Reaction Structure Profile : A Comparative Analysis of Metabolic Pathways Based on Important Substructures

Comparative analysis of organisms with metabolic pathways gives important information about functions within organisms. In this paper, we propose a new method for comparing the metabolic pathways with reaction structures that include important enzymes. In this method, subgraphs from pathways that include ‘choke point’ or ‘load point’ are extracted as important “reaction structures,” and a “reaction structure profile,” which represents whether extracted reaction structures are observed in the metabolic pathway of other organisms, is created. Distance regarding function within organisms between species is defined using the “reaction structure profile.” By applying the proposed method to the metabolic networks of 64 representative organisms selected from Archaea, Eubacteria and Eukaryote in the KEGG database, we succeed in reconstructing a phylogenetic tree, and confirm the effectiveness of the method.