Figure 2.

The combined metabolic network for M. tuberculosis. (a) The combined model. Shown is the combined model for M. tuberculosis generated by MetaMerge. The network was laid out with Cytoscape [34] and 12 isolated reactions were removed from the final figure. The color scheme is identical to that of Figure 1, with the Beste et al. model [13] used as model 1 and the Jamshidi and Palsson model [14] used as model 2. (b) Example pathways in the original and combined models. Shown are the pentose phosphate and glyoxylate metabolism pathways in the original models (model 1, labeled GB [13], and model 2, labeled JP [14]) and the combined model. The enzymes catalyzing each reaction are included as a top layer, and their names are shortened by removing Rv. Circles indicate metabolites (red, model 1; white, model 2; pink, combined); squares indicate reactions (turquoise, model 1; brown, model 2; dark green, combined); octagons indicate enzymes (light green, model 1; yellow, model 2; magenta, combined). The subnetworks were laid out with Cytoscape [34] and several currency metabolites were removed for visual clarity.

Chindelevitch et al. Genome Biology 2012 13:r6   doi:10.1186/gb-2012-13-1-r6
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