Question

In their article (Context-dependent optimal substitution matrices for exposed residues (Koshi-Goldstein, 1995)), more precisely in the substitution matrix displayed in Figure 2, one one hand, the legend says: "Graphical representation of the probability of a mutation from the amino acid in a given row to that in a given column during an evolutionary time of 40 point-accepted mutations per 100 residues"

And on the other hand, I've noticed it is a lot more likely for an amino acid to be deleted than to be inserted (cf. screenshot, blue is low probability, orange/red is high probability).Taken from: context-dependent optimal substitution matrices for exposed residues (Koshi-Goldstein, 1995)

How could one explain that? If that was true, all proteins sequence would slowly become smaller and smaller, right? Is it because it doesn't consider when proteins sequences merge? (I'm no biology expert, I'm sorry if the vocabulary I'm using is not exact. You are encouraged to correct me).

Answer 1

The substitution matrix in the article represents the probability of amino acid mutations over an evolutionary time. While it appears that amino acid deletion is more likely than insertion, this does not necessarily mean that all protein sequences will become smaller. The probability of deletion or insertion depends on various factors and contexts.

Step-by-step explanation:

The substitution matrix displayed in Figure 2 of the article represents the probability of a mutation from one amino acid to another during an evolutionary time of 40 point-accepted mutations per 100 residues. The legend explains that blue represents low probability, indicating that it is more likely for an amino acid to be deleted than to be inserted. This does not mean that all protein sequences would continually become smaller because it doesn't consider the merging of protein sequences. The probability of amino acid deletion or insertion depends on various factors such as evolutionary selection and the specific context.