PSEUDO growth predictions fall between FBA and MOMA. Predicted and measured yields are both normalized to a maximum of 1, corresponding to wild-type growth in these conditions. (A) Yields are plotted for 41 mutants for which growth predictions differ by more than 5% among the three methods. The diagonal line indicates equal predictions in PSEUDO and other methods. Note that MOMA predictions are consistently above the diagonal, and FBA consistently below. (B) Compared with measured growth rate data, PSEUDO growth predictions produce a rank correlation ρ of 0.63 with yield data, compared to 0.45 for the FBA method and 0.42 for MOMA. (C) PSEUDO predictions show no systematic bias. The error is the difference between prediction and measurement. The mean of the error distribution for PSEUDO was 0.06 with a 95% confidence interval of [0.13, -0.01] by bootstrap resampling. FBA predictions exceeded growth rates by 0.48 on average [0.39, 0.54]. The mean MOMA prediction error was -0.13 [-0.18, -0.08]. While the PSEUDO errors were unbiased, FBA and MOMA predictions were systematic over- and underestimates, respectively.