RegulonDB RegulonDB 11.1: Gene Form
   

ydcY gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydcZ ydcY ortT mnaT TSS_1818 (cluster) TSS_1818 (cluster) ydcYp3 ydcYp3

Gene      
Name: ydcY    Texpresso search in the literature
Synonym(s): ECK1440, G6757, b1446
Genome position(nucleotides): 1517648 --> 1517881
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.27
External database links:  
ASAP:
 ABE-0004821
ECHOBASE:
 EB3531
ECOLIHUB:
 ydcY
OU-MICROARRAY:
 b1446
STRING:
 511145.b1446
COLOMBOS: ydcY


Product      
Name: DUF2526 domain-containing protein YdcY
Synonym(s): YdcY
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 8.8
Isoelectric point: 5.893
Motif(s):
 
Type Positions Sequence Comment
1 -> 77 MSHLDEVIARVDAAIEESVIAHMNELLIALSDDAELSREDRYTQQQRLRTAIAHHGRKHKEDMEARHEQLTKGGTIL
54 -> 77 HHGRKHKEDMEARHEQLTKGGTIL UniProt: Disordered; Sequence Annotation Type: region of interest.
55 -> 69 HGRKHKEDMEARHEQ UniProt: Basic and acidic residues; Sequence Annotation Type: compositionally biased region.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P64455
DIP:
 DIP-47884N
ECOCYC:
 G6757-MONOMER
ECOLIWIKI:
 b1446
INTERPRO:
 IPR019671
PFAM:
 PF10735
PRIDE:
 P64455
REFSEQ:
 NP_415963
SMR:
 P64455
UNIPROT:
 P64455


Operon      
Name: ydcY         
Operon arrangement:
Transcription unit        Promoter
ydcY


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 ydcYp3 1517610 forward nd [COMP-AINF] [1]
  promoter TSS_1818 (cluster) 1517612 forward nd [RS-EPT-CBR] [2]


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] 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

 [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.

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