RegulonDB RegulonDB 10.10: Gene Form
   

xylR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

xylH xylR bax xylG terminator anti-terminator TSS_4171 TSS_4171 xylRp xylRp

Gene      
Name: xylR    Texpresso search in the literature
Synonym(s): ECK3558, EG20253, b3569
Genome position(nucleotides): 3734979 --> 3736157 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 48.77
External database links:  
ASAP:
 ABE-0011652
CGSC:
 3
ECHOBASE:
 EB4154
ECOLIHUB:
 xylR
OU-MICROARRAY:
 b3569
STRING:
 511145.b3569
COLOMBOS: xylR


Product      
Name: DNA-binding transcriptional dual regulator XylR
Synonym(s): XylR
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AraC/XylS
Cellular location: cytosol
Molecular weight: 44.869
Isoelectric point: 6.576
Motif(s):
 
Type Positions Sequence
288 -> 386 IQAMHYIRNHACKGIKVDQVLDAVGISRSNLEKRFKEEVGETIHAMIHAEKLEKARSLLISTTLSINEISQMCGYPSLQYFYSVFKKAYDTTPKEYRDV
309 -> 384 DAVGISRSNLEKRFKEEVGETIHAMIHAEKLEKARSLLISTTLSINEISQMCGYPSLQYFYSVFKKAYDTTPKEYR
353 -> 376 INEISQMCGYPSLQYFYSVFKKAY
113 -> 277 HLKEKGVNRFAFYGLPESSGKRWATEREYAFRQLVAEEKYRGVVYQGLETAPENWQHAQNRLADWLQTLPPQTGIIAVTDARARHILQVCEHLHIPVPEKLCVIGIDNEELTRYLSRVALSSVAQGARQMGYQAAKLLHRLLDKEEMPLQRILVPPVRVIERRST
305 -> 326 DQVLDAVGISRSNLEKRFKEEV

 
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 --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
GO:0000976 - transcription cis-regulatory region binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
External database links:  
ECOCYC:
 EG20253-MONOMER
ECOLIWIKI:
 b3569
INTERPRO:
 IPR028082
INTERPRO:
 IPR020449
INTERPRO:
 IPR018062
INTERPRO:
 IPR009057
INTERPRO:
 IPR018060
MODBASE:
 P0ACI3
PDB:
 4FE7
PDB:
 4FE4
PFAM:
 PF12833
PFAM:
 PF13377
PRIDE:
 P0ACI3
PRINTS:
 PR00032
PROSITE:
 PS01124
PROSITE:
 PS00041
REFSEQ:
 NP_418026
SMART:
 SM00342
SMR:
 P0ACI3
UNIPROT:
 P0ACI3


Operon      
Name: xylFGHR         
Operon arrangement:
Transcription unit        Promoter
xylFGHR
xylR


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, XylR, ArcA
Repressed by: Fis


RNA cis-regulatory element    
Attenuation: Transcriptional


Regulation by small RNA    
  Display Regulation
small RNA dicF


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_4171 3736974 reverse nd [RS-EPT-CBR] [1]


Evidence    

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


Reference(s)    

 [1] 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.

RegulonDB