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["Transcriptional responses of the bacterium Burkholderia terrae BS001 to the fungal host Lyophyllum sp. strain Karsten under soil-mimicking conditions\n\nIrshad Ul Haq* Francisco Dini-Andreote and Jan Dirk van Elsas\nMicrobial Ecology, Groningen Institute of Evolutionary Life Sciences (GELIFES), Nijenborgh 7, 9747 AG, University of Groningen, The Netherlands.\n\n*Corresponding author: Irshad Ul Haq, Microbial Ecology, Groningen Institute of Evolutionary Life Sciences (GELIFES), Nijenborgh 7, 9747 AG, University of Groningen, The Netherlands.\nE‒mail address: i.u.haq@rug.nl\n"]
{"$rows_empty":10}
[null,null,"Microbial Ecology"]
[null,null,"List of differentially expressed genes involved in various KEGG pathways at time point 1 (day 3)"]
[]
["Label","Gene","Product","Log2 fold change","p-value","EC number","KEGG Pathways"]
["AKAUv1_1000053","ampC","Beta-lactamase",-1.69,0.0153,"3.5.2.6","311: Penicillin and cephalosporin biosynthesis"]
["AKAUv1_1010080","_","Beta-galactosidase",-2.08,{"v":0.000155,"d":"0.0002"},"3.2.1.23","52: Galactose metabolism531: Glycosaminoglycan degradation600: Sphingolipid metabolism604: Glycosphingolipid biosynthesis - ganglio series"]
["AKAUv1_1080047","fbpC","Fe(3+) ions import ATP-binding protein FbpC 2",-1.56,0.0231,"3.6.3.30","230: Purine metabolism680: Methane metabolism"]
["AKAUv1_1080148","_","Acetolactate synthase 3, chloroplastic",-1.61,{"v":0.00387,"d":"0.0039"},"2.2.1.6","10: Glycolysis / Gluconeogenesis20: Citrate cycle (TCA cycle)290: Valine, leucine and isoleucine biosynthesis620: Pyruvate metabolism650: Butanoate metabolism660: C5-Branched dibasic acid metabolism770: Pantothenate and CoA biosynthesis"]
["AKAUv1_1080319","FAH","Fumarylacetoacetase",-1.95,0.0132,"3.7.1.2","350: Tyrosine metabolism643: Styrene degradation"]
["AKAUv1_1080349","_","putative molybdopterin oxidoreductase, alpha subunit (fdhA)",-2.17,{"v":0.00284,"d":"0.0028"},"1.2.1.2","630: Glyoxylate and dicarboxylate metabolism680: Methane metabolism"]
["AKAUv1_1080422","ugpC","sn-glycerol-3-phosphate import ATP-binding protein UgpC",-1.67,{"v":0.00399,"d":"0.0040"},"3.6.3.20","230: Purine metabolism680: Methane metabolism"]
["AKAUv1_1080428","_","Acetate CoA-transferase YdiF",-2.34,{"v":0.00299,"d":"0.0030"},"2.8.3.8","627: Aminobenzoate degradation640: Propanoate metabolism650: Butanoate metabolism"]
["AKAUv1_1150004","_","putative Aldehyde dehydrogenase (NAD(+))",-1.56,0.0211,"1.2.1.3","10: Glycolysis / Gluconeogenesis40: Pentose and glucuronate interconversions53: Ascorbate and aldarate metabolism71: Fatty acid metabolism280: Valine, leucine and isoleucine degradation310: Lysine degradation330: Arginine and proline metabolism340: Histidine metabolism380: Tryptophan metabolism410: beta-Alanine metabolism561: Glycerolipid metabolism620: Pyruvate metabolism625: Chloroalkane and chloroalkene degradation640: Propanoate metabolism903: Limonene and pinene degradation"]
["AKAUv1_1250022","_","putative hydroxymethylglutaryl-CoA lyase",-1.67,0.0262,"4.1.3.4","72: Synthesis and degradation of ketone bodies280: Valine, leucine and isoleucine degradation281: Geraniol degradation650: Butanoate metabolism"]
["AKAUv1_1250053","tmd","Trimethylamine dehydrogenase",-2.63,{"v":0.000339,"d":"0.0003"},"1.5.8.2","680: Methane metabolism"]
["AKAUv1_1250061","prkB","phosphoribulokinase",-2.12,{"v":0.00643,"d":"0.0064"},"2.7.1.19","710: Carbon fixation in photosynthetic organisms"]
["AKAUv1_1250067","mch","Methenyltetrahydromethanopterin cyclohydrolase",-1.58,0.0343,"3.5.4.27","680: Methane metabolism"]
["AKAUv1_1250081","ffsA","Formylmethanofuran--tetrahydromethanopterin formyltransferase",-1.96,{"v":0.00616,"d":"0.0062"},"2.3.1.101","680: Methane metabolism"]
["AKAUv1_1250084","glyA","serine hydroxymethyltransferase",-2.3,{"v":0.00154,"d":"0.0015"},"2.1.2.1","260: Glycine, serine and threonine metabolism460: Cyanoamino acid metabolism630: Glyoxylate and dicarboxylate metabolism670: One carbon pool by folate680: Methane metabolism"]
["AKAUv1_1250085","sgaA","Serine--glyoxylate aminotransferase",-2.53,{"v":0.000948,"d":"0.0009"},"2.6.1.45","260: Glycine, serine and threonine metabolism630: Glyoxylate and dicarboxylate metabolism680: Methane metabolism"]
["AKAUv1_1250087","sucC","succinyl-CoA synthetase, beta subunit",-1.55,0.0225,"6.2.1.5","20: Citrate cycle (TCA cycle)640: Propanoate metabolism660: C5-Branched dibasic acid metabolism720: Carbon fixation pathways in prokaryotes"]
["AKAUv1_1250093","_","putative Glutamate synthase, large subunit region 2 FMN-binding (GlxD)",-2.12,{"v":0.00483,"d":"0.0048"},"1.4.1.13","250: Alanine, aspartate and glutamate metabolism330: Arginine and proline metabolism471: D-Glutamine and D-glutamate metabolism910: Nitrogen metabolism"]
["AKAUv1_1250096","glnT","glutamine synthetase III",-1.79,0.0273,"6.3.1.2","250: Alanine, aspartate and glutamate metabolism330: Arginine and proline metabolism630: Glyoxylate and dicarboxylate metabolism910: Nitrogen metabolism"]
["AKAUv1_1250100","soxB","sarcosine oxidase beta subunit",-1.56,{"v":0.00969,"d":"0.0097"},"1.5.3.1","260: Glycine, serine and threonine metabolism"]
["AKAUv1_1390086","amaB","N-carbamoyl-L-amino acid hydrolase",-2.28,{"v":0.00705,"d":"0.0071"},"3.5.1.87","340: Histidine metabolism"]
["AKAUv1_1470024","phbB","Acetoacetyl-CoA reductase",-1.76,0.0174,"1.1.1.36","62: Fatty acid elongation630: Glyoxylate and dicarboxylate metabolism650: Butanoate metabolism"]
["AKAUv1_160018","_","Long-chain-fatty-acid--CoA ligase",-2.18,{"v":0.00635,"d":"0.0064"},"6.2.1.3","71: Fatty acid metabolism"]
["AKAUv1_160022","_","2-dehydropantoate 2-reductase",-1.56,0.0231,"1.1.1.169","770: Pantothenate and CoA biosynthesis"]
["AKAUv1_160091","andAa","Anthranilate 1,2-dioxygenase system ferredoxin--NAD(+) reductase component",-1.98,0.0125,"1.18.1.3","71: Fatty acid metabolism"]
["AKAUv1_160094","andAc","Anthranilate 1,2-dioxygenase large subunit",-1.56,0.0146,"1.14.12.1","627: Aminobenzoate degradation"]
["AKAUv1_160113","fadA","3-ketoacyl-CoA thiolase",-1.51,0.0201,"2.3.1.16","62: Fatty acid elongation71: Fatty acid metabolism280: Valine, leucine and isoleucine degradation281: Geraniol degradation360: Phenylalanine metabolism362: Benzoate degradation592: alpha-Linolenic acid metabolism642: Ethylbenzene degradation1040: Biosynthesis of unsaturated fatty acids"]
["AKAUv1_1780022","alc","allantoicase",-1.85,0.0232,"3.5.3.4","230: Purine metabolism"]
["AKAUv1_1880013","nirB","nitrite reductase, large subunit, NAD(P)H-binding",-1.81,{"v":0.00411,"d":"0.0041"},"1.7.1.4","910: Nitrogen metabolism"]
["AKAUv1_1880024","cynT","carbonic anhydrase",-1.85,0.0137,"4.2.1.1","910: Nitrogen metabolism"]
["AKAUv1_1890016","fadA","3-ketoacyl-CoA thiolase, Acetyl-CoA acetyltransferase",-2.18,{"v":0.00635,"d":"0.0064"},"2.3.1.16, 2.3.1.9","62: Fatty acid elongation71: Fatty acid metabolism72: Synthesis and degradation of ketone bodies280: Valine, leucine and isoleucine degradation281: Geraniol degradation310: Lysine degradation360: Phenylalanine metabolism362: Benzoate degradation380: Tryptophan metabolism592: alpha-Linolenic acid metabolism620: Pyruvate metabolism630: Glyoxylate and dicarboxylate metabolism640: Propanoate metabolism642: Ethylbenzene degradation650: Butanoate metabolism720: Carbon fixation pathways in prokaryotes900: Terpenoid backbone biosynthesis1040: Biosynthesis of unsaturated fatty acids"]
["AKAUv1_1950003","maeB","putative fused malic enzyme oxidoreductase ; putative phosphotransacetylase",-2.11,0.0082,"1.1.1.40, 2.3.1.8","430: Taurine and hypotaurine metabolism620: Pyruvate metabolism640: Propanoate metabolism680: Methane metabolism710: Carbon fixation in photosynthetic organisms720: Carbon fixation pathways in prokaryotes"]
["AKAUv1_1950013","gcl","glyoxylate carboligase",-2.12,{"v":0.00608,"d":"0.0061"},"4.1.1.47","630: Glyoxylate and dicarboxylate metabolism"]
["AKAUv1_1950033","glcB","malate synthase G",-1.75,0.0262,"2.3.3.9","620: Pyruvate metabolism630: Glyoxylate and dicarboxylate metabolism"]
["AKAUv1_2290010","_","putative epoxide hydrolase",-1.79,{"v":0.00826,"d":"0.0083"},"3.3.2.10","590: Arachidonic acid metabolism625: Chloroalkane and chloroalkene degradation"]
["AKAUv1_2410029","kdpA","potassium translocating ATPase, subunit A",-1.57,0.0162,"3.6.3.12","230: Purine metabolism680: Methane metabolism"]
["AKAUv1_2430010","kbaZ","tagatose 6-phosphate aldolase 1, kbaZ subunit",-1.99,{"v":0.00925,"d":"0.0093"},"4.1.2.40","52: Galactose metabolism"]
["AKAUv1_2430012","polS","Sorbitol dehydrogenase",-1.8,0.0184,"1.1.1.14","51: Fructose and mannose metabolism"]
["AKAUv1_2480045","metE","5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase",-1.61,{"v":0.02,"d":"0.0200"},"2.1.1.14","270: Cysteine and methionine metabolism450: Selenocompound metabolism"]
["AKAUv1_2530033","phtD","4,5-dihydroxyphthalate decarboxylase",-1.73,0.0117,"4.1.1.55","624: Polycyclic aromatic hydrocarbon degradation"]
["AKAUv1_2530036","athL","Pyrogallol hydroxytransferase large subunit",-1.65,{"v":0.00412,"d":"0.0041"},"1.97.1.2","627: Aminobenzoate degradation"]
["AKAUv1_2560053","lldD","L-lactate dehydrogenase [cytochrome]",-1.62,0.0146,"1.1.2.3","620: Pyruvate metabolism"]
["AKAUv1_2560057","aldH","NADP-dependent fatty aldehyde dehydrogenase",-1.86,0.0317,"1.2.1.4","10: Glycolysis / Gluconeogenesis620: Pyruvate metabolism930: Caprolactam degradation"]
["AKAUv1_2570013","_","putative epoxide hydrolase",-1.84,{"v":0.00942,"d":"0.0094"},"3.3.2.10","590: Arachidonic acid metabolism625: Chloroalkane and chloroalkene degradation"]
["AKAUv1_2570046","OPR","12-oxophytodienoate reductase 3",-1.62,{"v":0.00956,"d":"0.0096"},"1.3.1.42","592: alpha-Linolenic acid metabolism"]
["AKAUv1_2570080","ALD","Aldehyde dehydrogenase 5, mitochondrial",-2.28,{"v":0.00893,"d":"0.0089"},"1.2.1.3, 1.2.1.4","10: Glycolysis / Gluconeogenesis40: Pentose and glucuronate interconversions53: Ascorbate and aldarate metabolism71: Fatty acid metabolism280: Valine, leucine and isoleucine degradation310: Lysine degradation330: Arginine and proline metabolism340: Histidine metabolism380: Tryptophan metabolism410: beta-Alanine metabolism561: Glycerolipid metabolism620: Pyruvate metabolism625: Chloroalkane and chloroalkene degradation640: Propanoate metabolism903: Limonene and pinene degradation930: Caprolactam degradation"]
["AKAUv1_2570132","aroE","Shikimate dehydrogenase",-1.95,0.0116,"1.1.1.25","400: Phenylalanine, tyrosine and tryptophan biosynthesis"]
["AKAUv1_2570213","ydiF","Acetate CoA-transferase YdiF",-1.79,{"v":0.00826,"d":"0.0083"},"2.8.3.8","627: Aminobenzoate degradation640: Propanoate metabolism650: Butanoate metabolism"]
["AKAUv1_2700025","acs","acetyl-CoA synthetase",-1.98,{"v":0.000643,"d":"0.0006"},"6.2.1.1","10: Glycolysis / Gluconeogenesis620: Pyruvate metabolism640: Propanoate metabolism680: Methane metabolism720: Carbon fixation pathways in prokaryotes"]
["AKAUv1_2820093","rbsA","Ribose import ATP-binding protein RbsA 1",-1.87,0.0199,"3.6.3.17","230: Purine metabolism680: Methane metabolism"]
["AKAUv1_3020034","_","putative hydroxymethylglutaryl-CoA lyase",-1.58,0.0343,"4.1.3.4","72: Synthesis and degradation of ketone bodies280: Valine, leucine and isoleucine degradation281: Geraniol degradation650: Butanoate metabolism"]
["AKAUv1_3020072","bgaA","Beta-galactosidase BgaA",-2.33,{"v":0.000507,"d":"0.0005"},"3.2.1.23","52: Galactose metabolism531: Glycosaminoglycan degradation600: Sphingolipid metabolism604: Glycosphingolipid biosynthesis - ganglio series"]
["AKAUv1_3180006","gapA","glyceraldehyde-3-phosphate dehydrogenase A",-1.85,0.0288,"1.2.1.12","10: Glycolysis / Gluconeogenesis710: Carbon fixation in photosynthetic organisms"]
["AKAUv1_3190102","HPR","Glyoxylate/hydroxypyruvate reductase A HPR2",-1.5,0.0225,"1.1.1.79, 1.1.1.81","260: Glycine, serine and threonine metabolism620: Pyruvate metabolism630: Glyoxylate and dicarboxylate metabolism680: Methane metabolism"]
["AKAUv1_3230016","glyA","serine hydroxymethyltransferase",-1.58,0.0343,"2.1.2.1","260: Glycine, serine and threonine metabolism460: Cyanoamino acid metabolism630: Glyoxylate and dicarboxylate metabolism670: One carbon pool by folate680: Methane metabolism"]
["AKAUv1_400022","hisC","Histidinol-phosphate aminotransferase 2",-1.69,0.0242,"2.6.1.9","130: Ubiquinone and other terpenoid-quinone biosynthesis340: Histidine metabolism350: Tyrosine metabolism360: Phenylalanine metabolism400: Phenylalanine, tyrosine and tryptophan biosynthesis401: Novobiocin biosynthesis950: Isoquinoline alkaloid biosynthesis960: Tropane, piperidine and pyridine alkaloid biosynthesis"]
["AKAUv1_430029","quiA","quinate/shikimate dehydrogenase [Pyrroloquinoline-quinone] (NAD(P)-independent quinate dehydrogenase)",-2.4,{"v":0.00369,"d":"0.0037"},"1.1.5.8","400: Phenylalanine, tyrosine and tryptophan biosynthesis"]
["AKAUv1_480002","trpC","indole-3-glycerol phosphate synthase (IGPS)",-1.68,{"v":0.01,"d":"0.0100"},"4.1.1.48","400: Phenylalanine, tyrosine and tryptophan biosynthesis"]
["AKAUv1_500017","tauD","Alpha-ketoglutarate-dependent taurine dioxygenase",-1.56,0.0231,"1.14.11.17","430: Taurine and hypotaurine metabolism"]
["AKAUv1_540006","dhaS","putative aldehyde dehydrogenase DhaS",-1.74,0.0192,"1.2.1.3","10: Glycolysis / Gluconeogenesis40: Pentose and glucuronate interconversions53: Ascorbate and aldarate metabolism71: Fatty acid metabolism280: Valine, leucine and isoleucine degradation310: Lysine degradation330: Arginine and proline metabolism340: Histidine metabolism380: Tryptophan metabolism410: beta-Alanine metabolism561: Glycerolipid metabolism620: Pyruvate metabolism625: Chloroalkane and chloroalkene degradation640: Propanoate metabolism903: Limonene and pinene degradation"]
["AKAUv1_540041","chqB","Hydroxyquinol 1,2-dioxygenase",-1.68,{"v":0.01,"d":"0.0100"},"1.13.11.37","361: Chlorocyclohexane and chlorobenzene degradation362: Benzoate degradation"]
["AKAUv1_540113","hbdH","D-beta-hydroxybutyrate dehydrogenase",-1.69,0.0153,"1.1.1.30","72: Synthesis and degradation of ketone bodies650: Butanoate metabolism"]
["AKAUv1_540134","fadD","Long-chain-fatty-acid--CoA ligase",-2.61,{"v":0.00101,"d":"0.0010"},"6.2.1.3","71: Fatty acid metabolism"]
["AKAUv1_760183","lpd","Dihydrolipoyl dehydrogenase 3",-1.79,{"v":0.014,"d":"0.0140"},"1.8.1.4","10: Glycolysis / Gluconeogenesis20: Citrate cycle (TCA cycle)260: Glycine, serine and threonine metabolism280: Valine, leucine and isoleucine degradation380: Tryptophan metabolism620: Pyruvate metabolism630: Glyoxylate and dicarboxylate metabolism910: Nitrogen metabolism"]
["AKAUv1_760397","dhaS","putative aldehyde dehydrogenase DhaS",-1.73,{"v":0.00894,"d":"0.0089"},"1.2.1.3","10: Glycolysis / Gluconeogenesis40: Pentose and glucuronate interconversions53: Ascorbate and aldarate metabolism71: Fatty acid metabolism280: Valine, leucine and isoleucine degradation310: Lysine degradation330: Arginine and proline metabolism340: Histidine metabolism380: Tryptophan metabolism410: beta-Alanine metabolism561: Glycerolipid metabolism620: Pyruvate metabolism625: Chloroalkane and chloroalkene degradation640: Propanoate metabolism903: Limonene and pinene degradation"]
["AKAUv1_840018","cysI","Sulfite reductase (NADPH) hemoprotein beta-component",-2.18,0.0031,"1.8.1.2","920: Sulfur metabolism"]
["AKAUv1_910021","pdxA","4-hydroxythreonine-4-phosphate dehydrogenase",-1.77,0.0267,"1.1.1.262","750: Vitamin B6 metabolism"]
["AKAUv1_910026","mhpF","acetaldehyde-CoA dehydrogenase II, NAD-binding",-1.84,0.0408,"1.2.1.10","362: Benzoate degradation620: Pyruvate metabolism621: Dioxin degradation622: Xylene degradation650: Butanoate metabolism"]
["AKAUv1_910033","fahd","Acylpyruvase FAHD1, mitochondrial",-1.69,0.0242,"3.7.1.5","350: Tyrosine metabolism"]
["AKAUv1_970064","kdpB","potassium translocating ATPase, subunit B",-1.58,0.0231,"3.6.3.12","230: Purine metabolism680: Methane metabolism"]