| Fold | number of domains in representative set
| number of domains in representative set as a % | number of domains in entire database | number of domains in entire database as a % |
|---|
| "histone-like" proteins from arhaea from 3Dee | 1 | 0.06 | 2 | 0.01 |
| 2,3-Dihydroxybiphenyl dioxygenase (DHDB, BPHC enzyme) from 3Dee | 2 | 0.12 | 4 | 0.02 |
A DNA topoisomerase I domain from 3Dee  | 3 | 0.17 | 3 | 0.02 |
| ADP-ribosylation toxins from 3Dee | 4 | 0.23 | 34 | 0.18 |
| ATP-grasp sub-domain I from 3Dee | 5 | 0.29 | 12 | 0.06 |
| ATP-grasp sub-domain II from 3Dee | 5 | 0.29 | 12 | 0.06 |
| Aldehyde ferredoxin oxidoreductase, N-terminal domains from 3Dee | 1 | 0.06 | 2 | 0.01 |
| Anti-LPS factor/recA domain from SCOP | 1 | 0.06 | 9 | 0.05 |
| Astacin domain II from 3Dee | 1 | 0.06 | 6 | 0.03 |
| Bacteriophage T7 lysozyme (Zn amidase) from SCOP | 1 | 0.06 | 1 | 0.01 |
| C-type lectin from 3Dee | 3 | 0.17 | 105 | 0.56 |
| CI-2 family of serine protease inhibitors from SCOP | 1 | 0.06 | 28 | 0.15 |
| Cell cycle regulatory proteins from SCOP | 1 | 0.06 | 12 | 0.06 |
| Chorismate mutase from 3Dee | 1 | 0.06 | 36 | 0.19 |
| Class II aaRS and biotin synthetases from SCOP | 5 | 0.29 | 39 | 0.21 |
| Copper amino oxidase, domain 1 from 3Dee | 1 | 0.06 | 4 | 0.02 |
| Creatinase/methionine aminopeptidase from 3Dee | 2 | 0.12 | 10 | 0.05 |
| Cystatin-like from SCOP | 10 | 0.58 | 56 | 0.30 |
| Cysteine proteinases Domain I from 3Dee | 3 | 0.17 | 51 | 0.27 |
| Cysteine proteinases Domain II from 3Dee | 3 | 0.17 | 51 | 0.27 |
| Cytochrome b5 from SCOP | 1 | 0.06 | 16 | 0.08 |
| D-amino acid aminotransferase Domain I from 3Dee | 1 | 0.06 | 15 | 0.08 |
| D-amino acid aminotransferase Domain II from 3Dee | 1 | 0.06 | 15 | 0.08 |
| DCoH-like from SCOP | 2 | 0.12 | 42 | 0.22 |
| DNA clamp from SCOP | 5 | 0.29 | 16 | 0.08 |
| DNase I-like from SCOP | 2 | 0.12 | 5 | 0.03 |
| Elongation Factor domain III from 3Dee | 2 | 0.12 | 2 | 0.01 |
| Endonuclease from 3Dee | 1 | 0.06 | 2 | 0.01 |
| FAD-linked reductases, C-terminal domain from SCOP | 2 | 0.12 | 3 | 0.02 |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain from 3Dee | 2 | 0.12 | 56 | 0.30 |
| FKBP-like from SCOP | 3 | 0.17 | 26 | 0.14 |
| Fe,Mn superoxide dismutase (SOD), C-terminal domain from SCOP | 1 | 0.06 | 38 | 0.20 |
| Ferredoxin-like from SCOP | 20 | 1.17 | 202 | 1.07 |
| GMP synthetase, the C-terminal, dimerisation domain from 3Dee | 1 | 0.06 | 4 | 0.02 |
| Gelsolin-like (actin-severing protein) from 3Dee | 1 | 0.06 | 2 | 0.01 |
| Glutamine synthetase main domain from 3Dee | 1 | 0.06 | 14 | 0.07 |
| Glutamine synthetase smaller domain from 3Dee | 1 | 0.06 | 14 | 0.07 |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain from SCOP | 3 | 0.17 | 63 | 0.33 |
| Hedgehog/DD-peptidase from SCOP | 1 | 0.06 | 1 | 0.01 |
| Histidine decarboxylase from SCOP | 1 | 0.06 | 6 | 0.03 |
| Histidine-containing phosphocarrier proteins (HPr) from SCOP | 1 | 0.06 | 13 | 0.07 |
| IF3-like from SCOP | 3 | 0.17 | 12 | 0.06 |
| Interleukin 8-like chemokines from 3Dee | 2 | 0.12 | 64 | 0.34 |
| KH-domain from SCOP | 1 | 0.06 | 2 | 0.01 |
| Lactate & malate dehydrogenases, C-terminal domain from SCOP | 3 | 0.17 | 44 | 0.23 |
| Lysozyme-like from SCOP | 2 | 0.12 | 7 | 0.04 |
| Lysozyme-like Domain I from 3Dee | 2 | 0.12 | 492 | 2.60 |
| Lysozyme-like Domain II from 3Dee | 2 | 0.12 | 492 | 2.60 |
| MHC antigen-recognition domain from SCOP | 2 | 0.12 | 51 | 0.27 |
| Metzincins, catalytic (N-terminal) domain from 3Dee | 5 | 0.29 | 72 | 0.38 |
| Microbal ribonucleases from 3Dee | 3 | 0.17 | 137 | 0.73 |
| N-terminal domain of enolase & muconate-lactonizing enzyme from 3Dee | 3 | 0.17 | 28 | 0.15 |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) from SCOP | 1 | 0.06 | 30 | 0.16 |
| Nucleoside triphosphate pyrophosphorylase (MutT) from SCOP | 1 | 0.06 | 2 | 0.01 |
| Nucleotidyltransferases Domain II from 3Dee | 1 | 0.06 | 105 | 0.56 |
| Ornithine decarboxylase C-terminal domain from SCOP | 1 | 0.06 | 2 | 0.01 |
| P-loop containing nucleotide triphosphate hydrolases, inserted domain in Guanylate Kinase from 3Dee | 1 | 0.06 | 1 | 0.01 |
| P-loop containing nucleotide triphosphate hydrolases, small a+b insert from 3Dee | 1 | 0.06 | 8 | 0.04 |
| Phosphate binding protein-like inserted domain from 3Dee | 1 | 0.06 | 13 | 0.07 |
| Profilin-like from SCOP | 2 | 0.12 | 18 | 0.10 |
| Protein kinases (PK), catalytic core C terminal Domain from 3Dee | 2 | 0.12 | 53 | 0.28 |
| Protein kinases (PK), catalytic core N terminal Domain from 3Dee | 3 | 0.17 | 44 | 0.23 |
| RNA bacteriophage capsid protein from SCOP | 2 | 0.12 | 42 | 0.22 |
| Ribonuclease A-like from 3Dee | 2 | 0.12 | 95 | 0.50 |
| Ribosomal protein L7/12, C-terminal fragment from SCOP | 1 | 0.06 | 1 | 0.01 |
| Ribosomal protein S5 domain 2-like from SCOP | 2 | 0.12 | 4 | 0.02 |
| Ribosome inactivating proteins (RIP) Domain I from 3Dee | 1 | 0.06 | 27 | 0.14 |
| Ribosome inactivating proteins (RIP) Domain II from 3Dee | 2 | 0.12 | 27 | 0.14 |
| RuBisCO, small subunit from SCOP | 1 | 0.06 | 47 | 0.25 |
| S-adenosylmethionine synthetase. MAT inner domain from 3Dee | 1 | 0.06 | 8 | 0.04 |
| S-adenosylmethionine synthetase. MAT outer domain from 3Dee | 3 | 0.17 | 24 | 0.13 |
| SH2-like from SCOP | 1 | 0.06 | 64 | 0.34 |
| Subtilisin inhibitor from SCOP | 1 | 0.06 | 5 | 0.03 |
| Sugar phosphatases alpha+beta N terminal domain from 3Dee | 3 | 0.17 | 76 | 0.40 |
| TBP-like from SCOP | 2 | 0.12 | 30 | 0.16 |
| Tautomerase/MIF from SCOP | 2 | 0.12 | 21 | 0.11 |
| Tetrahydrobiopterin biosynthesis enzymes from 3Dee | 1 | 0.06 | 2 | 0.01 |
| The intermediate domain of GroEL from 3Dee | 1 | 0.06 | 36 | 0.19 |
| Thymidine phosphorylase Domain III from 3Dee | 1 | 0.06 | 1 | 0.01 |
| Thymidylate synthase from 3Dee | 1 | 0.06 | 69 | 0.37 |
| Thymidylate synthase Extra Domain from 3Dee | 1 | 0.06 | 14 | 0.07 |
| Ubiquitin conjugating enzyme from SCOP | 1 | 0.06 | 6 | 0.03 |
| Urease, gamma-subunit from SCOP | 1 | 0.06 | 19 | 0.10 |
| Virally encoded KP4 toxin from 3Dee | 1 | 0.06 | 2 | 0.01 |
| beta-Grasp from 3Dee | 8 | 0.47 | 76 | 0.40 |
| beta-Lactamase/D-ala carboxypeptidase Domain I from 3Dee | 1 | 0.06 | 23 | 0.12 |
| dsRBD & PDA domains from SCOP | 3 | 0.17 | 4 | 0.02 |
| Total | 193 | 11.25 | 3432 | 18.16 |
