XTMS: Pathway Search in an eXTended Metabolic Space: Tutorial

1. Submit compound query → 2. Select the target compound → 3. Select a pathway → 4. Get pathway information → 5. Get reaction information

Summary

The XTMS web server provides access to the set of available pathways that can be imported into E. coli based on an Extended Metabolic Space, i.e. on the set of potential in vivo biochemical transformations as modeled by extended connectivity fingerprints at the atom neighborhood diameters of d = 14, 12, and 10 (Carbonell et al., 2011).

Most promising routes are described in terms of metabolite exchange, maximum allowable pathway yield, toxicity, and enzyme efficiency.

References:
  • Carbonell, P., Parutto, P., Herisson, J., Pandit, S., Faulon, J.L. XTMS: Pathway design in an eXTended Metabolic Space. Nucleic Acids Research, 2014.
  • Carbonell, P., Parutto, P., Baudier, C., Junot, C., Faulon, J.L. Retropath: automated pipeline for embedded metabolic circuits. ACS Synthetic Biology, 2013. doi:10.1021/sb4001273
  • Carbonell, P., Fichera, D., Pandit, S.B., Faulon, J.L. Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Systems Biology, 6:10, 2012. doi:10.1186/1752-0509-6-10
  • Carbonell P., Planson A.G., Fichera D., Faulon J.L. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Systems Biology, 5:122, 2011. doi:10.1186/1752-0509-5-122