This repository contains the codes (in Jupyter Notebook) used for designing a pathway in P. putida KT2440 to convert methyl red to actinorhodin; analyze growth coupling possibilities in glucose and methyl red (or both) using cMCS; and evaluate the strain designs suggested. The models used in this study are derived from the genome-scale reconstruction iJN1462 (Nogales et al. 2020).
Nayyara P, Permana D, Ermawar RA, Fahayana R (2024) Computational analysis into the potential of azo dyes as a feedstock for actinorhodin biosynthesis in Pseudomonas putida. PLOS ONE 19(3): e0299128. https://doi.org/10.1371/journal.pone.0299128