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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.
I was thinking this too, if you have an open-ended 4x slot it can fit a 16x card but only runs at 4x.
TBH if you're running 10Gb you may want to look for a board with on-board 10Gb rather than a PCIE which will save you the slot. My HP server has a swapable daughter board for the nic so you can chose 4x1Gb or 4x10Gb.
I already have the server, it doesn't make any sense to change it. Above all, as someone else has pointed, the 4 lanes are enough for transcoding.