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Figure 2 | Genome Biology

Figure 2

From: MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis

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.

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