Network Analysis
We converted the metabolic model to a metabolite-metabolite graph of primary carbon metabolism using the method of Ranganathan and Maranas (2010). A full list of the nodes and edges is available on Zenodo (DOI: 10.5281/zenodo.3366934). We then used the networkx (version 1.10) package in python in order to iteratively identify pathways with fewer than 20 nodes connecting Rubisco and fumarate node. We checked these pathways against the flux sampling solutions of the Col-0 models and identified pathways which carried a flux substantial enough to account for fumarate accumulation in the model.