Table 1 List of parameters and similarity values for 37 metabolic pathways. The information on pathway IDs, names and categories was obtained from KEGG [2]. For each pathway reference graph, the diameter and average path length were calculated by regarding the graph as directed, and the clustering coefficient was calculated by regarding the graph as undirected. TopNet [36] was used to calculate the clustering coefficient. The prokaryote number refers to the number of studied prokaryotes containing the pathway, based on the definition of presence or absence of metabolic pathways given in Methods.

map00010

Glycolysis / Gluconeogenesis

Carbohydrate Metabolism

40

12

4.58

0.617

154

0.178

0.198

map00020

Citrate cycle (TCA cycle)

Carbohydrate Metabolism

23

9

3.06

0.594

118

0.13

0.121

map00030

Pentose phosphate pathway

Carbohydrate Metabolism

34

8

3.24

0.468

107

0.153

0.163

map00040

Pentose and glucuronate interconversions

Carbohydrate Metabolism

53

13

5.28

0.441

14

0.272

0.363

map00051

Fructose and mannose metabolism

Carbohydrate Metabolism

61

10

3.60

0.419

96

0.225

0.182

map00052

Galactose metabolism

Carbohydrate Metabolism

37

14

4.80

0.408

38

0.171

0.142

map00130

Ubiquinone biosynthesis

Metabolism of Cofactors and Vitamins

21

7

3.13

0.088

39

0.222

0.194

map00220

Urea cycle and metabolism of amino groups

Amino Acid Metabolism

33

13

4.46

0.285

110

0.112

0.121

map00230

Purine metabolism

Nucleotide Metabolism

97

16

3.78

0.481

164

0.236

0.204

map00240

Pyrimidine metabolism

Nucleotide Metabolism

59

9

2.95

0.408

170

0.149

0.161

map00251

Glutamate metabolism

Amino Acid Metabolism

35

5

1.83

0.622

148

0.172

0.172

map00252

Alanine and aspartate metabolism

Amino Acid Metabolism

38

7

2.50

0.626

139

0.213

0.198

map00260

Glycine, serine and threonine metabolism

Amino Acid Metabolism

55

14

4.09

0.556

116

0.238

0.212

map00271

Methionine metabolism

Amino Acid Metabolism

23

5

2.43

0.515

122

0.126

0.092

map00280

Valine, leucine and isoleucine degradation

Amino Acid Metabolism

32

9

3.16

0.402

40

0.297

0.270

map00330

Arginine and proline metabolism

Amino Acid Metabolism

70

10

4.14

0.502

70

0.238

0.268

map00340

Histidine metabolism

Amino Acid Metabolism

39

15

5.10

0.276

110

0.056

0.056

map00360

Phenylalanine metabolism

Amino Acid Metabolism

39

4

1.84

0.465

34

0.258

0.258

map00362

Benzoate degradation via hydroxylation

Biodegradation of Xenobiotics

44

9

3.02

0.202

19

0.250

0.187

map00400

Phenylalanine, tyrosine and tryptophan biosynthesis

Amino Acid Metabolism

31

10

3.48

0.464

149

0.075

0.089

map00450

Selenoamino acid metabolism

Metabolism of Other Amino Acids

19

7

2.70

0.253

52

0.142

0.122

map00500

Starch and sucrose metabolism

Carbohydrate Metabolism

74

12

4.23

0.283

82

0.189

0.164

map00520

Nucleotide sugars metabolism

Carbohydrate Metabolism

28

5

2.16

0.548

93

0.044

0.055

map00530

Aminosugars metabolism

Carbohydrate Metabolism

38

7

2.93

0.582

130

0.110

0.133

map00561

Glycerolipid metabolism

Lipid Metabolism

80

13

4.02

0.343

74

0.295

0.211

map00620

Pyruvate metabolism

Carbohydrate Metabolism

67

7

2.43

0.598

155

0.296

0.263

map00630

Glyoxylate and dicarboxylate metabolism

Carbohydrate Metabolism

58

8

3.10

0.618

57

0.129

0.166

map00640

Propanoate metabolism

Carbohydrate Metabolism

45

10

3.05

0.513

21

0.055

0.055

map00650

Butanoate metabolism

Carbohydrate Metabolism

52

13

3.90

0.429

32

0.275

0.275

map00670

One carbon pool by folate

Metabolism of Cofactors and Vitamins

24

4

1.57

0.80

157

0.103

0.116

map00710

Carbon fixation

Energy Metabolism

23

8

3.28

0.247

97

0.117

0.117

map00730

Thiamine metabolism

Metabolism of Cofactors and Vitamins

14

6

2.88

0.199

20

0.117

0.117

map00760

Nicotinate and nicotinamide metabolism

Metabolism of Cofactors and Vitamins

32

8

2.47

0.518

121

0.118

0.118

map00770

Pantothenate and CoA biosynthesis

Metabolism of Cofactors and Vitamins

27

10

3.43

0.320

92

0.134

0.157

map00790

Folate biosynthesis

Metabolism of Cofactors and Vitamins

25

7

2.69

0.322

124

0.115

0.115

map00860

Porphyrin and chlorophyll metabolism

Metabolism of Cofactors and Vitamins

60

20

6.37

0.171

90

0.241

0.183

map00910

Nitrogen metabolism

Energy Metabolism

63

5

1.87

0.508

137

0.231

0.186