  Unraveling the structure of complex biological networks and relating it to
their functional role is an important task in systems biology. Here we attempt
to characterize the functional organization of the large-scale metabolic
networks of three microorganisms. We apply flux balance analysis to study the
optimal growth states of these organisms in different environments. By
investigating the differential usage of reactions across flux patterns for
different environments, we observe a striking bimodal distribution in the
activity of reactions. Motivated by this, we propose a simple algorithm to
decompose the metabolic network into three sub-networks. It turns out that our
reaction classifier which is blind to the biochemical role of pathways leads to
three functionally relevant sub-networks that correspond to input, output and
intermediate parts of the metabolic network with distinct structural
characteristics. Our decomposition method unveils a functional bow-tie
organization of metabolic networks that is different from the bow-tie structure
determined by graph-theoretic methods that do not incorporate functionality.
