Table 2. Accuracy of S4 alignments for templates identified by PSI-BLAST.
| Psi-Blast E-value | # Pairs | S4 FDS2 (1000) | S4 FDS2 (100) | Psi FDS2 |
| EV<10−6 | 902 | 95.6 | 94.9 | 83.4 |
| 10−6<EV<10−3 | 164 | 92.1 | 91.4 | 62.1 |
| 10−3<EV<10 | 316 | 88.8 | 86.1 | 41.9 |
| No Hit | 1516 | 82.0 | 76.0 | N/A |
Alignment pairs have been separated into three regions: clear homology (E-value<10−6), intermediate homology (10−6<E-value<10−3), remote homology (10−3<E-value<10) and undetectable homology (template not among PSI-BLAST hits). A default maximum E-value of 10 was used in PSI-BLAST for all queries.