RegulonDB RegulonDB 10.10: Gene Form
   

rfaD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

waaF rfaD htrL TSS_4208 TSS_4208 TSS_4207 TSS_4207 TSS_4206 TSS_4206 rfaDp4 rfaDp4 rfaDp1 rfaDp1 TSS_4204 TSS_4204 rfaDp2 rfaDp2 rfaDp3 rfaDp3 yibBp6 yibBp6 yibBp9 yibBp9 yibBp8 yibBp8 TSS_4203 (cluster) TSS_4203 (cluster)

Gene      
Name: rfaD    Texpresso search in the literature
Synonym(s): ECK3609, EG10838, b3619, hldD, htrM, nbsB, waaD
Genome position(nucleotides): 3793987 --> 3794919 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.91
External database links:  
ASAP:
 ABE-0011843
CGSC:
 299
ECHOBASE:
 EB0831
ECOLIHUB:
 rfaD
OU-MICROARRAY:
 b3619
STRING:
 511145.b3619
COLOMBOS: rfaD


Shine dalgarno      
Sequence: tccataattcGAAGGTtacagttATG


Product      
Name: ADP-L-glycero-D-mannoheptose 6-epimerase
Synonym(s): HldD, HtrM, NbsB, RfaD, WaaD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,membrane
Molecular weight: 34.893
Isoelectric point: 4.546
Motif(s):
 
Type Positions Sequence
210 -> 210 D
178 -> 178 K
201 -> 204 FEGS
2 -> 236 IIVTGGAGFIGSNIVKALNDKGITDILVVDNLKDGTKFVNLVDLNIADYMDKEDFLIQIMAGEEFGDVEAIFHEGACSSTTEWDGKYMMDNNYQYSKELLHYCLEREIPFLYASSAATYGGRTSDFIESREYEKPLNVYGYSKFLFDEYVRQILPEANSQIVGFRYFNVYGPREGHKGSMASVAFHLNTQLNNGESPKLFEGSENFKRDFVYVGDVADVNLWFLENGVSGIFNLG
10 -> 11 FI

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.3 - lipopolysaccharide --> 1.6.3.2 - core region
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0016020 - membrane
molecular_function GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0008712 - ADP-glyceromanno-heptose 6-epimerase activity
GO:0050661 - NADP binding
GO:0070401 - NADP+ binding
biological_process GO:0005975 - carbohydrate metabolic process
GO:0009103 - lipopolysaccharide biosynthetic process
GO:0009244 - lipopolysaccharide core region biosynthetic process
GO:0097171 - ADP-L-glycero-beta-D-manno-heptose biosynthetic process
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-35958N
ECOCYC:
 EG10838-MONOMER
ECOLIWIKI:
 b3619
INTERPRO:
 IPR001509
INTERPRO:
 IPR011912
INTERPRO:
 IPR036291
MODBASE:
 P67910
PDB:
 2X6T
PDB:
 1EQ2
PFAM:
 PF01370
PRIDE:
 P67910
PRODB:
 PRO_000022904
REFSEQ:
 NP_418076
SMR:
 P67910
UNIPROT:
 P67910


Operon      
Name: rfaD-waaFCL         
Operon arrangement:
Transcription unit        Promoter
rfaDFCL
rfaDFCL
rfaDFCL
rfaDFCL


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_4203 (cluster) 3793712 reverse nd [RS-EPT-CBR] [1]
  promoter yibBp8 3793729 reverse nd [ICWHO] [2]
  promoter yibBp9 3793730 reverse nd [ICWHO] [2]
  promoter yibBp6 3793834 reverse nd [ICWHO] [2]
  promoter TSS_4204 3793935 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4206 3794418 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4207 3794433 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4208 3794859 forward nd [RS-EPT-CBR] [1]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight


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.

 [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

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