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Table 3 Structural assessment of the phylogenetic motif functional site predictionsa

From: Predicting functional sites with an automated algorithm suitable for heterogeneous datasets

Protein family PDB ID Correct Useful info Wrong
A. Proteins from Table 1
Acetyglucosamine-6-phoshate deacyetylaseb 1O12 6 1 0
Alcohol dehydrogenase 1JVB 2 1 1
CuZnSOD 1SPD 3 2 1
Cytochrome P450 1N4G 6 4 0
Enolase 2ONE 6 2 0
Glyceroladhyde-3-phosphate dehydrogenase 1DC4 2 2 3
Glycerol kinase 1B05 7 1 0
Glutamate dehydrogenase 1HWZ 7 0 0
Inorganic pyrophosphatase 1I6T 3 2 0
Myoglobin 1MBA 4 1 0
Succinate dehydrogenase – FAD 1NEK 4 1 2
Succinate dehydrogenase – Fe/S 1NEK 4 0 0
Succinate dehydrogenase – Heme 1NEK 5 0 0
TATA box binding protein 1TBP n/ac   
Triosephosphate isomerase 7TIM 3 4 1
B. Additional examples
Acetate kinase 1G99 4 4 0
Aconitase A 7ACN 8 3 5
Alanine racemase 1L6F 4 1 1
Arginyl-tRNA synthetase 1F7U 2 2 1
Biotin carboxylaseb 1DV2 3 3 2
Catalase 1GGF 9 0 0
Citrate synthase 1NXG 8 1 0
Isocitrate dehydrogenases 1IA2 3 0 0
Malate/lactate dehydrogenases 1EMD 6 1 0
Malate synthase 1P7T 6 0 0
Phosphomannomutase 1P5D 5 2 0
Selenocysteine lyase 1ECX 5 2 1
Threonine aldolase 1LW5 6 2 0
Thymidylate synthase 1AIQ 4 0 1
Transaldolase 1ONR 1 1 1
Trehalose-6-phosphate synthase 1UQU 5 3 3
  1. a A sequence window width of 5 is used for each of the above examples and gap range of {-1: -2}.
  2. b The known functional site defined in Acetyglucosamine-6-phoshate deacyetylase and biotin carboxylase is prohibitively incomplete; as such, functional sites indicated in [41] and [42], respectively, are also included. c Because so much of the TATA-box binding protein surface area directly interacts with its DNA substrate, the known functional site sphere encompasses nearly the entire protein, making the assessment unsporting because all predictions will trivially be correct.