Figure 4

Verification of pathway completeness using scenarios. A Petri net algorithm is used to find all possible paths through a subsystem's reactions to complete a given scenario. This can be executed in an organism-independent or dependent manner. Output of the tool includes those reactions that make up the path completing the scenario, the KEGG compounds used, and the stoichiometry of the overall inputs and outputs of the scenario. Each reaction is appended with an R or an L to indicate the direction of the reaction used in the context of the pathway. (A) The first example shows the results of an organism-independent execution of the algorithm for the scenario Gluconeogenesis in the Embden-Meyerhof and Gluconeogenesis subsystem. (B) The second example shows the results of an organism-dependent execution of the algorithm for the same scenario. Here the results indicate that S. aureus does not contain a complete path in this subsystem for gluconeogenesis. The output indicates where the failure occurred, which is the first reaction in the pathway converting pyruvate (highlighted in blue) to phosphoenolpyruvate. The conversion is performed by reaction R00199_R (highlighted in yellow). The Glycolysis and Gluconeogenesis and Pyruvate Metabolism KEGG maps with reactions highlighted in an organism-dependent manner for S. aureus give a visual context for the results of the algorithm. The reaction R00199 (indicated by a red circle) is not highlighted on the KEGG map; consulting the subsystem spreadsheet reveals that S. aureus does not contain the gene encoding phosphoenolpyruvate synthase (EC 2.7.9.2) (cf. Fig. 2, role 26).