RegulonDB RegulonDB 10.7: Gene Form
   

ydfA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dicA ydfA ydfB ydfAp6 ydfAp6 ydfAp8 ydfAp8 TSS_1868 TSS_1868

Gene      
Name: ydfA    Texpresso search in the literature
Synonym(s): ECK1565, EG11300, b1571
Genome position(nucleotides): 1648508 --> 1648663 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.08
External database links:  
ASAP:
ABE-0005251
ECHOBASE:
EB1277
OU-MICROARRAY:
b1571
PORTECO:
ydfA
REGULONDB:
b1571
STRING:
511145.b1571
M3D: ydfA
COLOMBOS: ydfA
PortEco: b1571


Product      
Name: Qin prophage; DUF1391 domain-containing protein YdfA
Synonym(s): YdfA
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 5.792
Isoelectric point: 4.825
Motif(s):
 
Type Positions Sequence
3 -> 47 TIDLGNNESLVYGVFPNQDGTFTAMTYTKSKTFKTENGARRWLER

 

Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
ECOCYC:
EG11300-MONOMER
ECOLIWIKI:
b1571
INTERPRO:
IPR009821
PFAM:
PF07151
PRIDE:
P0ACW8
PRODOM:
PD019047
PROTEINMODELPORTAL:
P0ACW8
REFSEQ:
NP_416089
UNIPROT:
P0ACW8


Operon      
Name: ydfABC         
Operon arrangement:
Transcription unit        Promoter
 


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_1868 1647948 forward nd [RS-EPT-CBR] [2]
  promoter ydfAp6 1648457 forward Similarity to the consensus
Read more >
[ICWHO] [3]


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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [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.

 [3] 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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