A regular gyudon is 633 calories at Yoshinoya and about 730 at Sukiya, because Sukiya serves a bit more rice. For around 500 yen that is one of the cheapest full meals in Japan, and the numbers are all published, which makes it easy to plan around. The rice is 250g and about 390 calories. The beef is fatty short plate cooked in sugar and soy, roughly 200 calories for the meat and 45 for the onion and sauce.
The size ladder is steep. Yoshinoya's small (komori) is about 490 calories, regular 633, atamono-omori (extra beef, same rice) about 740, omori about 850, and tokumori around 1,000. The 'mega' bowl at Sukiya is over 1,200. The chains price these only 100 to 200 yen apart, so people go up a size without thinking, and each step is roughly a bowl of miso soup's worth of rice or a burger's worth of beef.
Toppings change the picture. A raw egg is about 80 calories and 6g of protein, which is a reasonable add. Cheese is about 120. Kimchi is 20. The 'tsuyudaku' extra sauce order is mostly free in calories but adds salt. If you want the bowl to do more for you, the egg or the extra beef head is the better spend than the bigger rice.