RegulonDB RegulonDB 10.8:Regulon Page

YdfH DNA-binding transcriptional dual regulator

Synonyms: YdfH
YdfH belongs to the GntR transcription factor family [1] for which the consensus sequence is reported to be tnGTnnnACna [4] Although only one site was determined in a gel shift assay, it is possible that YfdH binds as a complex of flanking regions of the core sequence (-65 to -50) [3] YdfH is not a global repressor, and few genes are repressed by YdfH [3]

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YdfH Functional   [APPHINH], [HIFS], [IEP] [1], [2], [3]
Evolutionary Family: GntR
Connectivity class: Local Regulator
Gene name: ydfH
  Genome position: 1628352-1629038
  Length: 687 bp / 228 aa
Operon name: ydfH
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s)
Regulated operon(s)
First gene in the operon(s)
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor regulation    

Transcription factor binding sites (TFBSs) arrangements

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References

High-throughput Transcription factor binding sites (TFBSs)

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence (Confirmed, Strong, Weak) References
  YdfH repressor rspA-rspB tu nd
1655194 1655207 1655200.0 nd [BPP], [GEA] [3]

Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation



 [1] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [2] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [3] Sakihama Y., Mizoguchi H., Oshima T., Ogasawara N., 2012, YdfH identified as a repressor of rspA by the use of reduced genome Escherichia coli MGF-01., Biosci Biotechnol Biochem 76(9):1688-93

 [4] Rigali S., Derouaux A., Giannotta F., Dusart J., 2002, Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies., J Biol Chem 277(15):12507-15