Table 2.
Distribution comparison of sequence pairs between 10% and 30% identity detected with different E values
| BLAST (E = 10) | BLAST (E = 1000 | FASTA (E = 10) | FASTA (E = 100) | SSEARCH (E = 10) | SSEARCH (E = 100) | |
| Number of selected pairsa | 765 | 1316 | 852 | 2634 | 1115 | 4097 |
| Structurally similar (%)b | 93.6 | 66 | 58.1 | 25.1 | 53.5 | 20.1 |
| Structurally dissimilar (%) | 6.4 | 34 | 41.9 | 74.9 | 46.5 | 79.9 |
| Average alignment length | 163 | 145 | 151 | 135 | 149 | 135 |
| Average identity rate (%) | 23.9 | 22.4 | 22.1 | 20.3 | 21.5 | 19.8 |
E value is the expected value as defined in Altschul et al. (1997).
a All pairs sharing between 10% and 50% identity, >50 residues and exhibiting <10% gaps.
b Structurally similar pairs are proteins present in the FSSP database with a Z score > 2 and with at least 100 amino acids.