.13e-19

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: 72.81  E-value: 3.13e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1585564935  2 DVIDQANERAENMVQAALAQRTNTR-LAPSALWCEDCGEQIPEARRQAAPGCECCISCQELRE 63
Cdd:TIGR02419  1 DEFDRAQELEEELLERALAAARAKKvIGPSLRECEDCGEPIPEARREALPGVTRCVSCQEILE 63
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
33-64 8.39e-08

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 43.43  E-value: 8.39e-08
                         10        20        30
                 ....*....|....*....|....*....|..
gi 1585564935 33 WCEDCGEQIPEARRQAAPGCECCISCQELREY 64
Cdd:pfam01258  5 SCEDCGEPIPEARLRAVPGARLCIECQEKYER 36
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
2-68 1.54e-05

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 39.12  E-value: 1.54e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1585564935   2 DVIDQANERAENMVQAALAQRTNTRLAP--SAL---------WCEDCGEQIPEARRQAAPGCECCISCQELREYPARR 68
Cdd:COG1734    42 DPADRATEEEERELELALRDRERKLLRKidAALerieegtygICEECGEPIPLERLEARPTATLCIECKERQERRERR 119
 
Name Accession Description Interval E-value
PHA00080 PHA00080
DksA-like zinc finger domain containing protein
 1-63 8.94e-23

DksA-like zinc finger domain containing protein


Pssm-ID: 222775  Cd Length: 72  Bit Score: 82.11  E-value: 8.94e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1585564935  1 MDVIDQANERAENMVQAALAQRTNTRLAPSALWCEDCGEQIPEARRQAAPGCECCISCQELRE 63
Cdd:PHA00080   1 ADIIDRAAEIEELQRERALANRRNKYQAPSATHCEECGDPIPEARREAVPGCRTCVSCQEILE 63
C4_traR_proteo TIGR02419
phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Members of this family are ...
 2-63 3.13e-19

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: 72.81  E-value: 3.13e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1585564935  2 DVIDQANERAENMVQAALAQRTNTR-LAPSALWCEDCGEQIPEARRQAAPGCECCISCQELRE 63
Cdd:TIGR02419  1 DEFDRAQELEEELLERALAAARAKKvIGPSLRECEDCGEPIPEARREALPGVTRCVSCQEILE 63
PRK11019 PRK11019
DksA/TraR family C4-type zinc finger protein;
8-63 1.71e-12

DksA/TraR family C4-type zinc finger protein;


Pssm-ID: 182903  Cd Length: 88  Bit Score: 56.42  E-value: 1.71e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1585564935  8 NERAENMVQAALAQ-RTNTRLAPSALWCEDCGEQIPEARRQAAPGCECCISCQELRE 63
Cdd:PRK11019  12 QEQIDATVEDAIARaRSELPRGESLTECEECGEPIPEARRKAIPGVRLCVACQQEKD 68
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
33-64 8.39e-08

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 43.43  E-value: 8.39e-08
                         10        20        30
                 ....*....|....*....|....*....|..
gi 1585564935 33 WCEDCGEQIPEARRQAAPGCECCISCQELREY 64
Cdd:pfam01258  5 SCEDCGEPIPEARLRAVPGARLCIECQEKYER 36
PRK13715 PRK13715
conjugal transfer protein TraR; Provisional
 2-63 1.40e-05

conjugal transfer protein TraR; Provisional


Pssm-ID: 184270  Cd Length: 73  Bit Score: 38.42  E-value: 1.40e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1585564935  2 DVIDQANERAENMVQAAL---AQRTNTRLAPSALwCEDCGEQIPEARRQAAPGCECCISCQELRE 63
Cdd:PRK13715   3 DEADEAYSVTEQLTMTGInriRQKINAHGIPVYL-CEACGNPIPEARRKIFPGVTLCVECQAYQE 66
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
2-68 1.54e-05

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 39.12  E-value: 1.54e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1585564935   2 DVIDQANERAENMVQAALAQRTNTRLAP--SAL---------WCEDCGEQIPEARRQAAPGCECCISCQELREYPARR 68
Cdd:COG1734    42 DPADRATEEEERELELALRDRERKLLRKidAALerieegtygICEECGEPIPLERLEARPTATLCIECKERQERRERR 119
dksA TIGR02420
RNA polymerase-binding protein DksA; The model that is the basis for this family describes a ...
 33-61 1.19e-04

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: 36.84  E-value: 1.19e-04
                          10        20
                  ....*....|....*....|....*....
gi 1585564935  33 WCEDCGEQIPEARRQAAPGCECCISCQEL 61
Cdd:TIGR02420  82 YCEECGEEIGLRRLEARPTATLCIDCKTL 110
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH