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Supplemental Table 3. Summary of transcripts annotated to metabolic pathways and the number of transcripts total in each pathway. Pathway Short Name Metabolic pathways Biosynthesis of secondary metabolites Microbial metabolism in diverse environments ABC transporters Two-component system Biosynthesis of amino acids Aminoacyl-tRNA biosynthesis Ribosome Purine metabolism Nitrogen metabolism Phosphotransferase system (PTS) Flagellar assembly Glycolysis / Gluconeogenesis Pyrimidine metabolism Pyruvate metabolism Porphyrin and chlorophyll metabolism Arginine and proline metabolism Amino sugar and nucleotide sugar metabolism Fructose and mannose metabolism Bacterial chemotaxis Propanoate metabolism Starch and sucrose metabolism Pentose and glucuronate interconversions Glycine, serine and threonine metabolism Pentose phosphate pathway Methane metabolism Cysteine and methionine metabolism Glycerophospholipid metabolism Butanoate metabolism Oxidative phosphorylation Alanine, aspartate and glutamate metabolism Glyoxylate and dicarboxylate metabolism Galactose metabolism Phenylalanine metabolism Phenylalanine, tyrosine and tryptophan biosynthesis Glutathione metabolism Homologous recombination Selenocompound metabolism Sulfur metabolism Mismatch repair Base excision repair Glycerolipid metabolism Fatty acid biosynthesis Citrate cycle (TCA cycle) Lipopolysaccharide biosynthesis Valine, leucine and isoleucine degradation Number Of Transcripts 403 168 140 138 101 72 58 49 47 40 37 36 32 32 30 30 29 29 29 26 25 24 24 23 22 20 19 19 18 18 18 17 16 16 15 15 14 14 13 13 12 12 12 12 12 11 Fatty acid metabolism Histidine metabolism Folate biosynthesis Peptidoglycan biosynthesis Biotin metabolism Sulfur relay system One carbon pool by folate Ascorbate and aldarate metabolism beta-Alanine metabolism Ubiquinone and other terpenoid 2-Oxocarboxylic acid metabolism Tryptophan metabolism Benzoate degradation Inositol phosphate metabolism Nicotinate and nicotinamide metabolism Pantothenate and CoA biosynthesis Terpenoid backbone biosynthesis Lysine degradation Streptomycin biosynthesis Vitamin B6 metabolism Protein export RNA degradation Lysine biosynthesis Tyrosine metabolism Bacterial secretion system DNA replication Valine, leucine and isoleucine biosynthesis Cyanoamino acid metabolism Nucleotide excision repair Thiamine metabolism Aminobenzoate degradation Taurine and hypotaurine metabolism Limonene and pinene degradation Synthesis and degradation of ketone bodies Nitrotoluene degradation Chloroalkane and chloroalkene degradation Biosynthesis of unsaturated fatty acids Riboflavin metabolism C5-Branched dibasic acid metabolism Polyketide sugar unit biosynthesis Phosphonate and phosphinate metabolism Arachidonic acid metabolism D-Glutamine and D-glutamate metabolism D-Alanine metabolism Xylene degradation Other glycan degradation Caprolactam degradation Geraniol degradation Dioxin degradation RNA polymerase 11 11 11 10 10 9 9 9 9 9 9 8 8 8 8 7 7 7 7 6 6 6 6 6 6 6 6 5 5 5 5 5 4 4 4 4 4 4 4 4 4 3 3 3 3 3 3 3 3 2 Novobiocin biosynthesis Naphthalene degradation Biosynthesis of siderophore group nonribosomal peptides Sphingolipid metabolism alpha-Linolenic acid metabolism Toluene degradation 2 2 1 1 1 1
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