RegulonDB RegulonDB 11.1: Gene Form
   

rfbC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rfbX glf rfbD rfbA rfbC terminator TSS_2389 (cluster) TSS_2389 (cluster) rfbXp7 rfbXp7 rfbXp8 rfbXp8 rfbXp5 rfbXp5 rfbXp6 rfbXp6 TSS_2388 TSS_2388 rfcp11 rfcp11 rfcp7 rfcp7 rfcp10 rfcp10 rfcp8 rfcp8

Gene      
Name: rfbC    Texpresso search in the literature
Synonym(s): ECK2032, EG11979, b2038, rfbD, rmlC
Genome position(nucleotides): 2109581 <-- 2110138
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 38.71
External database links:  
ASAP:
 ABE-0006759
CGSC:
 38129
ECHOBASE:
 EB1922
ECOLIHUB:
 rfbC
OU-MICROARRAY:
 b2038
STRING:
 511145.b2038
COLOMBOS: rfbC


Product      
Name: dTDP-4-dehydrorhamnose 3,5-epimerase
Synonym(s): RfbC, RfbD, RmlC
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 21.27
Isoelectric point: 5.575
Motif(s):
 
Type Positions Sequence Comment
6 -> 176 TEIEDVLILEPRVFGDDRGFFYESFNQSAFEHILGYPVSFVQDNHSRSSKNVLRGLHFQRGEYAQDKLVRCTHGAVFDVAVDIRPNSVSFGKWVGVLLSADNKQQLWIPKGFAHGFLVLSDIAEFQYKTTNYYHPESDCGICWNDERIAIDWPQTSGLILSPKDERLFTLD
47 -> 49 QDN UniProt: Substrate binding; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.3 - lipopolysaccharide --> 1.6.3.1 - O antigen
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.10 - sugar nucleotide biosynthesis, conversions
  6 - cell structure --> 6.3 - surface antigens (ECA, O antigen of LPS)
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0016854 - racemase and epimerase activity
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity
biological_process GO:0005975 - carbohydrate metabolic process
GO:0006974 - cellular response to DNA damage stimulus
GO:0009103 - lipopolysaccharide biosynthetic process
GO:0009243 - O antigen biosynthetic process
GO:0046677 - response to antibiotic
GO:0045226 - extracellular polysaccharide biosynthetic process
GO:0009411 - response to UV
GO:0033692 - cellular polysaccharide biosynthetic process
GO:0019305 - dTDP-rhamnose biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Giraud MF., et al., 1999
External database links:  
ALPHAFOLD:
 P37745
DIP:
 DIP-10681N
ECOCYC:
 DTDPDEHYDRHAMEPIM-MONOMER
ECOLIWIKI:
 b2038
INTERPRO:
 IPR014710
INTERPRO:
 IPR011051
INTERPRO:
 IPR000888
MODBASE:
 P37745
PANTHER:
 PTHR21047
PFAM:
 PF00908
PRIDE:
 P37745
PRODB:
 PRO_000023729
REFSEQ:
 NP_416542
SMR:
 P37745
SWISSMODEL:
 P37745
UNIPROT:
 P37745


Operon      
Name: rfbBDACX         
Operon arrangement:
Transcription unit        Promoter
rfbACX
rfbBDACX


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 rfcp8 2107234 reverse nd [COMP-AINF] [2]
  promoter rfcp10 2107283 reverse nd [COMP-AINF] [2]
  promoter rfcp7 2107394 reverse nd [COMP-AINF] [2]
  promoter rfcp11 2107444 reverse nd [COMP-AINF] [2]
  promoter TSS_2388 2108494 reverse nd [RS-EPT-CBR] [3]
  promoter rfbXp6 2109586 reverse nd [COMP-AINF] [2]
  promoter rfbXp5 2109676 reverse nd [COMP-AINF] [2]
  promoter rfbXp8 2109716 reverse nd [COMP-AINF] [2]
  promoter rfbXp7 2109718 reverse nd [COMP-AINF] [2]
  promoter TSS_2389 (cluster) 2111073 reverse nd [RS-EPT-CBR] [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Giraud MF., Gordon FM., Whitfield C., Messner P., McMahon SA., Naismith JH., 1999, Purification, crystallization and preliminary structural studies of dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (RmlC), the third enzyme of the dTDP-L-rhamnose synthesis pathway, from Salmonella enterica serovar typhimurium., Acta Crystallogr D Biol Crystallogr 55(Pt 3):706-8

 [2] 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

 [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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