Overview of RELATCH framework for predicting metabolic flux distributions in perturbed microbial systems. (a) The metabolic flux distribution (w) and enzyme contributions (Wenz) in a reference state are first estimated using metabolic flux analysis (MFA), physiological measurements, and gene expression data. Variables are shown in bold blue letters and experimental measurements are shown in plain letters. (b) The metabolic flux distribution (v) in a perturbed state is predicted by minimizing the relative flux changes and latent pathway activation from the reference state. Two parameters are used to represent the extent of adaptation to perturbations, a penalty for latent pathway activation (α) and a limit on contribution increase in active enzymes (γ). (c) An illustrative example of using RELATCH to predict the effects of deleting an isozyme, where contributions of two isozymes are shown in green.