We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E. coli. We introduce novel clustering algorithm and compare it with mainstream module detection method based on simulated annealing. Both methods identify the similar modular core. Slight but significant increase in modularity is observed after regulatory interactions addition. We also identify new functional modules in the combined network, which cannot be detected in the metabolic network only. Regulatory loops in the modules are the source of their autonomy, and allow us to hypothesise about module function.

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