Overview of the method. First, compound nodes and enzyme nodes (a) are generalized into compound supernodes and enzyme supernodes (b). Two reactions of species 1 are aligned with two reactions of species 2 (c), by pairing the supernodes into compound hypernodes and enzyme hypernodes (d). Each pair of aligned reaction forms a building block, from which an aligned pathway can be assembled. The reaction directions are omitted in the figure for simplicity.