RegulonDB RegulonDB 11.1: Gene Form
   

ybdD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cstA hcxA ybdD ybdDp2 ybdDp2 TSS_727 TSS_727

Gene      
Name: ybdD    Texpresso search in the literature
Synonym(s): ECK0592, G0-10438, b4512
Genome position(nucleotides): 632182 --> 632379
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.02
External database links:  
ASAP:
 ABE-0285033
ECHOBASE:
 EB1098
ECOLIHUB:
 ybdD
STRING:
 511145.b4512
COLOMBOS: ybdD


Product      
Name: PF04328 family protein YbdD
Synonym(s): YbdD
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 7.467
Isoelectric point: 7.41
Motif(s):
 
Type Positions Sequence Comment
5 -> 65 LAKAGKYLGQAAKLMIGMPDYDNYVEHMRVNHPDQTPMTYEEFFRERQDARYGGKGGARCC

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P0AAS9
ECOCYC:
 MONOMER0-2660
ECOLIWIKI:
 b4512
INTERPRO:
 IPR007423
PANTHER:
 PTHR38453
PFAM:
 PF04328
PRIDE:
 P0AAS9
REFSEQ:
 YP_588442
UNIPROT:
 P0AAS9


Operon      
Name: ybdD         
Operon arrangement:
Transcription unit        Promoter
ybdD


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_727 629905 forward nd [RS-EPT-CBR] [1]
  promoter ybdDp2 631991 forward nd [COMP-AINF] [2]


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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