AGP is a totally different standard from PCI Express or PCIE. It is a different looking slot, with different number of pins, speed, etc... If you have an AGP port on your motherboard, you will surely not have a PCIE next to it.
Unfortunately bringing in this new standard makes the PC world running forward. No more AGP in the future, only PCIE! It has a 16x speed, so it could be AGP 16x, but not. Designers decided to give some fresh blood into the graphics card market, and to grab more of your money to be up to date. In the future, you cannot place a modern graphics card into an "old" mobo. You MUST buy a new mobo if you want to keep up with the technology race.