Overview of genome-scale metabolic reconstruction. (A) A typical process for generating genome-scale metabolic reaction networks. Arrows correspond to the four steps of the reconstruction process – Annotation, Assembly, Verification, and Testing. The types of information and methods used during each step are indicated to the left of the arrows in the diagram. Steps in the process that feed back to refine the initial annotation are depicted as arrows on the right side of the diagram to illustrate the iterative nature of the process. (B) Our approach to genome-scale metabolic reconstruction generates an organism-independent database of coherent reaction subnetworks for discrete components of central and intermediary metabolism. This database is used to generate an organism-specific set of coherent reaction subnetworks based on the genome annotation. This set is then combined with reaction subnetworks constructed for metabolic components not represented in the database, resulting in a preliminary reaction network. Each new metabolic reconstruction adds coherent reaction subnetworks specific to new metabolic components to the database (depicted as dashed, red arrows).