Table 1.
Mapping between the general and minor functional categories for 1,781 protein domains defined in structural classification of proteins (SCOP) 1.73 and the number of fold superfamilies (FSFs) corresponding to each minor category in our dataset of 965 organisms. A total of 135 FSFs could not be annotated. m/tr, metabolism and transport.
| Functional category | Minor categories | No. of FSF domains |
|---|---|---|
| Metabolism (533 FSFs) | Energy | 54 |
| Photosynthesis | 20 | |
| E- transfer | 31 | |
| Amino acids m/tr | 20 | |
| Nitrogen m/tr | 1 | |
| Nucleotide m/tr | 30 | |
| Carbohydrate m/tr | 30 | |
| Polysaccharide m/tr | 21 | |
| Storage | 0 | |
| Coenzyme m/tr | 50 | |
| Lipid m/tr | 17 | |
| Cell envelope m/tr | 8 | |
| Secondary metabolism | 11 | |
| Redox | 55 | |
| Transferases | 29 | |
| Other enzymes | 156 | |
| General (131 FSFs) | Small molecule binding | 27 |
| Ion binding | 13 | |
| Lipid/membrane binding | 4 | |
| Ligand binding | 3 | |
| General | 28 | |
| Protein interaction | 49 | |
| Structural protein | 7 | |
| Information (201 FSFs) | Chromatin structure | 7 |
| Translation | 92 | |
| Transcription | 24 | |
| DNA replication/repair | 68 | |
| RNA processing | 10 | |
| Nuclear structure | 0 | |
| Other (273 FSFs) | Unknown function | 200 |
| Viral proteins | 73 | |
| Extracellular processes (95 FSFs) | Cell adhesion | 31 |
| Immune response | 19 | |
| Blood clotting | 5 | |
| Toxins/defense | 40 | |
| Intracellular processes (208 FSFs) | Cell cycle, Apoptosis | 20 |
| Phospholipid m/tr | 6 | |
| Cell motility | 20 | |
| Trafficking/secretion | 0 | |
| Protein modification | 35 | |
| Proteases | 52 | |
| Ion m/tr | 21 | |
| Transport | 54 | |
| Regulation (205 FSFs) | RNA binding, m/tr | 19 |
| DNA-binding | 66 | |
| Kinases/phosphatases | 15 | |
| Signal transduction | 53 | |
| Other regulatory function | 34 | |
| Receptor activity | 18 |