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NimR DNA-binding transcriptional repressor

Synonyms: NimR
Summary:
NimR, formerly called YeaM, belongs to the AraC/XylS superfamily [4] It confers resistance to 2-nitroimidazole, an antibacterial and antifungal agent [1] NimR plays a regulatory role in divergent transcription of the nimT and nimR genes [1] NimR: regulator of nimT [1]


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NimR Functional   [AIFS], [APPHINH], [IEP] [1], [2]
Evolutionary Family: AraC/XylS
Connectivity class: Local Regulator
Gene name: nimR
  Genome position: 1874755-1875576
  Length: 822 bp / 273 aa
Operon name: nimR
TU(s) encoding the TF:
Transcription unit        Promoter
yeaM
nimRp


Regulon       
Regulated gene(s) nimR, nimT
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Transcription related (1)
transcriptional level (1)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
Regulated operon(s) nimR, nimT
First gene in the operon(s) nimR, nimT
Simple and complex regulons NimR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[NimR,-](2)


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
  NimR repressor nimRp nd -57.5 -82.0 nimR
gtcatatgctTCTCATTGTTACAAACGAGgctgtacctt
1875649 1875667 [BPP], [GEA], , [ICWHO] [1], [3]
  NimR repressor nimRp nd -29.5 -54.0 nimR
ctgtaccttaCCGTTTTTATTGTTAtgttgaatca
1875623 1875637 [BPP], [GEA], , [ICWHO] [1], [3]
  NimR repressor nimRp nd 17.0 -8.5 nimR
atgacaaattATCGCTAAGTTCGGACAAAATGatgcacaggt
1875574 1875595 [BPP], [GEA], , [ICWHO] [1], [3]
  NimR repressor nimTp nd -73.0 -88.5 nimT
acctgtgcatCATTTTGTCCGAACTTAGCGATaatttgtcat
1875574 1875595 [BPP], [GEA], , [ICWHO] [1], [3]
  NimR repressor nimTp nd -27.5 -43.0 nimT
tgattcaacaTAACAATAAAAACGGtaaggtacag
1875623 1875637 [BPP], [GEA], , [ICWHO] [1], [3]
  NimR repressor nimTp nd 1.5 -15.0 nimT
aaggtacagcCTCGTTTGTAACAATGAGAagcatatgac
1875649 1875667 [BPP], [GEA], , [ICWHO] [1], [3]


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


Evidence    

 [AIFS] Automated inference of function from sequence

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

 [IEP] Inferred from expression pattern

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [GS] genomic SELEX

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Ogasawara H., Ohe S., Ishihama A., 2015, Role of transcription factor NimR (YeaM) in sensitivity control of Escherichia coli to 2-nitroimidazole., FEMS Microbiol Lett 362(1):1-8

 [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] 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

 [4] Martin RG, Rosner JL, 2001, The AraC transcriptional activators., Curr Opin Microbiol, 2001 Apr



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