Additional File 1.

1 has been uploaded as a Microsoft Excel file containing eight worksheets: 1. Orthology prediction: List of orthologous gene pairs between L. lactis, E. coli, B. subtilis and L. plantarum. Orthologs were predicted by applying the Inparanoid algorithm, using default settings. 2. Overlap AUTOGRAPH and Oliveira: Orthologous groups of genes from the Oliveira network and their orthologs with associated reactions. The reactions associated to the L. lactis genes in the Oliveira network are indicated under "Oliveira". 3. Unique genes for AUTOGRAPH: Orthologous groups of genes containing the L. lactis query genes (from Genbank) which are not incorporated into the Oliveira network, and their orthologs with associated reactions. L. lactis genes were classified into three different groups: (i) transport: all genes associated to transport reactions (ii) specific: incorporation of these genes and their associated reactions would potentially lead to additional biochemistry and hence possibly different model predictions and (iii) choice: these genes and associated reactions would lead to a higher resolution of the network, i.e. would specify reactions that are lumped into an overall reaction in the Oliveira network. 4. Unique specific reactions: List of unique specific reactions that are associated to L. lactis genes which are not incorporated into the Oliveira network. 5. Examples and literature support: Examples of predicted orthologs with literature support for L. lactis genes which are not incorporated into the Oliveira network. 6. Abbreviations E. coli: Compound information (including compound abbreviations) of reactions which are associated to E. coli genes. 7. Abbreviations B. subtilis: Compound information (including compound abbreviations) of reactions which are associated to B. subtilis genes. 8. Abbreviations L. plantarum: Compound information (including compound abbreviations) of reactions which are associated to L. plantarum genes.

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Notebaart et al. BMC Bioinformatics 2006 7:296   doi:10.1186/1471-2105-7-296