From: Protein family comparison using statistical models and predicted structural information
 | Number of true | family-family | relationships | detected by |  |
---|---|---|---|---|---|
Type of false-positive | Gapped-BLAST | PSI-BLAST | prof _sim | prof _ss (predicted ss) | prof _ss (true ss) |
Different superfamily, same fold ("possible" relationship) | 116 | 146 | 173 | 178 | 272 |
Different fold, same class ("weak" relationship) | 116 | 148 | 173 | 178 | 274 |
Different class ("suspicious" relationship) | 124 | 153 | 189 | 209 | 328 |
Alpha ↔ Beta ("error" relationship) | 214 | 268 | 308 | >395 | >584 |