If the Konig USB 2.0 card looks like the one below, it's old fashioned PCI card, not modern PCI Express.
Do NOT try to plug a PCI card into a PCIe slot. For a start, it won't fit and more important, you'll probably kill the motherboard.
However, there's nothing to stop you plugging the Konig card into the PCI slot on your X79-UD3 motherboard. It's the slot with "Ultra Durable 3 ON/OFF Charge" silk screened on the PCB (see image below). Whether or not you find any drivers for your Operating System and such an old card is a different matter.
On close inspection, you should see the left hand end of the one and only PCI connector does not line up with the ends of all the other (PCIe) connectors. This is designed to make it more difficult to plug the wrong type of card into an incompatible slot.
As for the presence of one or two notches on a PCI card, they define whether the card is 5V only, 3.3V only or universal (5V and 3.3V). See quote from Wiki page below:-
Typical PCI cards have either one or two key notches, depending on their signaling voltage. Cards requiring 3.3 volts have a notch 56.21 mm from the card backplate; those requiring 5 volts have a notch 104.47 mm from the backplate. This allows cards to be fitted only into slots with a voltage they support. "Universal cards" accepting either voltage have both key notches.
https://en.wikipedia.org/wiki/Peripheral_Component_Interconnect
If the card fits into the PCI socket that's OK. If the card doesn't fit, it's not compatible.