Figure 2.

Representation of gene to protein to reaction (GPR) associations. Each gene included in the model is associated with at least one reaction. Examples of different types of associations are shown, where the top layer is the gene locus, the second layer is the translated peptide, the third layer is the functional protein and the bottom layer is the reaction (shown as its corresponding abbreviation listed in the additional data file). Subunits (for example, sdhABCD and gapC_1C_2) and enzyme complexes (for example, xylFGH) are connected to reactions with '&' associations, indicating that all have to be expressed for the reaction to occur. For sdhABCD, the '&' is shown above the functional protein level, denoting that all of these gene products are needed for the functional enzyme. With xylFGH the '&' association is shown above the reaction level, indicating that the different proteins form a complex that carries out the reaction. Isozymes (for example, gapC_1C_2 and gapA) are independent proteins which carry out identical reactions where only one of the isozymes needs to be present for the reaction to occur. Isozymes are shown as two or more arrows leaving different proteins but impinging on the same reaction.