In Nethack, your prayer timeout is a measure of how long it will be until you can safely pray. When it is at zero, you can pray successfully, subject to other criteria such as your luck and alignment. If you are in trouble, you can pray before your prayer timeout reaches zero (100 turns before for minor trouble, 200 for major trouble).

Outside of wizard mode, there is no way of telling exactly what your prayer timeout is. You can tell whether or not you can pray by enlightening yourself with a wand or potion of enlightenment, or by sacrificing on a coaligned altar and seeing what happens. (If your sacrifice is consumed but you get no other message, or you see a four-leafed clover, then it's safe to pray.)

Your prayer timeout decreases with time, and you can also decrease it faster by sacrificing. It increases when you pray, receive an artifact through sacrifice or make a wish.