In that case it should run no slower when in a 1x pcie slot.
Max bandwidth of 1 pcie channel is 5Gbps and max for USB3 is 4.8Gbps.
There are no USB3 devices which get anywhere near that yet.
A typical USB3 hard drive can only sustain about 1Gbps (ie
about 120 MB/S) although it may have tiny bursts faster than that
(not something you'll notice in the real world.)
HTH
--
Rob