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Comparision of the number of hits obtained in HMMSearch using models derived from regular multiple sequence alignments and structure based sequence alignments.
| Superfamily name | SCOP code | Hits obtained from PASS2 HMMs | Hits obtained from superfamily HMMs |
| Superoxide dismutase | 46609 | 152 | 137 |
| Anticodon-binding domain of class I aminoacyl-tRNA synthetases | 47323 | 220 | 182 |
| Cyclophilin (peptidylprolyl isomerase) | 50891 | 112 | 98 |
| Hemopexin-like domain | 50923 | 103 | 73 |
