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Fig. 2 | Journal of Cheminformatics

Fig. 2

From: A review of parameters and heuristics for guiding metabolic pathfinding

Fig. 2

a The degree of connectivity for a node (vertex) within a metabolic network can be described by the number edges that are incident to it. In this case, the degree for each node, or the total number of incoming and outgoing edges in the directed graph, is provided in each node. b The path length can be easily determined by counting the number of edges that must be traversed to complete a pathway from the starting (green) node to the target (red) node. This is directly analogous to the number of enzymatic steps that must be engineered to complete a biosynthetic pathway. c Atom mapping is a highly detailed interpretation of chemical transformation that occurs along each edge of the metabolic network. Here, the first step of the citric acid cycle can be both described as a simple network with two edges and three nodes, or as a balanced chemical reaction where atoms can be tracked between reactants and their corresponding products. Notice that the network ignores water and coenzyme A (CoA), whereas the atom mapped reaction can be used to identify what atoms from the reactants acetyl-CoA and oxaloacetic acid contributed to the product, citrate

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