Subsystem functional role table, spreadsheet and scenarios in the SEED. (A) The Functional Role table and Spreadsheet for the Embden-Meyerhof and Gluconeogenesis subsystem are depicted. The Functional Role table includes short abbreviations, functional role names and associated KEGG reaction identifiers. The Spreadsheet contains columns corresponding to functional roles and rows corresponding to specific genomes (only S. aureus subsp. N315 shown). The cells of the spreadsheet contain gene identifiers that have been annotated with the specified functional role. A column heading containing an asterisk (*) indicates that several related functional roles are grouped together in a column; subscripts after gene identifiers indicate which functional role the organism implements (e.g., 1571-6 for *pfk). (B) We have encoded scenarios in subsystems that represent segments of metabolic pathways. The elements of each scenario are input compounds, output compounds, the KEGG pathway maps that provide context for the scenario, and additional reactions.