Table 1.
Similarity for homologs and non-homologsa.
| 5PTP versus: | 1SGT | 2SGA | 1BEF | 1SBT | |
|---|---|---|---|---|---|
| DALI | Z | 32.7 | 13.7 | 8.8 | <2 |
| E(2775) | 10−14 | 10−4 | 0.02 | >100 | |
| Nalign (%id) | 209 (34) | 147 (19) | 131 (10) | NA | |
| RMSD (Å) | 1.4 | 2.8 | 2.9 | NA | |
| VAST | E(2775) | 10−21 | 0.017b | 1.94 | NA |
| Nalign (%id) | 208 (34) | 130 (22) | 122 (14) | NA | |
| RMSD (Å) | 1.5 | 2.3 | 2.8 | NA | |
| COMPASS | E(10 000) | 10−114 | 10−13 | 0.056 | 13 |
| PSI-BLAST | E(2775) | 10−48 | 2.5 | >10 | >10 |
| Nalign | 231 | 40 | NA | NA | |
| SSEARCH | E(10 000) | 10−19 | 2.6 | >10 | >10 |
| Nalign (%id) | 223 (36) | 181 (25) | 68 (33) | 159 (25) |
a
Nalign is the number of aligned residues, %id is the percent sequence identity and RMSD is the root mean square distance. E(N) is the expectation value, the number of times a score is expected by chance in a search of a database of size N. 5PTP, 1SGT and 2SGA are trypsin-like serine protease homologs; 1BEF is a viral protease that CATH says is not homologous to the trypsin-like proteases, but SCOP says is homologous to them. 1SBT is subtilisin, which has the same catalytic triad as the trypsin-like serine proteases, but a completely different global domain structure.
b
Based on alignment with 5SGA, which is 100% sequence identical to 2SGA. NA: not available — no alignment was calculated.