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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