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AlsR DNA-binding transcriptional repressor

Synonyms: AlsR, AlsR-D-allose
"Allose utilization regulator," AlsR, negatively controls the expression of genes involved in transport and catabolism of D-allose and low-affinity transport of D-ribose [1, 3] It is negatively autoregulated and coordinately represses transcription of the divergent gene rpiB, encoding an enzyme in the pentose pathway [3] Synthesis of alsR and rpiB genes is induced when Escherichia coli is grown on d-allose in the absence of glucose. Gene induction occurs when the physiological inducer, d-allose, binds to AlsR, liberating the repression effect caused by this protein [1, 2] As a member of the RpiR/YebK/YfhH family of transcriptional regulators, AlsR features an N-terminal domain containing a helix-turn-helix motif [3] Currently, no DNA-binding sites for this regulator have been reported in the literature.

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
AlsR Functional   Apo [AIFS], [GEA], [IPI] [1], [2], [3]
AlsR-D-allose Non-Functional Allosteric Holo [GEA], [IEP], [IHBCE], [IPI] [1], [2], [3]
Evolutionary Family: RpiR
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: alsR
  Genome position: 4312101-4312991
  Length: 891 bp / 296 aa
Operon name: alsRBACE
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) alsA, alsB, alsC, alsE, alsR, rpiB
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (6)
ABC superfamily ATP binding cytoplasmic component (1)
ABC superfamily, periplasmic binding component (1)
ABC superfamily, membrane component (1)
membrane (1)
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Regulated operon(s) alsRBACE, rpiB
First gene in the operon(s) alsR, alsR, rpiB
Simple and complex regulons AlsR
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
  AlsR repressor alsRp1 Sigma70 nd nd alsR, alsB, alsA, alsC, alsE nd nd [CV(GEA)], [CV(GEA)], [CV(GEA/GS)], [CV(GEA/GS)], [GEA], [GS] [1], [4]
  AlsR repressor alsRp2 Sigma70 nd nd alsR, alsB, alsA, alsC, alsE nd nd [CV(GEA)], [CV(GEA)], [CV(GEA/GS)], [CV(GEA/GS)], [GEA], [GS] [1], [4]
  AlsR repressor rpiBp Sigma70 nd nd rpiB nd nd [CV(GEA)], [CV(GEA)], [CV(GEA/GS)], [CV(GEA/GS)], [GEA], [GS] [2], [3], [4]

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


 [AIFS] Automated inference of function from sequence

 [GEA] Gene expression analysis

 [IPI] Inferred from physical interaction

 [IEP] Inferred from expression pattern

 [IHBCE] Inferred by a human based on computational evidence

 [CV(GEA)] cross validation(GEA)

 [CV(GEA/GS)] cross validation(GEA/GS)

 [GS] genomic SELEX


 [1] Kim C., Song S., Park C., 1997, The D-allose operon of Escherichia coli K-12., J Bacteriol 179(24):7631-7

 [2] Poulsen TS., Chang YY., Hove-Jensen B., 1999, D-Allose catabolism of Escherichia coli: involvement of alsI and regulation of als regulon expression by allose and ribose., J Bacteriol 181(22):7126-30

 [3] Sorensen KI., Hove-Jensen B., 1996, Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression., J Bacteriol 178(4):1003-11

 [4] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936