Elucidating the distribution of metabolic fluxes experimentally relies on (i) stable-isotope labeling experiments, and (ii) atom-level representations of metabolism (13C-MFA). Most of the currently used atom-maps (i) represent only the core metabolism and (ii) assume one single flux distribution, which limits the interpretation of labeling experiment outcomes.

Here, we tackle these two limitations, by (i) using systematic model reduction (redGEM, lumpGEM) and a labeling method based on biochemical reaction rules (iAM.NICE) to build a atom-level metabolic model of E. coli. With the aid of this framework, we determine the origin of each carbon atom in the Biomass Building Blocks (BBB), and we make the results available via an interactive database.