Superfamilies Unique for One of the Processed Proteomes or Group of Proteomes
| SCOP superfamily | N | R | Functional description |
| Human | |||
| MHC antigen-recognition domain | 57 | 62 | Immune system |
| Interleukin 8-like chemokines | 48 | 71 | Immune system, growth factors |
| 4-helical cytokines | 47 | 75 | Immune system, diverse range of interferons and interleukins |
| Crystallins/protein S/yeast-killer toxin | 20 | 144 | Eye lens component |
| Serum albumin | 19 | 150 | Major blood plasma component |
| Colipase-like | 11 | 202 | Enzyme regulation for pancreatic lipases, development |
| RNase A-like | 8 | 237 | Different ribonucleases found in pancreas, eosinophil granules, and involved in angeogenesis |
| PKD domain | 7 | 260 | Possibly involved in extracellular protein-protein interaction |
| Defensin-like | 7 | 260 | Small antibacterial, fungal, and viral protein |
| Uteroglobin-like | 5 | 294 | Binding of phospholipids, progesterone, inhibits phospholipase A2 (involved in metabolism of biomembranes) |
| Midkine | 4 | 328 | Growth factors |
| Fly | |||
| Insect pheromone/odorant-binding proteins | 26 | 81 | Hormone related, sex recognition |
| Scorpion toxin-like | 6 | 220 | Drosomycin and defensin, antibiotic, antifungicide |
| Worm | |||
| Plant lectins/antimicrobial peptides | 4 | 234 | Antimicrobial peptides, pathogen response, antifungicides Homologous to plant proteins |
| Osmotin, thaumatin-like protein | 4 | 234 | Same description as for lectins above |
| Yeast | |||
| Zn2/Cys6 DNA-binding domain | 53 | 11 | Transcription factors |
| DNA-binding domain of Mlu1-box binding protein MP1 | 4 | 155 | Transcription factors |
| Bacteria | |||
| TetR/NARL DNA-binding domain | 112 | 19 | Transcription factors |
| IIA domain of mannitol-specific and ntr phosphotransferase EII | 28 | 99 | Carbohydrate transport system: part of phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) |
| Prokaryotic DNA-binding protein | 18 | 157 | Bacterial histone-like proteins |
| Zn2+ DD-carboxypeptidase, N-terminal domain | 17 | 165 | Found in enzymes involved in bacterial cell wall degradation, possibly peptidoglycan-binding domain |
| Glucose permease domain IIB | 17 | 165 | Part of PTS |
| Regulatory protein AraC | 14 | 182 | Part of the transcription regulation of the arabinose operon |
| LexA/signal peptidase | 11 | 211 | 1. Transcriptional regulation of SOS repair genes, protease domain of the LexA protein 2. Cleaves the N-terminal signal peptides of secreted or periplasmic proteins. |
| Histidine-containing phosphocarrier proteins (HPr) | 11 | 211 | Part of PTS |
| Periplasmic chaperone C domain | 11 | 211 | Assembly of extracellular periplasmic macromolecular structures |
| Duplicated hybrid motif | 10 | 224 | Part of PTS |
| Aspartate receptor, ligand-binding domain | 10 | 224 | Found in different membrane integral sensor and chemotaxis proteins, often associated with kinase domains |
[i] The functional description is taken from PFAM/InterPro and SwissProt homologs. N and R are the same as in Table 1. For human, fly, worm, and yeast, the superfamilies with N >3 and for bacteria N >9 are listed.