Skip to main content

Table 3 Comparison of selected organism-specific pathway genome databases (PGDB)

From: Reconstruction of metabolic pathways for the cattle genome

Database statistics

Cattle

New PGDB without manual curation

BioCyc

 

Initial

Curated

Human

Mouse

Dog

E. coli

Human

Metabolic pathways

243

217

342

324

151

194

178

Enzymatic reactions

1,500

1,419

2,020

1,941

1,102

1,245

1,253

Enzymes

1,172

1,544

2,846

2,789

753

1,323

2,594

Compounds

1,116

1,021

1,390

1,325

794

1,202

975

Pathway holes (missing enzymes)

       

number of pathway holes

593

113

587

536

509

35

246

pathway holes as a percentage of total reactions in pathways

56%

14%

45%

43%

67%

5%

36%

pathways with no holes

59

165

134

128

17

169

67

pathways with 1 hole

51

28

64

65

30

15

35

pathways with 2 holes

32

11

40

41

22

7

37

pathways with 3 holes

21

1

36

25

15

3

15

pathways with 4 holes

14

6

18

18

15

0

11

pathways with >5 holes

66

6

50

47

52

0

13

total pathways with holes

184

52

208

196

134

25

111