The villain opposes the protagonist. This makes him the second most important character in the story. Villains are usually antagonists though not all antagonists are villains.
Alignments show what side the character is on. It tells us whether he is a good person, an evil person or something in between and how consistent he is. This is often used in games such as Dungeons and Dragons and the character is expected to behave according to his alignment. In fiction however, character alignment is not that black and white. Personalities are vague, people are never pure good or bad. The cast of a story is a matter of shades of grey.