An alternative to modifying the video card is to notch the back of the pcie x1 slot so that the pcie x16 card can plug into it. Both slots accept usb 30 cards and can be used to add usb 30 ports.
You have to make sure there is clear. There are two types of expansion slots on computers pci and pci express pcie. Pci express devices communicate via a logical connection called an interconnect or link.
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A link is a point to point communication channel between two pci express.