Table 4.
Divergent Results. It is impossible to assign these structures to consensus EC numbers based on ProMOL, BLAST, Pfam, and Dali results. All programs generated promising, yet varying, results. Six of seven alignments in ProMOL consisted of identical active site residue matches between the query and the motif template.
| Query | ProMOL: Assigned Function and EC | BLAST: Assigned Function and EC | Pfam: Assigned Function and EC | Dali: Assigned Function and EC |
|---|---|---|---|---|
| 1R3D | Hydrolase (3.1.1.3) | SHCHC synthase (4.2.99.20) | alpha/beta hydrolase (3) | SHCHC synthasea (4.2.99.20) |
| 2FBMb | lyase (4.2.1.24) | Y-like chromo domain (2.3.1.48) | enoyl-CoA hydratase (4.2.1.17) or isomerase (5.3.3.8) | Y-like chromadomainb (2.3.1.48) |
| 2I1S | isomerase (5.3.1.5) | plasmid pRiA4b ORF-3 family protein | plasmid pRiA4b ORF-3 family protein | No significant results |
| 3KK4 | hydrolase (3.1.3.7) | RHH-4 superfamily and COG4321 | RHH_4 super- family | No significant results |
| 3HFQ | Isomerase (5.5.1.5) | No significant results | 7-bladed beta- propeller lactonase family (EC 3.1.1.31) | No significant results |
| 3Q9D | hydrolase (3.2.2.1) | various hypothetical/ uncharacter-ized proteins and CT584 protein | no significant results | CT584 protein |
| 4EZI | hydrolase (3.4) | various hypothetical proteins | no significant results | esterase or lipase (3) |
For PDB entry 1R3D, the catalytic triad SER-HIS-ASP is typical of both alpha/beta hydrolases and SHCHC synthases [44].
For PDB entry 2FBM, ProMOL does not yet manage motifs of the size of the chromodomain. Regarding PDB entry 2FBM, many members of the crotonase (or enoyl-CoA hydratase) family have similar structures, but differing functions as they are from separate enzyme classes [45]. In vitro testing of these cases might prove the most interesting in establishing the value of each ProMOL functional assignment relative to BLAST, Pfam and Dali.