Yes and no. When it comes to proteins that are as separated as those from bacteria and mammalian it can be difficult.
How do you quantify similarity of shape and structure?
I am not sure if this is a rhetorical question or not. If so what is your point? If not, I will address it.
No, he's right - you sequence the amino acids and count the matches. I've done runs on proteins from organisms as different as E. coli and rhesus monkeys. This does not, however, measure secondary and tertiary structure, which is what you really need if you're to determing biological activities, but the amino count won't get you there by itself.