Functional prediction for proteins of bacteria.

Question

[m90]

Hello everyone,

I have a list of proteins that I am interested in for the same bacterial species but from different locations. They have variations such as insertions and substitutions. I would like to know if there is a tool available to annotate these variations and determine their influence on the proteins.

[dthorbur]

Can you be more specific about what kind of changes you are interested in? For example, are the biochemical changes or structural changes particularly interesting?

For the latter, you could use one of the many tools that predicts secondary structure from sequence to infer differences. You could also use AlphaFold2/3 to model the structures and cluster/compare them with something like FoldSeek.