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Table 3 Pathways significantly enriched in ‘core’ microbiome enzymes

From: Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality

Pathway name Pathway classa p valueb Core enzymes in pathway Total enzymes in pathway
Aminoacyl-tRNA biosynthesis O 3.57E-08 22 32
Purine metabolism NT 1.49E-06 44 100
Peptidoglycan biosynthesis G 4.30E-06 12 15
Glycolysis/gluconeogenesis C 2.89E-05 23 45
Alanine, aspartate and glutamate metabolism AA 4.24E-05 22 43
Valine, leucine and isoleucine biosynthesis AA 8.75E-05 12 18
Pyrimidine metabolism NT 2.89E-04 27 63
Phenylalanine, tyrosine and tryptophan biosynthesis AA 6.27E-04 15 29
Pentose phosphate pathway C 7.05E-04 17 35
Carbon fixation pathways in prokaryotes E 2.22E-03 17 38
One carbon pool by folate CO 3.21E-03 12 24
Lysine biosynthesis AA 3.32E-03 13 27
Pyruvate metabolism C 3.37E-03 24 62
Fatty acid biosynthesis L 3.88E-03 9 16
Citrate cycle (TCA cycle) C 4.76E-03 11 22
Amino sugar and nucleotide sugar metabolism C 5.66E-03 30 85
Oxidative phosphorylation E 8.48E-03 7 12
Drug metabolism—other enzymes X 2.34E-02 9 20
Cysteine and methionine metabolism AA 2.55E-02 21 61
Polyketide sugar unit biosynthesis T 2.74E-02 4 6
Streptomycin biosynthesis S 3.48E-02 8 18
Folate biosynthesis CO 3.61E-02 7 15
  1. aDefined according to KEGG. AA amino acid, C carbohydrate, CO co-factor, E energy, G glycan, L lipid, NT nucleotode, O other, S secondary metabolites, T terpenoids, X xenobiotics
  2. bHere, we used the hypergeometric test to examine enrichment of pathways compared to all KEGG defined pathways