Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns

Determining minimal media for the production of amino acids. (A) Network under consideration for computation of elementary flux patterns. Dark reactions belong to the subsystem. (B) Elementary flux patterns of the subsystem. The inflow reaction that is used and the amino acid that can be produced from this input medium are indicated. Examples of minimal and nonminimal media are provided by the synthesis of histidine, which can be produced from glutamate alone as well as from ammonia and glutamate, respectively. The latter elementary flux pattern is more efficient in terms of glutamate consumed. A list of abbreviations can be found in Supplemental material S2.