Empirical grouping, into seven regions, of submodules comprising the megamodule. Each color represents a submodule, while intermodular genes are shown in orange. Intermodular genes are placed inside the region that best associates with its most important physiological function. For example, the intermodular gene amtB, positively regulated by NtrC (region A) and GadX (region D), encodes an ammonium transporter under acidic growing conditions. Therefore, this gene was placed in the nitrogen and sulfur assimilation region (region A).