I have flagging, but nowadays to get it on a comment you need to click the permalink button on a post to get it.

And I'm glad of that, because up until now I've sent in 1 legitimate, intentional report and 10 or so cases of fat fingering the button on a mobile device (not catastrophic because of the unflag option, but still...)

Huh, I never noticed the flagging on comments before.

Are you able to downvote? I'm curious what the karma threshold is for that.

500 is often reported but is incorrect. As of today, it appears to be 501.

711 days ago, when there was a thread about karma levels and I just hit 500, I encountered the same phenomenon. I received a response saying that you don't get to downvote threads created prior to crossing 500. (Obviously, can't verify that, but here's the thread for context: https://news.ycombinator.com/item?id=3812967)

I just hit comment down voting within the past few karma. So around 775

It was 500 when I hit it, but occasionally goes up. Not sure what it is now.

I hit it at 500 a few weeks ago. Ok, not sure exactly but definitely not more than 510 :)

What algorithm are they using? Is the source open?

HN is in fact open source (an older version of it anyway): http://arclanguage.org/

However much of the "secret sauce" is, well, secret.