RegulonDB RegulonDB 11.2: Gene Form
   

yafD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yafC yafD yafE dkgB TSS_428 TSS_428 TSS_427 TSS_427 TSS_426 TSS_426 TSS_425 TSS_425 yafCp6 yafCp6 yafDp yafDp TSS_424 TSS_424 TSS_423 TSS_423 TSS_422 TSS_422

Gene      
Name: yafD    Texpresso search in the literature
Synonym(s): ECK0209, EG11650, b0209
Genome position(nucleotides): 231122 --> 231922
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.68
External database links:  
ASAP:
 ABE-0000700
ECHOBASE:
 EB1603
ECOLIHUB:
 yafD
OU-MICROARRAY:
 b0209
STRING:
 511145.b0209
COLOMBOS: yafD


Product      
Name: endonuclease/exonuclease/phosphatase domain-containing protein YafD
Synonym(s): YafD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 29.992
Isoelectric point: 9.94
Motif(s):
 
Type Positions Sequence Comment
49 -> 252 WNIYKQQRAEWLSVLKNYGKDAHLVLLQEAQTTPELVQFATANYLAADQVPAFVLPQHPSGVMTLSAAHPVYCCPLREREPILRLAKSALVTVYPLPDTRLLMVVNIHAVNFSLGVDVYSKQLLPIGDQIAHHSGPVIMAGDFNAWSRRRMNALYRFAREMSLRQVRFTDDQRRRAFGRPLDFVFYRGLNVSEASVLVTRASDH
112 -> 112 T UniProt: In Ref. 6..
223 -> 223 R UniProt: In Ref. 6..

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
molecular_function GO:0003824 - catalytic activity
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P0A8U2
DIP:
 DIP-47877N
ECOCYC:
 EG11650-MONOMER
ECOLIWIKI:
 b0209
INTERPRO:
 IPR022958
INTERPRO:
 IPR036691
INTERPRO:
 IPR005135
MODBASE:
 P0A8U2
PFAM:
 PF03372
PRIDE:
 P0A8U2
REFSEQ:
 NP_414745
UNIPROT:
 P0A8U2


Operon      
Name: yafDE         
Operon arrangement:
Transcription unit        Promoter
yafDE


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_422 230910 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_423 230912 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_424 230918 reverse nd [RS-EPT-CBR] [1]
  promoter yafCp6 231083 reverse nd [COMP-AINF] [2]
  promoter TSS_425 231274 forward nd [RS-EPT-CBR] [1]
  promoter TSS_426 231276 forward nd [RS-EPT-CBR] [1]
  promoter TSS_427 231280 forward nd [RS-EPT-CBR] [1]
  promoter TSS_428 231299 forward nd [RS-EPT-CBR] [1]


Evidence    

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

 [COMP-AINF] 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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