Details

Autor(en) / Beteiligte

• Mu, Fangping
• Williams, Robert F.
• Unkefer, Clifford J.
• Unkefer, Pat J.
• Faeder, James R.
• Hlavacek, William S.

Titel

Carbon-fate maps for metabolic reactions

Ist Teil von

• Bioinformatics, 2007-12, Vol.23 (23), p.3193-3199

Ort / Verlag

Oxford: Oxford University Press

Erscheinungsjahr

2007

Quelle

MEDLINE

Beschreibungen/Notizen

• Motivation: Stable isotope labeling of small-molecule metabolites (e.g. 13C-labeling of glucose) is a powerful tool for characterizing pathways and reaction fluxes in a metabolic network. Analysis of isotope labeling patterns requires knowledge of the fates of individual atoms and moieties in reactions, which can be difficult to collect in a useful form when considering a large number of enzymatic reactions. Results: We report carbon-fate maps for 4605 enzyme-catalyzed reactions documented in the KEGG database. Every fate map has been manually checked for consistency with known reaction mechanisms. A map includes a standardized structure-based identifier for each reactant (namely, an InChI™ string); indices for carbon atoms that are uniquely derived from the metabolite identifiers; structural data, including an identification of homotopic and prochiral carbon atoms; and a bijective map relating the corresponding carbon atoms in substrates and products. Fate maps are defined using the BioNetGen™ language (BNGL), a formal model-specification language, which allows a set of maps to be automatically translated into isotopomer mass-balance equations. Availability: The carbon-fate maps and software for visualizing the maps are freely available (http://cellsignaling.lanl.gov/FateMaps/). Contact: wish@lanl.gov Supplementary information: Supplementary data are available at Bioinformatics online.