Most of the large, healthy PHP-based sites I’ve worked on spend 5-20% of their average request time in the database. Which means PHP is chewing 80-95%. Which makes PHP the slow bit.
Not because PHP is bad: That’s a pretty reasonable figure for platforms based on Ruby, Python, PHP, etc. (Less so for Java and .NET.)
It's a really good rule of thumb: If you’re spending more time during each request doing database work rather than PHP work, then you’ve got a problem that needs to be fixed.
You’ve probably hit a database scalability limit, or tried to get the database to do something silly. (And hey, that’s easy to do with MySQL, which is fast primarily because it’s dumb.)
(By the way: WordPress, out of the box, doesn't spend much time in the database at all.)