Table 1.
Potential templates from the Protein Data Bank
| A. Gapped BLAST using BLOSUM62 Matrix | |||||||
| Accession no. | Description | Sequence length | Alignment length | E-value | Bit-score | Sequence identity (%) | Sequence similarity (%) |
| 1d2s_a | Sex hormone-binding globulin | 170 | 82 | 0.941166 | 26.7659 | 21 | 46 |
| 1qi7_a | N-glycosidase | 253 | 27 | 1.17302 | 26.4153 | 44 | 63 |
| 1dyk_a | Laminin α2 chain | 374 | 50 | 1.38631 | 26.0647 | 28 | 52 |
| 1quo_a | Laminin α2 chain | 181 | 69 | 3.14801 | 25.013 | 25 | 45 |
| 1ikp_a | Exotoxin A | 599 | 20 | 4.04452 | 24.6624 | 50 | 50 |
| 1aer_b | Exotoxin A | 195 | 20 | 5.07931 | 24.3119 | 50 | 50 |
| 1aer_a | Exotoxin A | 205 | 20 | 5.35662 | 24.3119 | 50 | 50 |
| 1wht_a | Serine carboxypeptidase II | 256 | 84 | 5.52182 | 24.3119 | 24 | 49 |
| 9gaf_c | Glycosylasparaginase | 292 | 62 | 6.88212 | 23.9613 | 24 | 45 |
| B. FUGUE Z-Score ≥6.0 (CERTAIN 99% confidence) | |||
| Accession no. | Description | Profile length | Z-score |
| (A) Gapped BLAST and (B) FUGUE were used to identify potential templates from PDB files available. The 223-amino-acid query sequence was used for Gapped BLAST using a BLOSUM62 Matrix. Potential templates are listed. Useful templates contain sequence that spans the 223-amino-acid query sequence and demonstrate maximum sequence identity. The FUGUE algorithm was used to detect templates not identified via Gapped BLAST. Z-scores ≥6.0 are marked as highly probable or “certain” templates. Adequate profile length while maximizing Z-score provides the criteria for selecting a template. Combining the two methods revealed the laminin α2 LG5 chain from 1dyk.pdb as the best template. | |||
| 1dyk | Laminin α2 chain | 213 | 17.08 |
| 1c4r | Neurexin-1 β | 180 | 15.09 |
| 1quo | Laminin α2 chain | 181 | 14.71 |
| 1d2s | Sex hormone-binding globulin | 170 | 10.02 |
| 1h30 | Growth-arrest-specific protein | 391 | 9.69 |