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. 2006 Jun 29;7:326. doi: 10.1186/1471-2105-7-326

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Copyright © 2006 Kleinman et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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 [57]. 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].