Skip to main content

Table 3 Tweaking set domain assignments by increasingly sensitive comparison tools.

From: SCOPmap: Automated assignment of protein structures to evolutionary superfamilies

Comparison Method

Number of Domains First Identified By This Method [4035 mapped domains plus 50 domains that are identified but not assigned (see Table 4)]

Average Sequence Identity Between Query and Closest Superfamily Representative

% of Domains Unmapped by Less Sensitive Methods that are Identified by This Method

BLAST

3163

80.1%

69.1%

RPS-BLAST

514

41.1%

36.3%

PSI-BLAST

104

26.1%

11.5%

COMPASS

26

27.2%

3.3%

MAMMOTH

100

29.7%

12.9%

DaliLite

124

17.4%

18.4%

correlation of conservation patterns

23

11.1%

4.2%

agreement of alignments produced by DaliLite and by gapped BLAST, RPS-BLAST, or PSI-BLAST

31

12.1%

5.9%