[squidfood]

Yep. Though it's still counted as a "calorie" that's stored in your body as a certain number of grams of protein. If your body later decides to lose that muscle, then the calorie is spent.

Since fat and protein each have different amounts of calories stored per gram, that's why if you want to get really accurate about weight loss/gain, you track your body's %fat & %muscle and not just your weight.

Edit: to clarify your analogy, just because we use wood to build a part of the house, doesn't mean we won't take it and burn it if we're desperate for heat and have used all the other fuel.