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 |
| Average | 44,057 | 167.7 | 66.4 | 486696 | 56.9 | 556884 | 83.6 | |
‡ After removing identical sequences and sequences that fail to align with at least 75% of the domain.
* Numbers in parentheses indicate the nodes retained after insignificant nodes were removed by the mcBPPS program.
† The log-likelihood ratio in nats.
§ The time (in minutes) is for Steps 2 and 3 of the algorithm only; Step 1 can be parallelized to run in less than 10% of the time shown.