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.