Phylogenetic Tree And Go Process Biology

Question

[User 0063]

Dear all, I've perfomed a phylogenetic analysis and among others, I get two distant groups of proteins supposed to interact each other and to bind the same ligand, as confirmed by bibliographic data. So I was wondering why my philogentic tree put them in two distant cluster. I noticed that they are clasisfied as proteins having the same GO function, but are involved in different GO process.

According to you, different GO process are sufficient to justify a philogenetic distance on the tree?

What do you suggest me to investigate further?

Thanks in advance

Answer 1

[Lars Juhl Jensen]

Not knowing the genes or GO terms in question, it is difficult to come with very concrete suggestions.

The only thing that comes to my mind is to check the basis of the GO annotations. If the GO annotations are themselves inferred by sequence similarity, they will not be of much use when it comes to evaluating a phylogenetic tree that is also based on sequence similarity.