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Conserved domains on  [gi|90111159|ref|NP_415211|]
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ribbon-helix-helix domain-containing protein YbfE [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

LexA regulated protein( domain architecture ID 10013860)

LexA regulated protein similar to Escherichia coli protein YbfE

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK11675 PRK11675
LexA regulated protein; Provisional
 1-90 1.29e-50

LexA regulated protein; Provisional


:

Pssm-ID: 183272  Cd Length: 90  Bit Score: 154.36  E-value: 1.29e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111159   1 MAKEQTDRTTLDLFAHERRPGRPKTNPLSRDEQLRINKRNQLKRDKVRGLKRVELKLNAEAVEALNELAESRNMSRSELI 80
Cdd:PRK11675  1 MAKEQTDRTTLDLFADERRPGRPKTNPLSRDEQLRINKRNQLKRDKVRGLKRVELKLNADLVDALNELAEARNISRSELI 80

                        90
                ....*....|
gi 90111159  81 EEMLMQQLAA 90
Cdd:PRK11675 81 EEILMKQLAA 90
 
Name Accession Description Interval E-value
PRK11675 PRK11675
LexA regulated protein; Provisional
 1-90 1.29e-50

LexA regulated protein; Provisional


Pssm-ID: 183272  Cd Length: 90  Bit Score: 154.36  E-value: 1.29e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111159   1 MAKEQTDRTTLDLFAHERRPGRPKTNPLSRDEQLRINKRNQLKRDKVRGLKRVELKLNAEAVEALNELAESRNMSRSELI 80
Cdd:PRK11675  1 MAKEQTDRTTLDLFADERRPGRPKTNPLSRDEQLRINKRNQLKRDKVRGLKRVELKLNADLVDALNELAEARNISRSELI 80

                        90
                ....*....|
gi 90111159  81 EEMLMQQLAA 90
Cdd:PRK11675 81 EEILMKQLAA 90
RHH_CopG_NikR-like cd21631
ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription ...
 51-91 9.36e-09

ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription factor NikR, and similar proteins; This family includes the ribbon-helix-helix (RHH) domains of transcriptional repressor CopG, nickel-responsive transcription factor NikR, several antitoxins such as Shewanella oneidensis CopA(SO), Burkholderia pseudomallei HicB, and Caulobacter crescentus ParD, and similar proteins. CopG, a homodimeric RHH protein of around 45 residues, constitutes one of the smallest natural transcriptional repressors characterized and is the prototype of a series of repressor proteins encoded by plasmids that exhibit a similar genetic structure at their leading strand initiation and control regions. It is involved in the control of plasmid copy number. NikR, which consists of the N-terminal DNA-binding RHH domain and the C-terminal metal-binding domain (MBD) with four nickel ions, regulates several genes; in Helicobacter pylori, NikR regulates the urease enzyme under extreme acidic conditions, and is involved in the intracellular physiology of nickel. Protein HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In Burkholderia pseudomallei, the HicAB system may play a role in disease by regulating the frequency of persister cells, while in Yersinia pestis HicB acts as an autoregulatory protein that inhibits HicA, which acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. The CopG family RHH domain, represented by this model, forms a homodimer and binds DNA.


Pssm-ID: 409020  Cd Length: 42  Bit Score: 46.73  E-value: 9.36e-09
                       10        20        30        40
               ....*....|....*....|....*....|....*....|.
gi 90111159 51 KRVELKLNAEAVEALNELAESRNMSRSELIEEMLMQQLAAL 91
Cdd:cd21631  1 KRVTIKLDDELLERLDELARKRGVSRSELIREALREYLERL 41
RHH_1 pfam01402
Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the ...
 52-89 7.17e-05

Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement. The helix-turn-helix-like structure is involved in dimerization and not DNA binding as might have been expected.


Pssm-ID: 426244  Cd Length: 39  Bit Score: 36.72  E-value: 7.17e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 90111159   52 RVELKLNAEAVEALNELAESRNMSRSELIEEMLMQQLA 89
Cdd:pfam01402  1 RVSISLDEELLERLDELARARGRSRSELIREALREYLE 38
 
Name Accession Description Interval E-value
PRK11675 PRK11675
LexA regulated protein; Provisional
 1-90 1.29e-50

LexA regulated protein; Provisional


Pssm-ID: 183272  Cd Length: 90  Bit Score: 154.36  E-value: 1.29e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 90111159   1 MAKEQTDRTTLDLFAHERRPGRPKTNPLSRDEQLRINKRNQLKRDKVRGLKRVELKLNAEAVEALNELAESRNMSRSELI 80
Cdd:PRK11675  1 MAKEQTDRTTLDLFADERRPGRPKTNPLSRDEQLRINKRNQLKRDKVRGLKRVELKLNADLVDALNELAEARNISRSELI 80

                        90
                ....*....|
gi 90111159  81 EEMLMQQLAA 90
Cdd:PRK11675 81 EEILMKQLAA 90
RHH_CopG_NikR-like cd21631
ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription ...
 51-91 9.36e-09

ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription factor NikR, and similar proteins; This family includes the ribbon-helix-helix (RHH) domains of transcriptional repressor CopG, nickel-responsive transcription factor NikR, several antitoxins such as Shewanella oneidensis CopA(SO), Burkholderia pseudomallei HicB, and Caulobacter crescentus ParD, and similar proteins. CopG, a homodimeric RHH protein of around 45 residues, constitutes one of the smallest natural transcriptional repressors characterized and is the prototype of a series of repressor proteins encoded by plasmids that exhibit a similar genetic structure at their leading strand initiation and control regions. It is involved in the control of plasmid copy number. NikR, which consists of the N-terminal DNA-binding RHH domain and the C-terminal metal-binding domain (MBD) with four nickel ions, regulates several genes; in Helicobacter pylori, NikR regulates the urease enzyme under extreme acidic conditions, and is involved in the intracellular physiology of nickel. Protein HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In Burkholderia pseudomallei, the HicAB system may play a role in disease by regulating the frequency of persister cells, while in Yersinia pestis HicB acts as an autoregulatory protein that inhibits HicA, which acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. The CopG family RHH domain, represented by this model, forms a homodimer and binds DNA.


Pssm-ID: 409020  Cd Length: 42  Bit Score: 46.73  E-value: 9.36e-09
                       10        20        30        40
               ....*....|....*....|....*....|....*....|.
gi 90111159 51 KRVELKLNAEAVEALNELAESRNMSRSELIEEMLMQQLAAL 91
Cdd:cd21631  1 KRVTIKLDDELLERLDELARKRGVSRSELIREALREYLERL 41
RHH_1 pfam01402
Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the ...
 52-89 7.17e-05

Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement. The helix-turn-helix-like structure is involved in dimerization and not DNA binding as might have been expected.


Pssm-ID: 426244  Cd Length: 39  Bit Score: 36.72  E-value: 7.17e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 90111159   52 RVELKLNAEAVEALNELAESRNMSRSELIEEMLMQQLA 89
Cdd:pfam01402  1 RVSISLDEELLERLDELARARGRSRSELIREALREYLE 38
 
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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