Table 1 |
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|
List of superfamilies used for FMALIGN benchmarking. |
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|
Superfamily code |
Superfamily name |
Structural Class |
Average length of proteins |
Average sequence identity(%) |
|
|
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|
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 |
|
|
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|
Chakrabarti et al. BMC Bioinformatics 2004 5:167 doi:10.1186/1471-2105-5-167 |
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