Hello again, first I would like to make a recommendation to open up a new section for whisch 
Even though it’s optional, I wanted to upload my protein’s alignment file to find the active sites. However the website HSSP_ID is not very user-friendly. Instead, I went and aligned the protein myself. In this situation I struggled with two questions;
What should I align with?
How many proteins should I align with?
So sorry if these question are simple. Thanks for your help in advance.