Context-dependent activity of biosynthetic pathways for the co-factor ubiquinone-8 (q8h2). Edges represent reactions, circular nodes represent metabolites. Black (thin) edges represent reactions predicted to be active both by FBA and by MD-FBA and green (thick) edges represent reactions predicted to be inactive by FBA and active by MD-FBA. MD-FBA correctly predicts the pathway to be activated under succinate minimal medium (where q8h2 is used in aerobic respiration) and to be inactivated under other media. FBA falsely predicts the inactivity of the pathway (downstream to 2ohph), as it does not account for the dilution demand for the production of q8h2, which is not included in its biomass reaction (as it is used only under some environments). 2ohph, 2-octaprenyl-6-hydroxyphenol; 2ombzl, 2-octaprenyl-6-methoxy-1,4-benzoquinol; 2omhmbl, 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol; 2ommbl, 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol; 2omph, 2-octaprenyl-6-methoxyphenol; 2oph, 2-octaprenylphenol; 3ophb, 3-octaprenyl-4-hydroxybenzoate; ahcys, s-adenosyl-l-homocysteine; amet, s-adenosyl-l-methionine; atp, adenosine-3-phosphate; co2, carbon dioxide; h, hydrogen; h2o, water; nad, nicotinamide-adenine-dinucleotide; nadh, nicotinamide-adenine-dinucleotide-reduced; o2, oxygen; pi, phosphate; q8h2, ubiquinone-8-reduced.
Benyamini et al. Genome Biology 2010 11:R43 doi:10.1186/gb-2010-11-4-r43