RegulonDB RegulonDB 10.10: Gene Form
   

ygiV gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ygiV ygiW mqsR QseB MqsA MqsA anti-anti-terminator anti-terminator terminator TSS_3326 (cluster) TSS_3326 (cluster) ygiVp3 ygiVp3 ygiVp2 ygiVp2 mqsRp mqsRp mqsRp2 mqsRp2 mqsAp2 mqsAp2 mqsAp9 mqsAp9 mqsAp1 mqsAp1

Gene      
Name: ygiV    Texpresso search in the literature
Synonym(s): ECK3014, G7573, b3023
Genome position(nucleotides): 3168749 <-- 3169231 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.21
External database links:  
ASAP:
ABE-0009928
ECHOBASE:
EB2842
ECOLIHUB:
ygiV
OU-MICROARRAY:
b3023
STRING:
511145.b3023
COLOMBOS: ygiV


Product      
Name: DNA-binding transcriptional repressor YgiV
Synonym(s): YgiV
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 17.827
Isoelectric point: 5.181
Motif(s):
 
Type Positions Sequence
104 -> 105 HV
7 -> 159 DVNIIDFPSIPVAMLPHRCSPELLNYSVAKFIMWRKETGLSPVNQSQTFGVAWDDPATTAPEAFRFDICGSVSEPIPDNRYGVSNGELTGGRYAVARHVGELDDISHTVWGIIRHWLPASGEKMRKAPILFHYTNLAEGVTEQRLETDVYVPL

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
biological_process GO:0045892 - negative regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [AUP] Assay of unpurified protein
[IEP] Inferred from expression pattern
Reference(s): [1] Zhang XS., et al., 2008
External database links:  
ECOCYC:
G7573-MONOMER
ECOLIWIKI:
b3023
INTERPRO:
IPR011256
INTERPRO:
IPR029442
INTERPRO:
IPR010499
MODBASE:
Q46866
PFAM:
PF06445
PRIDE:
Q46866
REFSEQ:
YP_026197
SMART:
SM00871
SMR:
Q46866
UNIPROT:
Q46866


Operon      
Name: ygiV         
Operon arrangement:
Transcription unit        Promoter
ygiV


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 mqsAp9 3168371 reverse nd [ICWHO] [2]
  promoter ygiVp2 3169287 reverse nd [ICWHO] [2]
  promoter ygiVp3 3169291 reverse nd [ICWHO] [2]
  promoter TSS_3326 (cluster) 3169416 reverse nd [RS-EPT-CBR] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Zhang XS., Garcia-Contreras R., Wood TK., 2008, Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)., ISME J 2(6):615-31

 [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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