Carbon-fate maps for metabolic reactions.
BACKGROUND
Stable isotope labeling of small-molecule metabolites (e.g. (13)C-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.


BACKGROUND
The carbon-fate maps and software for visualizing the maps are freely available (http://cellsignaling.lanl.gov/FateMaps/).
Mu
Fangping
F
Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Williams
Robert F
RF
Unkefer
Clifford J
CJ
Unkefer
Pat J
PJ
Faeder
James R
JR
Hlavacek
William S
WS
D000465:Algorithms; D002250:Carbon Radioisotopes / Q000737:chemistry* / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods*; D007553:Isotope Labeling / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D009097:Multienzyme Complexes / Q000737:chemistry* / Q000378:metabolism*; D010449:Peptide Mapping / Q000379:methods
D002250:Carbon Radioisotopes; D009097:Multienzyme Complexes