Table 3.
Query structures for which BLAST, Pfam, and Dali provided a consensus EC number while ProMOL reported a conflicting result. There were thirty structures for which all four programs gave promising results. These are the instances in which BLAST, Pfam, and Dali all returned similar results, but ProMOL did not. Twenty-eight of thirty-seven alignments in ProMOL consisted of identical active site residue matches between the query and the motif template.
| Query ID | Function Assigned by ProMOL | EC Number Assigned by ProMOL | Common function from Dali, BLAST, Pfam | EC Number Assigned by Dali, BLAST, Pfam |
|---|---|---|---|---|
| 1IUY | hydrolase | 3.2.1.15 | cullin family (ligase) | 6 |
| 1K77 | hydrolase | 3.1.1.29 | xylose isomerase; epimerase | 5.3.1.22 |
| 1NOG | oxidoreductase | 1.1.1.158 | adenosyltransferase | 2.5 |
| 1VQW | lyase | 4.2.1.24 | flavin monooxygenase | 1.14 |
| 1YEM | oxidoreductase | 1.1.1.85 | adenylate cyclase | 4.6.1.1 |
| 1YEY | hydrolase | 3.1.3.7 or 3.1.21.1 | mandelate racemase | 5.1.2.2 |
| 1YRE | hydrolase | 3.5.1.5 | acetyltransferase | 2.3 |
| 1YX3 | hydrolase | 3.2.1.14 | sulfite reductase | 1.8 |
| 1Z40 | transferase | 2.7.11.13 | apical membrane antigen 1 | N/Aa |
| 2DAF | hydrolase | 3.7.1.8 | ubiquitin-like domain | 1, 2, or 3 |
| 2DC4 | isomerase | 5.4.99.5 | adenylate cyclase | 4.6.1.1 |
| 2DEC | hydrolase | 3.5.2.6 | phosphosugar isomerase | 5.3 |
| 2F06 | oxidoreductase | 1.5.1.34 | aspartokinase | 2.7.2.4 |
| 2GGE | ligase | 6.3.2.9 | isomerase; mandelate racemase | 5 or 5.1.2.2 |
| 2KFL | transferase | 2.6.1.16 | prion protein | N/Aa |
| 2Q4D | hydrolase | 3.7.1.9 | lysine decarboxylase | 4.1.1.18 |
| 2R85 | hydrolase | 3.5.1.11 | formate-phosphoribosylaminoimidazole carboxamide ligase | 6.3 |
| 2YWO | transferase | 2.3.1.118 | thiol-disulfide isomerase; alkyl hydroperoxide reductase | 5.3.1.11 |
| 2Z0J | oxidoreductase | 1.1.1.158 | 2-phosphosulpholactate phosphatase | 3 |
| 2Z6V | isomerase | 5.3.3.10 | sulfotransferase | 2.8 |
| 2ZBV | hydrolase | 3.2.1.45 | S-adenosyl-1-methionine hydroxide adenosyltransferase | 2.5.1 |
| 3EC6 | isomerase | 5.3.3.1 | general stress protein; pyridoxamine 5′-phosphate oxidase | N/A or 1 |
| 3E8X | isomerase | 5.1.3.20 | oxidoreductase or NADP binding | 1 |
| 3FLJ | hydrolase | 3.1.3.7 | SnoaL_2 domain or steroid delta-isomerase | 5 |
| 3NRN | transferase | 2.1.1.184 | oxidoreductase | 1 |
| 3RE2 | transferase | 2.3.3.1 | menin | N/Aa |
| 3S5E | lyase | 4.2.1.24 | mitochondrial frataxin | N/Aa |
| 3TB2 | hydrolase | 3.1.3.7 | 1-cys peroxidoxin | N/Aa |
| 4ILS | hydrolase | 3.8.1.5 | alanine racemase | 5.1.1.1 |
| 4J10 | hydrolase | 3.5.1.77 | secreted protein | N/Aa |
a
Dali, BLAST and Pfam all agreed on the putative nonenzymatic functions for these protein structures; N/A indicates that no EC number is provided in these cases.