RegulonDB RegulonDB 11.1: Gene Form
   

ydfK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pinQ ydfK ynfT TSS_1861 TSS_1861 pinQp1 pinQp1 ydfKp5 ydfKp5

Gene      
Name: ydfK    Texpresso search in the literature
Synonym(s): ECK1537, G6818, b1544
Genome position(nucleotides): 1633072 --> 1633305
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 35.47
External database links:  
ASAP:
 ABE-0005161
ECHOBASE:
 EB3584
ECOLIHUB:
 ydfK
OU-MICROARRAY:
 b1544
STRING:
 511145.b1544
COLOMBOS: ydfK


Product      
Name: Qin prophage; cold shock protein YdfK
Synonym(s): YdfK
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 8.778
Isoelectric point: 10.292
Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
biological_process GO:0009409 - response to cold
Note(s): Note(s): ...[more].
Evidence: [COMP-AINF-FN-FROM-SEQ] Automated inference of function from sequence
Reference(s): [1] Perez-Rueda E., et al., 2004
External database links:  
ALPHAFOLD:
 P76154
ECOCYC:
 G6818-MONOMER
ECOLIWIKI:
 b1544
PRIDE:
 P76154
REFSEQ:
 NP_416062
UNIPROT:
 P76154


Operon      
Name: ynfT-ydfK         
Operon arrangement:
Transcription unit        Promoter
yntF-ydfK


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 ydfKp5 1632985 forward nd [COMP-AINF] [2]
  promoter pinQp1 1633584 forward nd [COMP-AINF] [2]
  promoter TSS_1861 1633598 forward 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] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [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.

RegulonDB