Table 1 Comparison of curated and automatically-generated domain hierarchies
CDD | Protein superfamily | number | length | Manually curated | Automatically generated | |||
|---|---|---|---|---|---|---|---|---|
Ident. |  | seqs‡ |  | nodes* | LLR†| nodes* | LLR†| time§ |
cd00030 | C2 | 23,452 | 102 | 106 (103) | 236574 | 78(73) | 223857 | 19.4 |
cd00138 | PLDc_SF | 16,765 | 119 | 105 (102) | 241766 | 36(34) | 192876 | 10.0 |
cd00142 | PI3Kc_like | 2,409 | 219 | 22 | 34129 | 16 | 34563 | 4.5 |
cd00159 | RhoGAP | 4,815 | 169 | 39(38) | 55604 | 32 | 53540 | 7.97 |
cd00173 | SH2 | 5,917 | 79 | 111 (101) | 49274 | 39 | 40075 | 3.5 |
cd00180 | Protein kinases | 104,912 | 215 | 280(260) | 1378273 | 107(104) | 1536991 | 241.0 |
cd00229 | SG NH_hydrolase | 14,635 | 187 | 30 | 180667 | 29 | 183822 | 14.95 |
cd00306 | S8/S53 peptidase | 10,960 | 241 | 36 | 161685 | 45(44) | 173693 | 30.90 |
cd00368 | Molybdopterin-Binding | 9,540 | 374 | 26 | 177569 | 44 | 209704 | 39.3 |
cd00397 | DNA_BRE_C | 25,824 | 164 | 27 (26) | 187382 | 39(37) | 211739 | 16.9 |
cd00761 | Glycosyltransferase A (GT-A) | 66,260 | 156 | 71 (70) | 944727 | 123(110) | 1048396 | 193.8 |
cd00768 | Class II aaRS-like core | 37,160 | 211 | 17 | 674454 | 31 | 833691 | 54.3 |
cd00838 | MPP_superfamily | 33,753 | 131 | 61 | 402297 | 55(54) | 399553 | 65.1 |
cd00900 | PH-like | 22,593 | 99 | 81 | 211812 | 99(98) | 274945 | 52.3 |
cd01067 | Globin_like | 9,933 | 117 | 4 (1) | 11133 | 26 (25) | 73808 | 4.3 |
cd01391 | Periplasmic_Binding_Protein_1 | 36,330 | 269 | 142(140) | 619713 | 68(65) | 580753 | 169.1 |
cd01494 | AAT_I (Pyrodoxal-PO4-binding) | 114,781 | 170 | 16 | 1086328 | 92(84) | 2027660 | 249.67 |
cd01635 | Glycosyltransferase GTB | 44,366 | 229 | 45 | 723443 | 95(93) | 881414 | 232.7 |
cd02156 | Class I aaRS-like core √ | 53,605 | 105 | 34 | 522962 | 61(57) | 698273 | 41.4 |
cd02883 | Nudix_Hydrolase | 32,046 | 123 | 55 (54) | 321636 | 61(60) | 367819 | 43.2 |
cd03128 | GAT-1 (mcBPPS vs pmcBPPS) | 46,514 | 92 | 34(32) | 319515 | 64(62) | 388621 | 42.2 |
cd03440 | hot_dog | 30,162 | 100 | 22(18) | 141990 | 70 (69) | 345298 | 39.1 |
cd03873 | Zinc peptidases | 24,455 | 237 | 81 | 596408 | 69(66) | 590521 | 43.9 |
cd05466 | Periplasmic_Binding_Protein_2 | 45,287 | 197 | 76(73) | 523941 | 49(41) | 411445 | 31.7 |
cd06587 | Glo_EDI_BRP_like | 36,165 | 112 | 60 (58) | 335848 | 94(91) | 479522 | 54.8 |
cd06663 | Biotinyl-lipoyl | 25,013 | 73 | 4 | 53038 | 25(18) | 66571 | 4.53 |
cd06846 | Adenylation_DNA_ligase_like | 3,833 | 182 | 14 | 43276 | 20 | 48,475 | 4.8 |
cd08555 | PI-PLCc_GDPD_SF | 8,707 | 179 | 74 (73) | 143201 | 37(32) | 123075 | 6.9 |
cd08772 | GH43_62_32_68 (β propellers) | 6,760 | 286 | 28 | 111336 | 51(50) | 176701 | 30.0 |
cl09931 | Rossmann fold proteins | 424,764 | 93 | 361 (347) | 4110907 | 145(130) | 4029120 | 757.2 |
| Â | Average | 44,057 | 167.7 | 66.4 | 486696 | 56.9 | 556884 | 83.6 |