RegulonDB RegulonDB 10.7: Gene Form
   

idnR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yjgR idnT idnR terminator terminator TSS_5118 TSS_5118 idnRp idnRp yjgRp3 yjgRp3 TSS_5117 TSS_5117

Gene      
Name: idnR    Texpresso search in the literature
Synonym(s): ECK4257, G7891, b4264, gntH, gntS?, yjgS
Genome position(nucleotides): 4490141 <-- 4491139 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
47.05
External database links:  
ASAP:
ABE-0013966
ECHOBASE:
EB2427
OU-MICROARRAY:
b4264
PORTECO:
idnR
REGULONDB:
b4264
STRING:
511145.b4264
M3D: idnR
COLOMBOS: idnR
PortEco: b4264


Product      
Name: DNA-binding transcriptional dual regulator IdnR
Synonym(s): GntH, IdnR, YjgS
Sequence: Get amino acid sequence Fasta Format
Regulator Family: GalR/LacI
Cellular location: cytosol
Molecular weight: 37.567
Isoelectric point: 6.678
Motif(s):
 
Type Positions Sequence
176 -> 329 LEKRVRHKILYLGSKDDTRDEQRYQGYCDAMMLHNLSPLRMNPRAISSIHLGMQLMRDALSANPDLDGVFCTNDDIAMGALLLCRERNLAVPEQISIAGFHGLEIGRQMIPSLASVITPRFDIGRMAAQMLLSKIKNNDHNHNTVDLGYQIYHG
8 -> 27 LQDIATLAGVTKMTVSRYIR
6 -> 60 ISLQDIATLAGVTKMTVSRYIRSPKKVAKETGERIAKIMEEINYIPNRAPGMLLN

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0019521 - D-gluconate metabolic process
Reference(s): [1] Isturiz T., et al., 2001
External database links:  
ECOCYC:
G7891-MONOMER
ECOLIWIKI:
b4264
INTERPRO:
IPR010982
INTERPRO:
IPR028082
INTERPRO:
IPR000843
MODBASE:
P39343
PFAM:
PF00356
PRIDE:
P39343
PRODB:
PRO_000022996
PROSITE:
PS50932
PROSITE:
PS00356
PROTEINMODELPORTAL:
P39343
REFSEQ:
NP_418685
SMART:
SM00354
SMR:
P39343
UNIPROT:
P39343


Operon      
Name: idnDOTR         
Operon arrangement:
Transcription unit        Promoter
idnR
idnDOTR


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, IdnR
Repressed by: GntR


RNA cis-regulatory element    
Attenuation: Translational


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_5117 4490083 reverse nd [RS-EPT-CBR] [2]
  promoter yjgRp3 4490085 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter TSS_5118 4491570 reverse nd [RS-EPT-CBR] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Isturiz T., Diaz-Benjumea R., Rodriguez N., Porco A., 2001, Involvement of gntS in the control of GntI, the main system for gluconate metabolism in Escherichia coli., J Basic Microbiol 41(2):75-83

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78


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