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Conserved domains on  [gi|447201434|ref|WP_001278690|]
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MULTISPECIES: conjugal transfer protein TraR [Enterobacteriaceae]

Protein Classification

conjugal transfer protein TraR( domain architecture ID 10014366)

conjugal transfer protein TraR is a RNA polymerase-binding protein and DksA homolog that mimics the effects of ppGpp/DksA on RNAP, modifying the kinetics of transcription initiation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13715 PRK13715
conjugal transfer protein TraR; Provisional
 1-73 4.60e-51

conjugal transfer protein TraR; Provisional


:

Pssm-ID: 184270  Cd Length: 73  Bit Score: 153.60  E-value: 4.60e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447201434  1 MSDEADEAYSVTEQLTMTGINRIRQKINAHGIPVYLCEACGNPIPESRRKIFPGVTLCVECQAYQERQRKHYA 73
Cdd:PRK13715  1 MSDEADEAYSVTEQLTMTGINRIRQKINAHGIPVYLCEACGNPIPEARRKIFPGVTLCVECQAYQERQRKHYA 73
 
Name Accession Description Interval E-value
PRK13715 PRK13715
conjugal transfer protein TraR; Provisional
 1-73 4.60e-51

conjugal transfer protein TraR; Provisional


Pssm-ID: 184270  Cd Length: 73  Bit Score: 153.60  E-value: 4.60e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447201434  1 MSDEADEAYSVTEQLTMTGINRIRQKINAHGIPVYLCEACGNPIPESRRKIFPGVTLCVECQAYQERQRKHYA 73
Cdd:PRK13715  1 MSDEADEAYSVTEQLTMTGINRIRQKINAHGIPVYLCEACGNPIPEARRKIFPGVTLCVECQAYQERQRKHYA 73
C4_traR_proteo TIGR02419
phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Members of this family are ...
 3-66 4.03e-20

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: 75.12  E-value: 4.03e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 447201434   3 DEADEAYSVTEQL--TMTGINRIRQKINAHgipVYLCEACGNPIPESRRKIFPGVTLCVECQAYQE 66
Cdd:TIGR02419  1 DEFDRAQELEEELleRALAAARAKKVIGPS---LRECEDCGEPIPEARREALPGVTRCVSCQEILE 63
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
3-71 2.54e-09

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 49.13  E-value: 2.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201434   3 DEADEAYSVTEQ-LTMTGINRIR---QKINA---------HGIpvylCEACGNPIPESRRKIFPGVTLCVECQAYQERQR 69
Cdd:COG1734   42 DPADRATEEEEReLELALRDRERkllRKIDAalerieegtYGI----CEECGEPIPLERLEARPTATLCIECKERQERRE 117


                 ..
gi 447201434  70 KH 71
Cdd:COG1734  118 RR 119
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
37-67 6.32e-09

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 46.12  E-value: 6.32e-09
                         10        20        30
                 ....*....|....*....|....*....|.
gi 447201434  37 CEACGNPIPESRRKIFPGVTLCVECQAYQER 67
Cdd:pfam01258  6 CEDCGEPIPEARLRAVPGARLCIECQEKYER 36
 
Name Accession Description Interval E-value
PRK13715 PRK13715
conjugal transfer protein TraR; Provisional
 1-73 4.60e-51

conjugal transfer protein TraR; Provisional


Pssm-ID: 184270  Cd Length: 73  Bit Score: 153.60  E-value: 4.60e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447201434  1 MSDEADEAYSVTEQLTMTGINRIRQKINAHGIPVYLCEACGNPIPESRRKIFPGVTLCVECQAYQERQRKHYA 73
Cdd:PRK13715  1 MSDEADEAYSVTEQLTMTGINRIRQKINAHGIPVYLCEACGNPIPEARRKIFPGVTLCVECQAYQERQRKHYA 73
C4_traR_proteo TIGR02419
phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Members of this family are ...
 3-66 4.03e-20

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: 75.12  E-value: 4.03e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 447201434   3 DEADEAYSVTEQL--TMTGINRIRQKINAHgipVYLCEACGNPIPESRRKIFPGVTLCVECQAYQE 66
Cdd:TIGR02419  1 DEFDRAQELEEELleRALAAARAKKVIGPS---LRECEDCGEPIPEARREALPGVTRCVSCQEILE 63
PRK11019 PRK11019
DksA/TraR family C4-type zinc finger protein;
10-70 2.37e-15

DksA/TraR family C4-type zinc finger protein;


Pssm-ID: 182903  Cd Length: 88  Bit Score: 63.74  E-value: 2.37e-15
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 447201434 10 SVTEQLTMT---GINRIRQKInAHGIPVYLCEACGNPIPESRRKIFPGVTLCVECQAYQERQRK 70
Cdd:PRK11019 10 AVQEQIDATvedAIARARSEL-PRGESLTECEECGEPIPEARRKAIPGVRLCVACQQEKDLQQA 72
PHA00080 PHA00080
DksA-like zinc finger domain containing protein
 2-71 1.89e-10

DksA-like zinc finger domain containing protein


Pssm-ID: 222775  Cd Length: 72  Bit Score: 50.91  E-value: 1.89e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201434  2 SDEADEAYSVTEQLTMTGINRIRQKINahGIPVYLCEACGNPIPESRRKIFPGVTLCVECQAYQERQRKH 71
Cdd:PHA00080  1 ADIIDRAAEIEELQRERALANRRNKYQ--APSATHCEECGDPIPEARREAVPGCRTCVSCQEILELKSYQ 68
DksA COG1734
RNA polymerase-binding transcription factor DksA [Transcription];
3-71 2.54e-09

RNA polymerase-binding transcription factor DksA [Transcription];


Pssm-ID: 441340  Cd Length: 119  Bit Score: 49.13  E-value: 2.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447201434   3 DEADEAYSVTEQ-LTMTGINRIR---QKINA---------HGIpvylCEACGNPIPESRRKIFPGVTLCVECQAYQERQR 69
Cdd:COG1734   42 DPADRATEEEEReLELALRDRERkllRKIDAalerieegtYGI----CEECGEPIPLERLEARPTATLCIECKERQERRE 117


                 ..
gi 447201434  70 KH 71
Cdd:COG1734  118 RR 119
zf-dskA_traR pfam01258
Prokaryotic dksA/traR C4-type zinc finger;
37-67 6.32e-09

Prokaryotic dksA/traR C4-type zinc finger;


Pssm-ID: 426162 [Multi-domain]  Cd Length: 36  Bit Score: 46.12  E-value: 6.32e-09
                         10        20        30
                 ....*....|....*....|....*....|.
gi 447201434  37 CEACGNPIPESRRKIFPGVTLCVECQAYQER 67
Cdd:pfam01258  6 CEDCGEPIPEARLRAVPGARLCIECQEKYER 36
bacill_yteA TIGR02890
regulatory protein, yteA family; Members of this predicted regulatory protein are found only ...
 20-70 4.98e-07

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: 43.87  E-value: 4.98e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 447201434   20 INRIRQKINA--HGIpvylCEACGNPIPESRRKIFPGVTLCVECQAYQERQRK 70
Cdd:TIGR02890  74 IEHALQKIENgtYGI----CEVCGKPIPYERLEAIPTATTCVECQNRKEVKND 122
 
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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