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Research Article

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes

  • Adam Alexander Thil Smith mail,

    aatsmith@orange.fr (AATS); vallenet@genoscope.cns.fr (DV)

    Affiliations: CEA, DSV, IG, Genoscope, Evry, France, CNRS-UMR8030, Evry, France, Université d'Evry Val d'Essonne, Evry, France

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  • Eugeni Belda,

    Affiliations: CEA, DSV, IG, Genoscope, Evry, France, CNRS-UMR8030, Evry, France, Université d'Evry Val d'Essonne, Evry, France

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  • Alain Viari,

    Affiliation: INRIA Grenoble-Rhône-Alpes, Team BAMBOO, Montbonnot, France

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  • Claudine Medigue,

    Affiliations: CEA, DSV, IG, Genoscope, Evry, France, CNRS-UMR8030, Evry, France, Université d'Evry Val d'Essonne, Evry, France

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  • David Vallenet mail

    aatsmith@orange.fr (AATS); vallenet@genoscope.cns.fr (DV)

    Affiliations: CEA, DSV, IG, Genoscope, Evry, France, CNRS-UMR8030, Evry, France, Université d'Evry Val d'Essonne, Evry, France

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  • Published: May 31, 2012
  • DOI: 10.1371/journal.pcbi.1002540

Reader Comments (1)

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on the possible sequencing error

Posted by gplunkett3 on 01 Jun 2012 at 19:44 GMT

We have noticed that the gene sequence of ECK0512/ylbE presents a frameshift which is absent in all other sequenced E. coli strains and may be due, according to UniProt, to a sequencing error.
http://ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002540#article1.body1.sec3.sec3.p4

While the pseudogene ylbE was thought to be a domestication mutant allele, resequencing data does seem to support the possibility of a sequencing error. See:

Nahku R, Peebo K, Valgepea K, Barrick JE, Adamberg K, Vilu R (2011) Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture. Microbiology 157(Pt 9):2604-2610 [PMID: 21700661]

Freddolino PL, Amini S, Tavazoie S (2012) Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. J Bacteriol 194(2):303-306 [PMID: 22081388]

No competing interests declared.