Biophysics and Physicobiology
Review Article
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis
Masaaki KoteraSusumu Goto
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JOURNALS FREE ACCESS

Volume 13 (2016) Pages 195-205

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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 predicted de novo from chemical transformations of the putative substrate-product pair. This review summarizes studies involving reference-based and de novo metabolic pathway reconstruction and discusses the importance of the classification and structure-function relationships of enzymes.

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© 2016 THE BIOPHYSICAL SOCIETY OF JAPAN
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