Evolution amino acid difference matrices

The I vaginalis hydrogenosomal presequences are generally short, ranging from 5 to 14 amino acid residues for those that have been proven experimentally, and up to 17 residues for the predicted presequences (Table 1). The presequences are enriched in the amino acid residues Ser (20%), Leu (14%), Arg (11%), Ala (8%), Phe (7%), Val (6%), Thr (6%) and Asn (5%). The other amino acids are significantly under-represented. Incidentally, or accidentally, the three amino acids most commonly found in these presequences, Ser, Leu and Arg, are the ones that are each encoded by six codons. This may have been relevant in the evolution of these presequences. The mitochondrial matrix N-terminal presequences are enriched in Arg (14%), Leu (12%), Ser (11%) and Ala (14%). On the other hand, chloroplast leader peptides have a different amino acid composition with 19% Ser and 9% Thr (von Heijne et al. 1989). Markedly under-represented in hydrogenosomal presequences are the acidic residues, as in the case of both mitochondrial and plastidic presequences (von Heijne et al. 1989). 

---