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The stoichiometry of reactions that describe protein degradation in anaerobic treatment systems were investigated. A methodology was developed to describe protein degradation to organic acids using a single reaction step. The reactions for individual amino acid fermentation and their mediating organisms were reviewed. The dominant fermentation pathways were selected based on a number of assumptions. Using the amino acid content of a model protein, it was then possible to determine stoichiometric coefficients for each major organic acid product in the overall degradation of the protein. The theoretical coefficients were then compared to those determined from two experimental runs on a continuously-fed, well-mixed, laboratory-scale anaerobic wastewater treatment system. In general, the coefficients compared well thus validating the use of a single reaction step for the overall catabolic reaction of protein degradation to organic acids. Furthermore, even when the protein concentration in feed or the feed flow rate was doubled, the amino acid fermentation pathways were found to occur predominantly by only one pathway. Although the choice of Stickland reactions over uncoupled degradation provided good comparisons, an electron balance showed that only about 40% of the amino acids could have proceeded coupled to other amino acid reactions. Uncoupled degradation of the remaining amino acids must have relied on the uptake of hydrogen produced from these reactions by hydrogen-consuming methane bacteria.