Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

Table 4 F-to-E/Q/K replacements versus all 190 possible replacement patterns

	all pairs	F-to-E/Q/K	F-to-E	F-to-K	F-to-Q
replacements*	5,918,700	15,454	5,922	5,815	3,717
average probability**	0.641	0.567	0.563	0.564	0.577
distinct families	1,820	1,457	1,142	1,160	1,068
average members/family	46.9	54.1	60	60.8	62.5
distinct alignment sites	491,794	13,169	5,347	5,181	3,424
average substitution rate/site	1.12	1.48	1.44	1.49	1.52
sites with PDB data	442,102	12,101	4,932	4,734	3,172
protein surface sites	54%	72%	73%	74%	65%
distinct branches	148,522	11,800	5,235	5,089	3,456
average branch length	0.207	0.697	0.807	0.782	0.761

*Detected as sites where the most probable parent and child residues were different.
**The average product of probabilities for the parent and child residues.

ISSN: 1471-2105