Analysis of Genetic Code Ambiguity Arising from Nematode-Specific Misacylated tRNAs
(A) Scatterplot of the frequencies of amino acids contained in all nonredundant peptides identified with a normal database search (x-axis) versus the total number of predicted amino acid misincorporations (y-axis) for each codon. The black line in the center denotes the linear regression line. The outer, light blue lines denote the 95% confidence interval for an individual predicted value. The red and green dots correspond to the GGG and AUA codons, respectively. The dots located outside the 95% confidence interval are shown in gray. (B) Heat map indicating the degree of predicted amino acid misincorporation (error rate) for each codon. The error rate was predicted by calculating the abundance of misincorporated amino acids relative to the total number of amino acids contained in the whole proteome. The matrix plots in the Gly (GGG) and Ile (AUA) row and in the ‘Xle’ (i.e., Ile or Leu) column are boxed. The total numbers of predicted misincorporations for each codon are indicated as a bar chart.