Figure 1
From: Low degree metabolites explain essential reactions and enhance modularity in biological networks
(a) UP-UC metabolites in the E. coli metabolic network forming a UP-UC cluster of 10 reactions. (b) UP-UC metabolites in the S. aureus metabolic network forming a UP-UC cluster of 6 reactions. Rectangles represent reactions and ovals metabolites. Yellow ovals represent UP-UC metabolites. Arrows to (from) metabolites represent their production (consumption) in reactions. A blue (red) link represents the production (consumption) of a UP (UC) metabolite. Note that UP-UC clusters are not strictly linear pathways. For example, in part (a) the reactions in the cluster are not all in a single chain and in part (b) there is a cycle inside the UP-UC cluster. Nevertheless fixing the flux of any one reaction in a UP-UC cluster fixes the fluxes of all other reactions in the cluster in any steady state, since the production rate of every UP-UC metabolite must be the same as its consumption rate. Hence, in part (a), fixing the flux of reaction GCALD fixes the flux of reaction DHNPA2 (because of the intermediate UP-UC metabolite gcald), which in turn fixes the fluxes of reactions HPPK2 and DNMPPA, and so on. All reactions in part (a) and (b) are globally essential in E. coli and S. aureus respectively. To reduce clutter, nodes corresponding to h (proton) and h2o have been omitted. Abbreviation of metabolite and reaction names in part (a) are as in [4] and in part (b) as in [5]. The figures have been drawn using Graphviz software.