RegulonDB RegulonDB 11.1: Gene Form
   

ygiW gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

qseB ygiV ygiW qseC QseB BasR QseB anti-anti-terminator ygiWp5 ygiWp5 qseBp1 qseBp1 qseBp2 qseBp2 ygiWp7 ygiWp7 TSS_3326 (cluster) TSS_3326 (cluster) ygiVp3 ygiVp3 ygiVp2 ygiVp2

Gene      
Name: ygiW    Texpresso search in the literature
Synonym(s): ECK3015, G7574, b3024, visP
Genome position(nucleotides): 3169284 <-- 3169676
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.91
External database links:  
ASAP:
 ABE-0009930
ECHOBASE:
 EB2843
ECOLIHUB:
 ygiW
OU-MICROARRAY:
 b3024
STRING:
 511145.b3024
COLOMBOS: ygiW


Product      
Name: BOF family protein YgiW
Synonym(s): VisP, YgiW, stress-induced protein
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 14.011
Isoelectric point: 4.863
Motif(s):
 
Type Positions Sequence Comment
1 -> 20 MKKFAAVIAVMALCSAPVMA
21 -> 130 AEQGGFSGPSATQSQAGGFQGPNGSVTTVESAKSLRDDTWVTLRGNIVERISDDLYVFKDASGTINVDIDHKRWNGVTVTPKDTVEIQGEVDKDWNSVEIDVKQIRKVNP UniProt: Protein YgiW.
25 -> 44 GFSGPSATQSQAGGFQGPNG UniProt: Disordered; Sequence Annotation Type: region of interest.
26 -> 44 FSGPSATQSQAGGFQGPNG UniProt: Polar residues; Sequence Annotation Type: compositionally biased region.

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
biological_process GO:0070301 - cellular response to hydrogen peroxide
GO:0044011 - single-species biofilm formation on inanimate substrate
GO:0071276 - cellular response to cadmium ion
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Lee J., et al., 2010
External database links:  
ALPHAFOLD:
 P0ADU5
DIP:
 DIP-47914N
ECOCYC:
 G7574-MONOMER
ECOLIWIKI:
 b3024
INTERPRO:
 IPR016052
INTERPRO:
 IPR036700
INTERPRO:
 IPR005220
MODBASE:
 P0ADU5
PDB:
 1NNX
PFAM:
 PF04076
PRIDE:
 P0ADU5
REFSEQ:
 NP_417496
SMR:
 P0ADU5
SWISSMODEL:
 P0ADU5
UNIPROT:
 P0ADU5


Operon      
Name: ygiW         
Operon arrangement:
Transcription unit        Promoter
ygiW


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 ygiVp2 3169287 reverse nd [COMP-AINF] [2]
  promoter ygiVp3 3169291 reverse nd [COMP-AINF] [2]
  promoter TSS_3326 (cluster) 3169416 reverse nd [RS-EPT-CBR] [3]
  promoter ygiWp7 3169688 reverse nd [COMP-AINF] [2]
  promoter ygiWp5 3169887 reverse nd [COMP-AINF] [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] Lee J., Hiibel SR., Reardon KF., Wood TK., 2010, Identification of stress-related proteins in Escherichia coli using the pollutant cis-dichloroethylene., J Appl Microbiol 108(6):2088-102

 [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.

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