RegulonDB RegulonDB 10.10: Gene Form
   

yodD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yodD dsrB dsrA terminator anti-terminator anti-anti-terminator dsrAp dsrAp TSS_2272 TSS_2272 dsrBp5 dsrBp5 TSS_2271 TSS_2271

Gene      
Name: yodD    Texpresso search in the literature
Synonym(s): ECK1951, G7046, b1953
Genome position(nucleotides): 2024986 --> 2025213 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 48.68
External database links:  
ASAP:
 ABE-0006488
ECHOBASE:
 EB4130
ECOLIHUB:
 yodD
OU-MICROARRAY:
 b1953
STRING:
 511145.b1953
COLOMBOS: yodD


Product      
Name: stress-induced protein
Synonym(s): YodD
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 8.579
Isoelectric point: 4.329
Motif(s):
 
Type Positions Sequence
18 -> 75 DVDALLAAINEISESEVHRSQNDSEHVSVDGREYHTWRELADAFELDIHDFSVSEVNR

 
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)  
biological_process GO:0070301 - cellular response to hydrogen peroxide
GO:0044011 - single-species biofilm formation on inanimate substrate
GO:0071468 - cellular response to acidic pH
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Lee J., et al., 2010
External database links:  
DIP:
 DIP-48227N
ECOCYC:
 G7046-MONOMER
ECOLIWIKI:
 b1953
INTERPRO:
 IPR019669
PFAM:
 PF10733
PRIDE:
 P64519
REFSEQ:
 NP_416463
UNIPROT:
 P64519


Operon      
Name: yodD         
Operon arrangement:
Transcription unit        Promoter
yodD


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_2271 2024841 reverse nd [RS-EPT-CBR] [2]
  promoter dsrBp5 2024843 reverse nd [ICWHO] [3]
  promoter TSS_2272 2024844 reverse nd [RS-EPT-CBR] [2]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight


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] 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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