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YebK DNA-binding transcriptional dual regulator

Synonyms: YebK-2-dehydro-3-deoxy-D-gluconate 6-phosphate, YebK
Summary:
YebK is a transcriptional regulator implicated in the adaptation to the transition from rich medium to cellobiose minimal medium, reducing the length of the lag phase [2] Expression of YebK is higher in cellobiose minimal medium than in glucose minimal medium. DNA binding of YebK is reversed by 2-keto-3-deoxygluconate-6-phosphate (KDPG) [2]


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YebK Functional   [AIFS], [AIFSO], [APPHINH], [HIFS] [1], [2], [3], [4]
YebK-2-dehydro-3-deoxy-D-gluconate 6-phosphate Non-Functional   nd nd
Evolutionary Family: RpiR
Connectivity class: Local Regulator
Gene name: yebK
  Genome position: 1936652-1937521
  Length: 870 bp / 289 aa
Operon name: yebK
TU(s) encoding the TF:
Transcription unit        Promoter
null
null


Regulon       
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 Growth Condition Evidence (Confirmed, Strong, Weak) References
  YebK repressor nd nd nd nd nd nd [BPP], [GEA], [IBAA] [2]


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


Evidence    


Reference(s)    

 [1] Leyn SA., Li X., Zheng Q., Novichkov PS., Reed S., Romine MF., Fredrickson JK., Yang C., Osterman AL., Rodionov DA., 2011, Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis., J Biol Chem 286(41):35782-94

 [2] Parisutham V., Lee SK., 2015, Novel Functions and Regulation of Cryptic Cellobiose Operons in Escherichia coli., PLoS One 10(6):e0131928

 [3] 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

 [4] 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



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