The blue slot on the M5A97 LE R2.0 board is PCIe 2.0 x16, the black one is PCIe 2.0 x4. Big GPUs should achieve near to their to* F@h performance in the blue slot, but will fold somewhat slower in the black slot. The degree of performance degradation in the 2.0 x4 slot will depend on the size of the GPU and on the OS: While Windows and Linux are both affected, Window takes a bigger hit.
(I don't have own experience with slots with lower lane count. I use most of my Pascal GPUs in PCIe 3.0 x8 mode, some in x16 mode, all on Linux. For that, PCIe 3.0 x8 is completely adequate.)
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*) edit, typo: their top F@h performance