An overview of the data processing pipeline developed in this work is given in Fig. . The numbering of the individual steps corresponds to the subsection numbering in the following. In general, we denote molecules (substrates, products, cofactors) by SMILES strings, and reactions by pairs of SMILES strings separated by "»". Enzymes were represented via their Enzyme Commission number (EC numbers/classes), as well as (if available) organism information and protein identifiers. The EC number is a numerical classification scheme which groups enzymatic reactions and does not specify the specific enzyme, its sequence or origin organism. For a given reaction we recommend to query an enzyme database, or tools like BridgIt to identify genes for enzymatic reactions if this information is not available.