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Figure 3 | Genome Biology

Figure 3

From: FOCAL: an experimental design tool for systematizing metabolic discoveries and model development

Figure 3

Various FOCAL statistics for genome-scale models. (a) Percentage of blocked, coupled, and uncoupled network reactions for each model evaluated. (b) Percentage of unblocked reactions from each model that require 0 to 5 deletions to become coupled with biomass. Reactions with zero gene deletions can be coupled solely by modifying the media composition. For all models, except iJO1366, the number of deletions is the number of necessary gene deletions. For iJO1366, additional isozyme deletions may be necessary (the total number of gene deletions needed for iJO1366 can be found in Figure S3 in Additional file 2). (c) Distribution of iJR904 reactions belonging to a given coupling category (coupled, uncoupled or blocked) across metabolite subsystems. The percentage (left) or number (right) of reactions within a given coupling category that belong to a particular subsystem is shown. The fully coupled metabolic subsystem in (c) is composed of metabolic subsystems in which all reactions could be coupled to biomass, and contains the citric acid cycle, pentose phosphate cycle, nitrogen, pyruvate and methylglyoxal metabolism, purine and pyrimidine biosynthesis, anaplerotic, and putative reaction pathways.

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