RegulonDB RegulonDB 11.1: Gene Form
   

yhdV gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

acrF yhdX yhdW yhdV NtrC NtrC terminator anti-terminator anti-anti-terminator yhdWp yhdWp yhdVp9 yhdVp9 TSS_3599 TSS_3599

Gene      
Name: yhdV    Texpresso search in the literature
Synonym(s): ECK3254, G7695, b3267
Genome position(nucleotides): 3418390 --> 3418611
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.05
External database links:  
ASAP:
 ABE-0010728
ECHOBASE:
 EB2682
ECOLIHUB:
 yhdV
OU-MICROARRAY:
 b3267
STRING:
 511145.b3267
COLOMBOS: yhdV


Product      
Name: lipoprotein YhdV
Synonym(s): YhdV
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 7.452
Isoelectric point: 7.351
Motif(s):
 
Type Positions Sequence Comment
4 -> 24 LIPVALLTALLAGCAHDSPCV UniProt: Helical.
51 -> 71 AGAIAGGAAAVAGLTMGIIAL UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
Note(s): Note(s): ...[more].
Reference(s): [1] Rao S., et al., 2020
External database links:  
ALPHAFOLD:
 P64622
ECOCYC:
 G7695-MONOMER
ECOLIWIKI:
 b3267
PRIDE:
 P64622
PROSITE:
 PS51257
REFSEQ:
 NP_417733
SMR:
 P64622
UNIPROT:
 P64622


Operon      
Name: yhdV         
Operon arrangement:
Transcription unit        Promoter
yhdV


RNA cis-regulatory element    
Attenuation: Transcriptional


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_3599 3417381 forward nd [RS-EPT-CBR] [2]
  promoter yhdVp9 3418196 forward nd [COMP-AINF] [3]


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] Rao S., Bates GT., Matthews CR., Newport TD., Vickery ON., Stansfeld PJ., 2020, Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations., Structure 28(4):475-487.e3

 [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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