Predicting metabolic pathways by sub-network extraction

Methods Mol Biol. 2012;804:107-30. doi: 10.1007/978-1-61779-361-5_7.


Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more enzyme-coding genes, graph analysis methods can be applied to extract a metabolic pathway that interconnects them. We describe here the way to use the Pathway extraction tool available on the NeAT Web server ( ) to piece together the metabolic pathway from a group of associated, enzyme-coding genes. The tool identifies the reactions that can be catalyzed by the products of the query genes (seed reactions), and applies sub-graph extraction algorithms to extract from a metabolic network a sub-network that connects the seed reactions. This sub-network represents the predicted metabolic pathway. We describe here the pathway prediction process in a step-by-step way, give hints about the main parametric choices, and illustrate how this tool can be used to extract metabolic pathways from bacterial genomes, on the basis of two study cases: the isoleucine-valine operon in Escherichia coli and a predicted operon in Cupriavidus (Ralstonia) metallidurans.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Cupriavidus / genetics
  • Enzymes / genetics*
  • Enzymes / metabolism
  • Escherichia coli / genetics
  • Genome, Bacterial / genetics*
  • Metabolic Networks and Pathways / genetics*
  • Metabolic Networks and Pathways / physiology
  • Models, Biological*
  • Operon / genetics
  • Software*
  • Systems Biology / methods*


  • Enzymes