fix(config): consider partial genes in mmseqs

[pbelmann]

This PR updates the default mmseqs cov mode from 0 to two in our config files. Coverage mode two demands that the alignment covers at least 80 percent of the query. This way partial genes are better represented in a mmseqs search.

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[pbelmann]

In addition to the coverage mode update explained in my initial comment, the coverage threshold is now also set to 0.