RegulonDB RegulonDB 10.10: Gene Form
   

ygiN gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

parE mdaB ygiN TSS_3329 TSS_3329 TSS_3328 (cluster) TSS_3328 (cluster) ygiNp2 ygiNp2

Gene      
Name: ygiN    Texpresso search in the literature
Synonym(s): ECK3020, EG12657, b3029
Genome position(nucleotides): 3173142 --> 3173456 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.48
External database links:  
ASAP:
 ABE-0009948
ECHOBASE:
 EB2525
ECOLIHUB:
 ygiN
OU-MICROARRAY:
 b3029
STRING:
 511145.b3029
COLOMBOS: ygiN


Product      
Name: putative quinol monooxygenase YgiN
Synonym(s): YgiN
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 11.532
Isoelectric point: 6.224
Motif(s):
 
Type Positions Sequence
1 -> 87 MLTVIAEIRTRPGQHHRQAVLDQFAKIVPTVLKEEGCHGYAPMVDCAAGVSFQSMAPDSIVMIEQWESIAHLEAHLQTPHMKAYSEA
4 -> 4 V
2 -> 100 LTVIAEIRTRPGQHHRQAVLDQFAKIVPTVLKEEGCHGYAPMVDCAAGVSFQSMAPDSIVMIEQWESIAHLEAHLQTPHMKAYSEAVKGDVLEMNIRIL

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016491 - oxidoreductase activity
GO:0004497 - monooxygenase activity
GO:0042803 - protein homodimerization activity
biological_process GO:0010447 - response to acidic pH
External database links:  
ECOCYC:
 EG12657-MONOMER
ECOLIWIKI:
 b3029
INTERPRO:
 IPR011008
INTERPRO:
 IPR007138
MODBASE:
 P0ADU2
PDB:
 1R6Y
PDB:
 1TUV
PFAM:
 PF03992
PRIDE:
 P0ADU2
PROSITE:
 PS51725
REFSEQ:
 NP_417501
SMR:
 P0ADU2
SWISSMODEL:
 P0ADU2
UNIPROT:
 P0ADU2


Operon      
Name: ygiN         
Operon arrangement:
Transcription unit        Promoter
ygiN


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 ygiNp2 3173078 forward nd [ICWHO] [1]
  promoter TSS_3328 (cluster) 3173120 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3329 3174907 reverse nd [RS-EPT-CBR] [2]


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] 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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