RegulonDB RegulonDB 10.8: Gene Form
   

allR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gcl allR allA AllR terminator anti-terminator TSS_673 TSS_673 TSS_672 TSS_672 gclp gclp TSS_671 TSS_671 TSS_670 TSS_670 TSS_669 TSS_669 TSS_668 TSS_668 TSS_667 (cluster) TSS_667 (cluster)

Gene      
Name: allR    Texpresso search in the literature
Synonym(s): ECK0499, G6276, b0506, glxA3, ybbU
Genome position(nucleotides): 533011 --> 533826 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.57
External database links:  
ASAP:
 ABE-0001750
ECHOBASE:
 EB3382
OU-MICROARRAY:
 b0506
PortEco:
 allR
STRING:
 511145.b0506
COLOMBOS: allR


Product      
Name: DNA-binding transcriptional repressor AllR
Synonym(s): AllR, YbbU
Sequence: Get amino acid sequence Fasta Format
Regulator Family: IclR
Cellular location: cytosol
Molecular weight: 29.27
Isoelectric point: 6.033
Motif(s):
 
Type Positions Sequence
141 -> 263 MCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDIST
23 -> 73 ALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD
215 -> 215 L
98 -> 267 VLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRFVSQGELVRDTARDISTALGL
135 -> 142 CKSMVRMC

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0003700 - DNA-binding transcription factor activity
GO:0042802 - identical protein binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006974 - cellular response to DNA damage stimulus
GO:0045892 - negative regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [AUP] Assay of unpurified protein
[IEP] Inferred from expression pattern
Reference(s): [1] Cusa E., et al., 1999
[2] Rintoul MR., et al., 2002
External database links:  
DIP:
 DIP-47907N
ECOCYC:
 G6276-MONOMER
ECOLIWIKI:
 b0506
INTERPRO:
 IPR014757
INTERPRO:
 IPR036390
INTERPRO:
 IPR036388
INTERPRO:
 IPR029016
INTERPRO:
 IPR005471
MODBASE:
 P0ACN4
PDB:
 1TF1
PFAM:
 PF01614
PFAM:
 PF09339
PRIDE:
 P0ACN4
PRODB:
 PRO_000022083
PROSITE:
 PS51078
PROSITE:
 PS51077
REFSEQ:
 NP_415039
SMART:
 SM00346
SMR:
 P0ACN4
UNIPROT:
 P0ACN4


Operon      
Name: allR         
Operon arrangement:
Transcription unit        Promoter
allR


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_667 (cluster) 532964 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [3]
  promoter TSS_668 532972 forward nd [RS-EPT-CBR] [3]
  promoter TSS_669 532977 forward nd [RS-EPT-CBR] [3]
  promoter TSS_670 532983 forward nd [RS-EPT-CBR] [3]
  promoter TSS_671 533637 forward nd [RS-EPT-CBR] [3]
  promoter TSS_672 534816 forward nd [RS-EPT-CBR] [3]
  promoter TSS_673 534825 forward nd [RS-EPT-CBR] [3]


Evidence    

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


Reference(s)    

 [1] Cusa E., Obradors N., Baldoma L., Badia J., Aguilar J., 1999, Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli., J Bacteriol 181(24):7479-84

 [2] Rintoul MR., Cusa E., Baldoma L., Badia J., Reitzer L., Aguilar J., 2002, Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS., J Mol Biol 324(4):599-610

 [3] 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.

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