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Table 1 List of the enzymes/genes and microorganisms detected in AB1 microcosm involved in diverse metabolism of carbohydrates

From: Detection of carbohydrate-active enzymes and genes in a spent engine oil-perturbed agricultural soil

Pathway Enzymes/genes Microorganisms
Glycolysis/gluconeogenesis Glucokinase; glucose-6-phosphate isomerase; fructose 1,6-bisphosphatase; phosphoglycerate kinase; pyruvate dehydrogenase E1 component; pyruvate dehydrogenase E1 component α-subunit; pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase); alcohol dehydrogenase; aldehyde dehydrogenase (NAD+); acetyl-CoA synthetase; pyruvate carboxylase phosphomannomutase/phosphoglucomutase; glucose-6-phosphate 1-epimerase Thioploca, Achromobacter, Colwellia, Massilia, Thauera, Acidiphilium, Methylobacterium, Stenotrophomonas, Caulobacter, Comamonas, Paracoccus, Azotobacter, Pseudomonas
Citric acid (TCA) cycle Aconitate hydratase 2/2-methylisocitrate dehydratase; 2-oxoglutarate dehydrogenase E2 component (dihydrolipoamide succinyltransferase); succinyl-CoA:acetate-CoA transferase; succinate dehydrogenase/fumarate reductase, flavoprotein subunit; fumarate reductase, flavoprotein subunit; fumarate hydratase, class I; malate dehydrogenase; pyruvate dehydrogenase E1 component; pyruvate dehydrogenase E1 component α-subunit; pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) Novosphingobium, Sphingobium, Azorhizobium, Candidatus Symbiobacter, Steroidobacter, Xanthomonas, Acidiphilium, Thauera, Methylobacterium, Stenotrophomonas
Pentose phosphate pathway Glucose-6-phosphate isomerase; glucose-6-phosphate 1-dehydrogenase; 6-phosphogluconolactonase; 6-phosphogluconate dehydrogenase; ribulose-phosphate 3-epimerase; xylulose-5-phosphate/fructose-6-phosphate phosphoketolase; ribokinase; phosphomannomutase/phosphoglucomutase; fructose 1,6-bisphosphatase I Achromobacter, Brevundimonas, Xanthomonas, Nitrospira, Pseudanabaena, Methylophaga, Sinorhizobium, Ensifer, Pseudomonas, Caulobacter, Colwellia, Symbiobacterium
Pentose and glucuronate interconversions 2-Deoxy-d-gluconate-3-dehydrogenase; tagaturonate reductase; ribulose-phosphate-3-epimerase; l-arabinose isomerase; l-rhamnose isomerase/sugar isomerase Chelativorans, Klebsiella, Pseudanabaena, Granulicella, Novosphingobium
Fructose and mannose metabolism Mannose-6-phosphate isomerase; phosphomannomutase/phosphoglucomutase, l-rhamnose isomerase; l-rhamnose isomerase/sugar isomerase; fructose 1,6-bisphosphatase I; mannitol-1-phosphate/altronate dehydrogenases Raoultella, Pseudomonas, Klebsiella, Novosphingobium, Caulobacter, Colwellia
Galactose metabolism UDP-glucose-4-epimerase; phosphomannomutase/phosphoglucomutase; glucokinase; d-tagatose 1,6-bisphosphate aldolase; α-glucosidase Niastella, Pseudomonas, Thioploca, Stenotrophomonas, Citrobacter
Amino sugar and nucleotide sugar metabolism β-N-Acetylhexosaminidase; anomeric MURNAc/GlcNAc kinase; UDP-N-acetylglucosamine-2-epimerase; N-acetylglucosamine-6-phosphate deacetylase; glucosamine-6-phosphate deaminase; α-N-arabinofuranosidase; UDP-4-amino-4-deoxy-l-arabinose formyltransferase/UDP-glucuronic acid dehydrogenase; UDP-glucuronate decarboxylase; glucokinase; glucose-6-phosphate isomerase; phosphomannomutase/phosphoglucomutase; UDP-glucose-4-epimerase; mannose-6-phosphate isomerase Azorhizobium, Magnetospira, Comamonadaceae bacterium A1, Terriglobus, Microterricola, Symbiobacterium, Sphingomonas, Kosakonia, Pseudomonas, Sphingobium, Thioploca, Achromobacter, Niastella, Raoultella
Starch and sucrose metabolism α-Glucosidase; β-glucosidase; trehalose-6-phosphate synthase; α, α-trehalase; maltose-α-d-glucosyltransferase/α-amylase; glycogen operon protein; α-d-glucan-1-α-d-glucosylmutase; UDP-glucuronate decarboxylase; isoamylase; glucokinase; glucose-6-phosphate isomerase; 4-α-glucanotransferase; cellulose synthase (UDP-forming); endoglucanase; endo-1,4-β-xylanase; phosphomannomutase/phosphoglucomutase, type II secretory pathway pullulanase PulA and related glycosidases (glycogen debranching enzyme) Citrobacter, Sphingobium, Agrobacterium, Azotobacter, Pseudomonas, Acidobacterium, Desulfurivibrio, Methylocella, Paraburkholderia, Sphingomonas, Thioploca, Achromobacter, Rhodospirillum, Terriglobus
Pyruvate metabolism Acetyl-CoA synthetase; pyruvate dehydrogenase E1 component; pyruvate dehydrogenase E1 component α-subunit; pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase); acetyl-CoA carboxylase carboxyl transferase α-subunit; acetyl-CoA carboxylase, biotin carboxylase subunit; aldehyde dehydrogenase (NAD+); succinyl-CoA:acetate-CoA transferase; l-lactate dehydrogenase (cytochrome); pyruvate dehydrogenase (quinone); glyoxylate/hydroxypyruvate reductase A; malate dehydrogenase; fumarate hydratase class I; fumarate reductase flavoprotein subunit; isopropylmalate synthase Azotobacter, Acidiphilium, Thauera, Methylobacterium, Stenotrophomonas, Dyella, Novosphingobium, Comamonas, Paracoccus, Azorhizobium, Sphingobium, Paraburkholderia, Xanthomonas, Steroidobacter, Frateuria
Glyoxylate and dicarboxylate metabolism Isocitrate lyase; malate dehydrogenase; aconitate hydratase 2/2-methylisocitrate dehydratase; acetoacetyl-CoA reductase; propionyl-CoA carboxylase β-chain; catalase; phosphoglycolate phosphatase; glycine dehydrogenase subunit 1 and 2; glyoxylate/hydroxypyruvate reductase A; formate dehydrogenase major subunit; formyltetrahydrofolate deformylase Sphingobium, Sphingomonas, Beijerinckia, Pseudomonas, Altererythrobacter, Xanthomonas, Novosphingobium, Caedibacter, Lysobacter, Caulobacter, Paraburkholderia, Rhizobium, Burkholderia
Propanoate metabolism Acetyl-CoA synthetase; acyl-CoA dehydrogenase; acrylyl-CoA reductase (NADPH); 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase/3-hydroxybutyryl-CoA epimerase/enoyl-CoA isomerase; acetyl-CoA carboxylase carboxyl transferase subunit alpha; acetyl-CoA carboxylase, biotin carboxylase subunit; propionyl-CoA carboxylase β-chain; aconitate hydratase 2/2-methylisocitrate dehydratase Azotobacter, Alkanivorax, Desulfurispirillum, Pseudomonas, Dyella, Novosphingobium, Sphingobium
Butanoate metabolism 3-Hydroxyacyl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase/3-hydroxybutyryl-CoA epimerase/enoyl-CoA isomerase; enoyl-CoA hydratase; butyryl-CoA dehydrogenase; poly (3-hydroxybutyrate) depolymerase; acetoacetyl-CoA reductase; fumarate reductase flavoprotein subunit; succinate semialdehyde dehydrogenase/glutarate semialdehyde dehydrogenase; succinyl-CoA:acetate CoA-transferase; acetolactate synthase I/II/II large subunit Novosphingobium, Cupriavidus, Xanthomonas, Pseudomonas,
Chloracidobacterium, Burkholderia,
Sphingomonas, Caedibacter, Steroidobacter, Chromohalobacter,
Azorhizobium,
Klebsiella
Sugar transport systems and signal transduction ABC-type sugar transport system, ATPase component; ABC-type sugar transport systems, permease components; ABC-type sugar transport system, periplasmic component; ribose transport system, substrate binding protein; l-fucose:H+ symporter permease; phosphotransferase system, HPr-related proteins; Na+/melibiose symporter and related transporters; sugar phosphate permease; TRAP-type C4-dicarboxylate transport system, small permease component; aerobic C4-dicarboxylate transport protein; maltoporin (maltose/maltodextrin high affinity phage lambda receptor protein); C4-dicarboxylate ABC transporter; histidine kinase regulating citrate/malate metabolism; histidine kinase regulating C4-dicarboxylate transport system Bradyrhizobium, Roseobacter, Hamadaea, Dyella, Kluyvera, Desulfosporosinus, Luteibacter, Sphingobium, Enterobacter, Burkholdera, Paraburkholderia, Pseudoxanthomonas, Sphingomonas, Klebsiella, Novosphingobium, Pseudomonas, Bosea