Table 4. Top 20 most populated DNA-binding domains detected in the human genome.
| SCOP ID | DBD-T | Pfam | Nc | SCOP Superfamily Description |
| 57667 | 5504/674 | 6071/688 | 4485/655 | C2H2 and C2HC zinc fingers |
| 46689 | 311/263 | 314/276 | 266/246 | Homeodomain-like |
| 46785 | 148/143 | 102/98 | 101/98 | Winged helix DBD |
| 57716 | 93/58 | 68/62 | 54/54 | Glucocorticoid receptor-like DBD |
| 47459 | 87/87 | 104/103 | 85/85 | Helix-loop-helix DBD |
| 47113 | 68/67 | 56/56 | 54/54 | Histone-fold |
| 47095 | 57/38 | 61/50 | 40/38 | HMG-box |
| 47413 | 53/50 | 21/21 | 19/19 | λ repressor-like DNA-binding domains |
| 57959 | 49/49 | 45/45 | 44/44 | Leucine zipper domain |
| 47954 | 44/26 | 4/2 | 4/2 | Cyclin-like |
| 49417 | 42/41 | 42/42 | 39/39 | p53-like transcription factors |
| 56672 | 31/28 | 21/21 | 21/21 | DNA/RNA polymerases |
| 52540 | 23/22 | 21/19 | 19/19 | P-loop containing nucleoside triphosphate hydrolases |
| 56219 | 22/19 | 26/26 | 19/19 | DNase I-like |
| 46894 | 22/22 | 0/0 | 0/0 | C-term domain of the bipartite response regulators |
| 117018 | 17/17 | 3/3 | 3/3 | ATP-dependent DNA ligase DBD |
| 56091 | 17/17 | 3/3 | 3/3 | DNA ligase/mRNA capping enzyme, catalytic domain |
| 50249 | 16/16 | 3/3 | 3/3 | Nucleic acid-binding proteins |
| 53098 | 12/12 | 10/10 | 10/10 | Ribonuclease H-like |
| 81296 | 11/11 | 27/22 | 10/10 | E set domains |
The numbers of domains/proteins detected by DBD-Threader and by Pfam are given for each SCOP Superfamily. The results of Pfam were obtained from the UniProt knowledge base and mapped to SCOP superfamilies (see text). Nc denotes the numbers of domain/proteins detected by both methods.