interpretation of 'fident' output

[LLehner]

Hello, thank you for this great tool.

Currently we are trying to redo the HFSP curve using foldseek instead of mmseqs2. When using identical data we noticed a shift downwards in % sequence identity using foldseek compared to mmseqs2.

My question is: Is 'fident' reported by foldseek based on the AA residues in protein sequences (like mmseqs2) or is it based on the new structural alphabet of 3Di states?

Edit: we noticed a downwards shift in foldseek, not upwards, in terms of % sequence identity