Metris et al. BMC Genomics 2011, 12:535 http://www.biomedcentral.com/1471-2164/12/535 165 In vitro transposition 35 26 8 FBA Stahl and Stintzi (in vitro transposition) 16 116 Page 8 of 14 143 Figure 3 Genes predicted to be essential by FBA and by two independent transposon mutageneses. The essential genes determined by FBA include “metabolic genes” only, shown in green. The “non-metabolic genes” are indicated in red. The genes predicted to be essential by transposon mutagenesis were those with no insert in the transposon mutagenesis in this study and in the study of Stahl and Stintzi [20]. nucleotide pathways. It was also found that the pathway for sulphur assimilation is not obvious from the genome annotation. A malate synthase activity was an assumption in our model, and this activity has been demonstrated in H. pylori [29]. Based on the annotation, the genome does not encode a malate synthase, and extensive BLAST searching using both the malate synthase A (aceB) and malate synthase G (glcB) sequences did not reveal any match in the H. pylori or C. jejuni genomes or any gen- ome from the epsilon sub-division of Proteobacteria. A new class of malate synthase enzymes may be present in H. pylori and possibly in this clade of life, that does not have sequence homology to known characterised malate synthase enzymes from other bacteria, although this requires further biochemical evidence. The reconstruc- tion of the model was mainly based on conventional genome annotation employing BLAST searches. More sophisticated annotation methods have been proposed to address functional divergence amongst proteins that share sequence similarity [50,51]. For instance, we com- pared the EC numbers obtained with the EFICAz [52] and PRIAM [53] tools to the EC numbers of the reac- tions linked to a unique gene in our model (287 reac- tions) and found discrepancies for 30 and 27 reactions respectively. Based on the original genome annotation, some enzymes in our model could catalyse diverse reac- tions, while the more sophisticated annotation tools