Section: New Results

Finding candidate genes for orphan enzymes

Of all biochemically characterized metabolic reactions formalized by the IUBMB, over one out of four have yet to be associated with a nucleic or protein sequence, i.e. are sequence-orphan enzymatic activities. Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploiting context-dependent rather than sequence-dependent data, and none are readily accessible and propose result integration across multiple genomes. We introduced CanOE (Candidate genes for Orphan Enzymes), a four-step bioinformatics strategy that proposes ranked candidate genes for sequence-orphan enzymatic activities (or orphan enzymes for short) [26] . Our strategy found over 60,000 genomic metabolons in more than 1,000 prokaryote organisms from the MicroScope platform developed by the group of Claudine Médigue from the Génoscope with whom this work was done, generating candidate genes for many metabolic reactions, of which more than 70 distinct orphan reactions. A computational validation of the approach was discussed and we presented a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12.