Table 1

List of superfamilies used for FMALIGN benchmarking.

Superfamily code

Superfamily name

Structural Class

Average length of proteins

Average sequence identity(%)


02.01.001

Globin-like

All α

142

15.2

02.01.023

Putative DNA-binding domain

All α

76

10.0

02.01.050

Cytochromes

All α

122

22.0

02.01.060

ACP-like

All α

80

23.5

02.01.101

SAM/Pointed domain

All α

84

13.3

02.02.027

C2 domain(Calcium/lipid-binding domain, CaLB)

All β

75

11.4

02.02.042

Galactose-binding domain-like

All β

185

12.6

02.02.058

ISP domain

All β

136

23.4

02.02.094

Acid proteases

All β

217

20.4

02.02.152

Hedgehog/intein (Hint) domain

All β

177

16.9

02.03.018

Phosphatidylinositol-specific phospholipase C (PI-PLC)

α and β

286

13.6

02.03.059

Ferredoxin reductase-like, C-terminal NADP-linked domain

α and β

132

21.6

02.03.073

Thiamin diphosphate-binding fold (THDP-binding)

α and β

236

12.1

02.03.148

"Helical backbone" metal receptor

α and β

320

14.4

02.04.010

Chromo domain-like

α and β

68

26.3

02.04.088

Regulatory domain in the amino acid metabolism

α and β

90

12.2

02.04.218

Ribosome inactivating proteins (RIP)

α and β

253

22.1

02.07.017

Leech antihemostatic proteins

α and β

47

19.1


Chakrabarti et al. BMC Bioinformatics 2004 5:167   doi:10.1186/1471-2105-5-167

Open Data