Those slots are (depending on a jumper setting) either:
x4 physical, x1 electrical
x16 physical, x16 electrical
x1 physical, x1 electrical
x16 physical, x2 electrical
or
x4 physical, x4 electrical
x16 physical, x8 electrical
x1 physical, NOT USABLE
x16 physical, x8 electrical

In theory you can use all four of them for GPUs with the first setting, the x1/x4 ones with extenders of course.