Fig. 1

Data from genome-scale metabolic models (GEMs) and modules are available in MicrobeRX. a Schematic representation of the sources of the metabolic reactions is included in this project. b Top 20 metabolic pathways (gray: gut microbes, white: human Recon3D). c Cellular localization of the metabolic reactions obtained from humans (white bar, Recon3D) and gut microbes (gray bar, 6286 strain-resolved GEMs from AGORA2). d Decomposition of the metabolic reaction into chemically specific reaction rules (CSRRs) with varying atom numbers. The central bar plot shows the CSRRs produced per biosystem (dark gray: microbes, white: human, light gray: both). The reactive atom in the metabolic reaction scheme is highlighted with a gray box (carbon: black, nitrogen: blue, oxygen: red, hydrogen: white). The structure added (methane for example) is highlighted with an orange box. The brace in the prediction scheme indicates the substructure shared by the query and the substrate in the CSRR (three heteroatoms “C = C–N”). e Plots available in the MetaboliteVisualizer module include PubChem annotation, 3D scoring plot, metabolic accessibility diagram, isotopic mass decomposition, bioavailability (Lipinski’s rule of five), ADMETox (BOILED-Egg), and Sankey for relationships between origin, enzyme, and metabolite. See Fig. S6 for examples of real plots from MetaboliteVisualizer. f Plots available in the OmicsIntegrator module include sunburst of microorganisms per reaction/enzyme, cluster map of pairwise protein sequence comparisons for homology analysis, multiple sequence alignment with the consensus sequence (protein logo), and protein family search in InterPro. See Fig. S7 for examples of real plots from OmicsIntegrator