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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.

From: Phylophenetic properties of metabolic pathway topologies as revealed by global analysis

pathway ID pathway name category vertex number diameter average path length clustering coefficient prokaryote number similarity to 16S rRNA based tree a similarity to 16S rRNA based tree b
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
  1. a Pathway-based phylophenetic trees were derived by using distance definition in equation 3.
  2. b Pathway-based phylophenetic trees were derived by using Heymans and Singh's distance definition [5].