Site-specific profiles. Sequence logos of site-specific profiles induced on an alpha-aminotransferase ([PDB:1GDE], chain A), using a contact + solvent accessibility (14 classes) potential. From top to bottom: (a) marginal profiles, (b) leave-one-out profiles, (c) empirical profiles from a multiple sequence alignment of 162 sequences [see Additional file 4], and (d) native sequence of the reference protein. Secondary structure representation was taken from PDBsum . Red dot: residue interaction with ligand. Only the first 100 amino acids are shown; sequence logos for the whole protein are available as supplementary material [see Additional file 5] [see Additional file 6].