Metabolic Pathway Databases

Abstract

Metabolic pathway databases may draw on enzyme, compound and gene databases, but usually go beyond them to show how enzyme reactions link to one another and ultimately form pathways for catabolism, anabolism or other necessary cellular functions. Public metabolic databases may contain information on pathways shared by many organisms; these may omit specialized metabolism. Others may limit themselves to share or unique pathways found in specific organisms, or specialized metabolism. Metabolic pathway databases are a resource for metabolic engineering. Genetic material from microbes, plants and animals is being modified at the present time; these modifications are often based on information mined from a pathway database. Mining of metabolic data is still in its infancy. Based on information stored in today's metabolic databases, it may be possible in the future to predict metabolic pathways for the biodegradation of novel environmental toxins or biosynthesis of needed specialty chemicals.

Key concepts:

  • Metabolic databases contain information on enzymes, compounds and genes organized in metabolic pathways.

  • Metabolic databases may contain information on pathways shared by many organisms, or may limit themselves to pathways in specific organisms or to specific types of pathways.

  • Metabolic databases are a resource for metabolic engineering, which needs information on the genes, enzymes and pathways found in target organisms.

Keywords: metabolism; databases; world wide web

Figure 1.

A portion of a Kyoto Encyclopedia of Genes and Genomes (KEGG) benzoate degradation map, with catechol highlighted. Enzymes are designated by their EC codes; compounds are named. In the complete map, each would link to enzyme and compound entries, respectively, in the LIGAND database. The complete map with catechol highlighted is at: http://www.genome.ad.jp/dbget‐bin/show_pathway?map00362+C00090. Reproduced with permission.

Figure 2.

A portion of Roche Applied Science ‘Biochemical Pathways’ which includes catechol. Enzymes are named and, in the larger map, link to entries in the ExPASy ENZYME database. Metabolite structures and cofactors are shown. The larger map is at: http://www.expasy.ch/cgi‐bin/show_image?E3. Reproduced with permission.

Figure 3.

A portion of the most detailed MetaCyc pathway map for the catechol degradation I pathway (metacleavage). In the complete map, compound information links to compound pages, enzyme information links to enzyme pages and gene information links to gene pages. The complete pathway is found at: http://BioCyc.org/META/NEW‐IMAGE?type=PATHWAY&object=PWY‐5415&detail‐level=4&detail‐level=3. Reproduced with permission.

Figure 4.

A portion of the University of Minnesota Biocatalysis Biodegradation Database (UM‐BBD) pathway map for nitrobenzene catabolism, which includes the compound catechol. Enzymes are named; metabolites are named and their structures are shown. In the complete map, enzyme names link to UM‐BBD reaction entries and metabolite names link to UM‐BBD compound entries. The complete map is at: http://umbbd.msi.umn.edu/nb/nb_image_map.html. Reproduced with permission.

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Further Reading

Coffee CJ (1997) Metabolism. Madison, CT: Fence Creek.

Cortassa S (2002) An Introduction to Metabolic and Cellular Engineering. River Edge, NJ: World Scientific.

Holmes FL and Heilbron JL (eds) (1992) Between Biology and Medicine: The Formation of Intermediary Metabolism. Berkeley: University of California Office of History of Science and Technology.

Mathews CK and van Holde KE (2000) Biochemistry, 3rd edn. Menlo Park: Benjamin/Cummings.

Michael G (ed.) (1999) Biomedical Pathways: An Atlas of Biochemistry and Molecular Biology. New York: Wiley.

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How to Cite close
Ellis, Lynda BM(Mar 2010) Metabolic Pathway Databases. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003036.pub2]