RegulonDB RegulonDB 11.1: Gene Form
   

agaR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

kbaZ agaR yhaV AgaR AgaR CRP AgaR AgaR AgaR kbaZp kbaZp TSS_3412 (cluster) TSS_3412 (cluster) agaRp agaRp TSS_3411 TSS_3411 TSS_3410 (cluster) TSS_3410 (cluster)

Gene      
Name: agaR    Texpresso search in the literature
Synonym(s): ECK3119, G7630, b3131, yhaW
Genome position(nucleotides): 3277856 <-- 3278665
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.22
External database links:  
ASAP:
 ABE-0010291
ECHOBASE:
 EB2615
ECOLIHUB:
 agaR
OU-MICROARRAY:
 b3131
STRING:
 511145.b3131
COLOMBOS: agaR


Product      
Name: DNA-binding transcriptional repressor AgaR
Synonym(s): AgaR, YhaW
Sequence: Get amino acid sequence Fasta Format
Regulator Family: DeoR
Cellular location: cytosol
Molecular weight: 29.572
Isoelectric point: 5.219
Motif(s):
 
Type Positions Sequence Comment
15 -> 70 TSERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGALI UniProt: HTH deoR-type.
18 -> 74 RREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGALICDST
32 -> 51 VQVNDLSALYGVSTVTIRND UniProt: H-T-H motif.
89 -> 247 NTAMKRSVAKAAVELIQPGHRVILDSGTTTFEIARLMRKHTDVIAMTNGMNVANALLEAEGVELLMTGGHLRRQSQSFYGDQAEQSLQNYHFDMLFLGVDAIDLERGVSTHNEDEARLNRRMCEVAERIIVVTDSSKFNRSSLHKIIDTQRIDMIIVDE

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.12 - amino sugar conversions
  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
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP] Inferred from expression pattern
Reference(s): [1] Ray WK., et al., 2004
External database links:  
ALPHAFOLD:
 P0ACK2
DIP:
 DIP-48095N
ECOCYC:
 G7630-MONOMER
ECOLIWIKI:
 b3131
INTERPRO:
 IPR001034
INTERPRO:
 IPR037171
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
INTERPRO:
 IPR018356
INTERPRO:
 IPR014036
MODBASE:
 P0ACK2
PFAM:
 PF00455
PFAM:
 PF08220
PRIDE:
 P0ACK2
PROSITE:
 PS51000
PROSITE:
 PS00894
REFSEQ:
 NP_417600
SMART:
 SM00420
UNIPROT:
 P0ACK2


Operon      
Name: agaR         
Operon arrangement:
Transcription unit        Promoter
agaR


Transcriptional Regulation      
Display Regulation             
Repressed by: AgaR


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_3410 (cluster) 3278324 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3411 3278701 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3412 (cluster) 3278705 reverse nd [RS-EPT-CBR] [2]


Evidence    

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


Reference(s)    

 [1] Ray WK., Larson TJ., 2004, Application of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in N-acetylgalactosamine metabolism in Escherichia coli K-12., Mol Microbiol 51(3):813-26

 [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.

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