Examples of gene-protein-reaction associations that represent the detailed logical relationships between open reading frames (ORFs), transcripts, proteins, and reactions in the model. (A) A multifunctional protein, such as Ole1p, can catalyze more than one reaction. (B) Pyc1p and Pyc2p are examples of isozymes, or proteins that can catalyze the same reaction independently. (C) Idhp is an example of a multimeric protein; it is formed by the association of two transcripts. (D) Proteins Pxa1p and Pxa2p form a protein complex. Both proteins are required to catalyze the reactions. All the gene-protein-reaction associations in Saccharomyces cerevisiae iND750 are found in the Supplemental materials as well as at http://systemsbiology.ucsd.edu.