Figure 1. Framework for including enzymes as metabolites in a genome‐scale model.

1. GECKO uses a genome‐scale model and includes enzymes as part of reactions.
2. Expansion of the stoichiometric matrix. M refers to metabolites, E to enzymes, v to metabolic fluxes, and e to enzyme usage. Note that 4 submatrices appear inside the new stoichiometric matrix: The upper left submatrix is equivalent to the original stoichiometric matrix, the upper right submatrix has only zeros, the lower left submatrix has the kinetic information, and the lower right submatrix is the identity matrix.