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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. In order to identify the modular structure we introduce clustering algorithm based on a novel vertex similarity measure for bipartite graphs. We also apply a standard module identification method based on simulated annealing. Both methods identify the same modular core each of them with different resolution. We observe slight but still statistically significant increase of modularity after regulatory interactions addition. Enrichment of the metabolic network with the regulatory information leads to identification of new functional modules, which cannot be detected in the metabolic network only. Regulatory loops in the modules are the source of their self-control, i.e. autonomy, and allow to make hypothesis about module function. This study demonstrates that incorporation of regulatory information is important component in defining functional units of the metabolic network.