Protein reannotations and optimization of signal peptide prediction parameters influencing the classes of orthologous groups. (A) Reclassification of groups based on signal peptide prediction due to reannotation of proteins from Mixed groups. Default PlasmoDB settings were used to consider positive signal peptide predictions: NN-Sum ≥ 3 or D-Score ≥ 0.5 or HMM probability ≥ 0.5. (B) Further reclassification of groups due to optimization of signal peptide threshold prediction parameters. The lowest number of Mixed groups was achieved by resetting thresholds to: NN-Sum = 4; D-Score = 0.48 and HMM probability = 0.9.