XTMS, a web-based pathway analysis platform available at http://xtms.micalis.inrae.fr, which provides full access to the set of pathways that can be imported into a chassis organism such as E. coli through the application of an Extended Metabolic Space modeling framework. The XTMS approach consists on determining the set of biochemical transformations that can potentially be processed in vivo as modeled by molecular signatures, a specific coding system for derivation of reaction rules for metabolic reactions and enumeration of all the corresponding substrates and products. Most promising routes are described in terms of metabolite exchange, maximum allowable pathway yield, toxicity, and enzyme efficiency.
Featured in Cell, “Designer Genes and Engineered Circuits”, 157:999, 2014.
“XTMS …may serve as the starting point for many projects seeking to make new metabolites.”
P. Carbonell, P. Parutto, J. Herisson, S. Pandit, J.L. Faulon. XTMS: Pathway design in an eXTended Metabolic Space. Nucleic Acids Research, 2014. | doi: 10.1093/nar/gku362