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YpdB DNA-binding transcriptional activator

Synonyms: YpdB-Phosphorylated
A mutant containing a deletion of both ypdA and ypdB does not show a significant phenotype when measured by phenotype microarray [2]. While wild-type E. coli shows significantly decreased swarming motility upon exposure to volatile organic compounds (VOCs) produced by Bacillus subtilis, a ypdB null mutant shows no significant difference in swarming motility upon VOC treatment [3].

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YpdB-Phosphorylated Functional   [APPHINH], [IEP], [IHBCE], [IPI] [1]
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: ypdB
  Genome position: 2500383-2501117
  Length: 735 bp / 244 aa
Operon name: ypdABC
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) yhjX
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
Regulated operon(s) yhjX
First gene in the operon(s) yhjX
Simple and complex regulons YpdB
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
  YpdB-Phosphorylated activator yhjXp Sigma70 -73.5 -110.0 yhjX
3712112 3712122 [BPP], [SM] [1]
  YpdB-Phosphorylated activator yhjXp Sigma70 -52.5 -89.0 yhjX
3712091 3712101 [BPP], [SM] [1]

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


 [APPHINH] Assay of protein purified to homogeneity from its native host

 [IEP] Inferred from expression pattern

 [IHBCE] Inferred by a human based on computational evidence

 [IPI] Inferred from physical interaction

 [BPP] Binding of purified proteins

 [SM] Site mutation


 [1] Fried L., Behr S., Jung K., 2013, Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli., J Bacteriol 195(4):807-15

 [2] Zhou L., Lei XH., Bochner BR., Wanner BL., 2003, Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems., J Bacteriol 185(16):4956-72

 [3] Kim KS., Lee S., Ryu CM., 2013, Interspecific bacterial sensing through airborne signals modulates locomotion and drug resistance., Nat Commun 4:1809