Metris et al. BMC Genomics 2011, 12:535 http://www.biomedcentral.com/1471-2164/12/535 Page 9 of 14 Figure 4 The shikimate pathway. The pathway shows the biosynthesis of aromatic amino acids, via shikimate, as suggested by the genome annotation. Each step is annotated to show the following: the enzyme (’Cj’ number and gene symbol), the prediction of essentiality based on FBA and transposon mutagenesis, the number of interactions in the PPI network, and the direction of expression from microarray data from a piglet model of infection. Predicted essential steps are shown in bold. suggested more metabolic specificity. An example is cj0324, originally annotated as a ubiquinone/menaqui- none methyltransferase (EC 2.1.1.-) [23], the PRIAM tool [53] suggests specifically demethylmenaquinone methyltransferase activity (EC 2.1.1.163), which is more likely as menaquinone and a methyl substituted menaquinone have been isolated in C. jejuni rather than ubiquinone [34]. We also checked our metabolic model against the ‘expert community’ subsystem annotation presented in The SEED [54], which returned discrepan- cies for 20 of the reactions considered above. For some genes, the precise annotation depends on the method