title: Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis.
abstract: Metabolic pathway reconstruction presents a challenge for understanding metabolic pathways in organisms of interest. Different strategies,i.e., reference-based vs.de novo, must be used for pathway reconstruction depending on the availability of well-characterized enzymatic reactions. If at least one enzyme is already known to catalyze a reaction, its amino acid sequence can be used as a reference for identifying homologous enzymes in the genome of an organism of interest. Where there is no known enzyme able to catalyze a corresponding reaction, however, the reaction and the corresponding enzyme must be predictedde novofrom chemical transformations of the putative substrate-product pair. This review summarizes studies involving reference-based andde novometabolic pathway reconstruction and discusses the importance of the classification and structure-function relationships of enzymes.
authors.affiliation: School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Kotera
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
keywords: chemical transformation; enzyme; genome; metabolome; substrate-product pair