RegulonDB RegulonDB 10.9:Regulon Page
   

YdcI DNA-binding transcriptional activator

Synonyms: YdcI
Summary:
Based on results with purified YdcI protein with a DNA probe in a gel shift assay, YdcI was shown to be a DNA-binding transcriptional repressor which negatively regulates its own expression in Salmonella enterica serovar Typhimurium [4]. YdcI was confirmed as a TF through an integrated workflow comprised of computational prediction, knowledge-based classification, and experimental validation of candidate TFs at the genome scale [1]. YdcI is involved in pH homeostasis and acetate metabolism [1]. YdcI belongs to the LysR family of transcriptional regulators, which is found in a wide range of Gram-negative bacteria and is involved in a number of Salmonella enterica serovar Typhimurium phenotypes [4] YdcI regulates a number of genes involved in aspects of bacterial biology related to survival, stress responses, and cell interactions [4] Regulation of the expression of genes in the YdcI regulon has evolved differently in different bacteria [4] YdcI appears to regulate genes with different cellular functions in E.
Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YdcI Functional   [APPHHH], [HIFS], [IPI] [1], [2], [3], [4]
Connectivity class: Local Regulator
Gene name: ydcI
  Genome position: 1494148-1495071
  Length: 924 bp / 307 aa
Operon name: ydcI
TU(s) encoding the TF:
Transcription unit        Promoter
ydcI
ydcIp


Regulon       
Regulated gene(s) flu, isrC
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
prophage genes and phage related functions (1)
RNA related (1)
Regulated operon(s) isrC-flu
First gene in the operon(s) isrC
Simple and complex regulons DksA,OxyR,YdcI,ppGpp
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[YdcI,+](1)


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
  YdcI activator flup Sigma70 nd nd isrC, flu nd nd [BPP], [GEA], [IGI] [5]



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
  YdcI activator smrB Transcription-Unit nd
nd
nd nd nd nd [BPP], [GEA], [IGI] [5]
  YdcI activator iraP Gene nd
nd
nd nd nd nd [BPP], [GEA], [IGI] [5]


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






RegulonDB