Is the x4 slot full length? Because the graphics card will likely work fine in an x4 slot. Especially if you are just using it for transcoding. PCI Express is backwards compatible, is just going to limit performance.
PCIe 2.0 with 4 lanes gets you 2GB/s. Which should be more than enough for video transcoding.
If it's not a full length slot you can buy a riser that converts it. Some x4 slots have a cutout at the end though to allow them to accept full length cards.