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. Author manuscript; available in PMC: 2017 Sep 15.
Published in final edited form as: Cell Rep. 2017 Sep 12;20(11):2666–2677. doi: 10.1016/j.celrep.2017.08.066

Figure 1. Framework for reconstruction and analysis of the small molecule regulatory network (SMRN).

Figure 1

The BRENDA and BioCyc databases were mined for each reaction taking place in E. coli. The identified entries (including data on EC numbers, enzyme names, activating or inhibiting small molecule – enzyme interactions, metabolite names, Km and KI values) were stored and then matched by EC number to reactions in the most recent genome-scale reconstruction of E. coli, iJO1366. This dataset was searched and analyzed for regulatory small molecules, yielding a comprehensive Small Molecule Regulatory Network (SMRN). The SMRN was used as the primary resource for the remainder of the analysis. We analyzed the topological properties of the SMRN, evaluated the similarities and differences in the kinetic properties of reactions and interactions, and used published metabolite concentration data in order to evaluate the functional role of inhibitory small molecule/enzyme interactions.