Metris et al. BMC Genomics 2011, 12:535 http://www.biomedcentral.com/1471-2164/12/535 as the H. pylori orthologs as appropriate. The reactions are associated to genes with Boolean rules. The reactions were categorised in pathways similarly to the model of H. pylori. Additional file 2: This table shows the substrates that were predicted to be metabolised according to the proposed model and compared to experimental data from the literature. Additional file 3: This table shows whether genes were predicted to be dispensable by different methods: FBA predictions, number of inserts of the transposon mutagenesis for the two transposon libraries of this study and whether inserts were present in the transposon mutagenesis of an independent study [20]. The degrees of the protein in the PPI network and known mutants are also indicated. Additional file 4: This table is a list of the proteins encoded by genes without a transposon insert as determined in this study (putative essential genes), classified according to the KEGG, BioCyc, and JCVI databases. Additional file 5: Table of substrates allowed in the system to determine essential genes in silico. Acknowledgements The work was supported by the Institute Strategic Programme Grant of the BBSRC to the IFR. Authors’ contributions AM reconstructed the metabolic network, carried out the FBA simulations and PPI network analysis. MR participated in the reconstruction of the metabolic network and analysed the results. DHJG carried out the transposon mutagenesis. AM, MR and DHJG drafted the manuscript. JB and AHMV conceived the study and critically revised the manuscript. All authors read and approve the final manuscript. Received: 18 August 2011 Accepted: 1 November 2011 Published: 1 November 2011 References 1. 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