Figure 1

Metabolic networks. (a) A set of related metabolic reactions can be represented as a network. M1, M2, and so on are metabolites and E1, E2, and so on are the enzymes that catalyze the conversion of one metabolite into another. The arrows represent the direction of the reaction. (b) Different ways of representing a metabolic network: left, with the metabolites as nodes; right, with the enzymes as nodes. (c) Representation of seed compounds in a hypothetical metabolic network. The metabolic boundary of the organism is represented by the gray oval. Metabolites (the nodes in the network) are represented by colored circles. The set of compounds that cannot be internally synthesized but must be obtained from the environment is referred to as the seed set, and is represented here as red circles. Seed metabolites form the interface between the environment and the metabolic system and link the metabolic habitats of an organism with its core metabolic processes. In this hypothetical network, it is possible to reach any of the internal nodes (open green nodes) from any other node except those that have to be obtained from the environment (blue arrows).