Minimal Gene Set includes well conserved housekeeping genes for basic metabolism and macromolecular synthesis, many of which are essential genes
(the list of these genes is taken from Gil R, Silva FJ, Peretó J, «Moya A. Determination of the core of a minimal bacterial gene set.»
Microbiol Mol Biol Rev. 2004 Sep ;68(3):518-37).
To find the homologs, the tool analyses the similarity results between the genes of each organism and the set of 206 genes from 7 genomes (Escherichia coli K12, Bacillus subtilis 168, Candidatus Blochmania floridanus,
Buchnera aphidicola APS, Buchnera aphidicola Bp, Buchnera aphidicola Sg and Mycoplasma genitalium G37).
The candidate genes have to fill one of the 2 following conditions :
share a BBH relationship with a minLRap > 0.5
belong to a synteny group
E. coli has numerous representatives of genes present in the oldest living ancestor genome as deduced by these methods.
The minimal set of genes obtained is a function of which and how many genomes are chosen for the analysis. As more E. coli genomes are completed, the Common Core will be more defined.
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