RegulonDB RegulonDB 11.1: Gene Form
   

rfbD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rfbB rfbD galF rfbA Cis-reg terminator TSS_2398 TSS_2398 TSS_2397 TSS_2397 TSS_2396 TSS_2396 TSS_2395 TSS_2395 TSS_2394 TSS_2394 TSS_2393 TSS_2393 TSS_2392 TSS_2392 TSS_2391 TSS_2391 TSS_2390 TSS_2390 TSS_2389 (cluster) TSS_2389 (cluster)

Gene      
Name: rfbD    Texpresso search in the literature
Synonym(s): ECK2034, EG12411, b2040, rmlD
Genome position(nucleotides): 2111077 <-- 2111976
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 46.56
External database links:  
ASAP:
 ABE-0006764
CGSC:
 295
ECHOBASE:
 EB2310
ECOLIHUB:
 rfbD
OU-MICROARRAY:
 b2040
STRING:
 511145.b2040
COLOMBOS: rfbD


Product      
Name: dTDP-4-dehydrorhamnose reductase
Synonym(s): RfbD, RmlD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 32.694
Isoelectric point: 5.626
Motif(s):
 
Type Positions Sequence Comment
1 -> 293 MNILLFGKTGQVGWELQRALAPLGNLIAFDVHSTDYCGDFSNPEGVAETVRSIRPDIIVNAAAHTAVDKAESEPEFAQLINATSVEAIAKAANEVGAWVIHYSTDYVFPGNGDMPWLETDATAPLNVYGETKLAGEKALQEYCAKHLIFRTSWVYAGKGNNFAKTMLRLAKEREELAVINDQFGAPTGAELLADCTAHAIRVALNKPDVAGLYHLVASGTTTWYDYAALVFEEARKAGIPLALNKLNAVPTTAYPTPARRPHNSRLNTEKFQQNFALVLPDWQVGVKRMLNEL
10 -> 12 GQV UniProt: NADH.
11 -> 12 QV UniProt: NADPH.
39 -> 40 DF UniProt: NADH.
63 -> 65 AHT UniProt: NADH.

 
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:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity
biological_process GO:0005975 - carbohydrate metabolic process
GO:0009103 - lipopolysaccharide biosynthetic process
GO:0009243 - O antigen biosynthetic process
GO:0045226 - extracellular polysaccharide biosynthetic process
GO:0019305 - dTDP-rhamnose biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Du J., et al., 2017
[2] Kim BG., et al., 2012
External database links:  
ALPHAFOLD:
 P37760
ECOCYC:
 DTDPDEHYRHAMREDUCT-MONOMER
ECOLIWIKI:
 b2040
INTERPRO:
 IPR036291
INTERPRO:
 IPR029903
INTERPRO:
 IPR005913
MODBASE:
 P37760
PANTHER:
 PTHR10491
PFAM:
 PF04321
PRIDE:
 P37760
PRODB:
 PRO_000023730
REFSEQ:
 NP_416544
SMR:
 P37760
SWISSMODEL:
 P37760
UNIPROT:
 P37760


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 TSS_2389 (cluster) 2111073 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2390 2112120 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2391 2112295 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2392 2113123 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2393 2113226 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2394 2113233 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2395 2113235 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2396 2113809 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2397 2113829 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2398 2113953 reverse 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] Du J., Zhang A., Hao J., Wang J., 2017, Biosynthesis of di-rhamnolipids and variations of congeners composition in genetically-engineered Escherichia coli., Biotechnol Lett 39(7):1041-1048

 [2] Kim BG., Kim HJ., Ahn JH., 2012, Production of bioactive flavonol rhamnosides by expression of plant genes in Escherichia coli., J Agric Food Chem 60(44):11143-8

 [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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