Experiment set8IT036 for Burkholderia phytofirmans PsJN

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Phenylacetic acid 5 mM carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Phenylacetic acid (5 mM), pH=7
Culturing: BFirm_ML3a, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Growth plate: Bfirm_deoxyribosePlus_plate D5

Specific Phenotypes

For 8 genes in this experiment

For carbon source Phenylacetic acid in Burkholderia phytofirmans PsJN

For carbon source Phenylacetic acid across organisms

SEED Subsystems

Subsystem #Specific
Aromatic amino acid interconversions with aryl acids 2
Aromatic Amin Catabolism 1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
benzoyl-CoA biosynthesis 3 3 2
phenylacetate degradation I (aerobic) 9 9 5
3-oxoadipate degradation 2 2 1
acetoacetate degradation (to acetyl CoA) 2 2 1
superpathway of phenylethylamine degradation 11 11 5
2-methyl-branched fatty acid β-oxidation 14 9 6
adipate degradation 5 5 2
adipate biosynthesis 5 4 2
5,6-dehydrokavain biosynthesis (engineered) 10 6 4
fatty acid β-oxidation II (plant peroxisome) 5 3 2
ketolysis 3 3 1
ethanol degradation II 3 3 1
polyhydroxybutanoate biosynthesis 3 3 1
ethanol degradation IV 3 3 1
valproate β-oxidation 9 6 3
ethanol degradation III 3 2 1
hypotaurine degradation 3 2 1
histamine degradation 3 1 1
oleate β-oxidation 35 29 11
benzoyl-CoA degradation I (aerobic) 7 6 2
fatty acid β-oxidation I (generic) 7 5 2
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 2
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 3
phytol degradation 4 3 1
(2S)-ethylmalonyl-CoA biosynthesis 4 3 1
putrescine degradation III 4 2 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
penicillin G and penicillin V biosynthesis 4 1 1
phenylacetate degradation II (anaerobic) 4 1 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 5 2
ketogenesis 5 4 1
pyruvate fermentation to acetone 5 3 1
4-hydroxybenzoate biosynthesis III (plants) 5 3 1
glutaryl-CoA degradation 5 3 1
fatty acid β-oxidation IV (unsaturated, even number) 5 3 1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 3 1
octane oxidation 5 3 1
mitochondrial NADPH production (yeast) 5 3 1
3-phenylpropanoate degradation 10 5 2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 2
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
dopamine degradation 5 2 1
isopropanol biosynthesis (engineered) 5 2 1
fatty acid β-oxidation VII (yeast peroxisome) 5 1 1
ethylbenzene degradation (anaerobic) 5 1 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 1 1
pyruvate fermentation to hexanol (engineered) 11 7 2
catechol degradation III (ortho-cleavage pathway) 6 6 1
fatty acid salvage 6 5 1
L-isoleucine degradation I 6 4 1
propanoate fermentation to 2-methylbutanoate 6 4 1
pyruvate fermentation to butanol II (engineered) 6 4 1
methyl ketone biosynthesis (engineered) 6 3 1
3-methyl-branched fatty acid α-oxidation 6 3 1
4-ethylphenol degradation (anaerobic) 6 1 1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast) 6 1 1
alkane oxidation 6 1 1
jasmonic acid biosynthesis 19 5 3
noradrenaline and adrenaline degradation 13 4 2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 2
superpathway of salicylate degradation 7 7 1
acetyl-CoA fermentation to butanoate 7 6 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 2
4-methylcatechol degradation (ortho cleavage) 7 4 1
pyruvate fermentation to butanoate 7 3 1
serotonin degradation 7 3 1
ceramide degradation by α-oxidation 7 2 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 2
mevalonate pathway II (haloarchaea) 7 1 1
mevalonate pathway I (eukaryotes and bacteria) 7 1 1
limonene degradation IV (anaerobic) 7 1 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 6 1
2-deoxy-D-ribose degradation II 8 5 1
pyruvate fermentation to butanol I 8 4 1
aromatic biogenic amine degradation (bacteria) 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
2-methylpropene degradation 8 2 1
mevalonate pathway III (Thermoplasma) 8 1 1
isoprene biosynthesis II (engineered) 8 1 1
mevalonate pathway IV (archaea) 8 1 1
androstenedione degradation I (aerobic) 25 6 3
aromatic compounds degradation via β-ketoadipate 9 9 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 6 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 1
benzoyl-CoA degradation III (anaerobic) 9 3 1
4-oxopentanoate degradation 9 2 1
superpathway of testosterone and androsterone degradation 28 6 3
L-glutamate degradation V (via hydroxyglutarate) 10 5 1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) 10 4 1
L-lysine fermentation to acetate and butanoate 10 3 1
methyl tert-butyl ether degradation 10 3 1
superpathway of cholesterol degradation I (cholesterol oxidase) 42 9 4
toluene degradation III (aerobic) (via p-cresol) 11 7 1
ethylmalonyl-CoA pathway 11 3 1
Spodoptera littoralis pheromone biosynthesis 22 4 2
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 9 4
L-glutamate degradation VII (to butanoate) 12 3 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 8 1
platensimycin biosynthesis 26 6 2
androstenedione degradation II (anaerobic) 27 4 2
L-tryptophan degradation III (eukaryotic) 15 10 1
glycerol degradation to butanol 16 11 1
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 3 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 10 1
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 4 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 3 1
mandelate degradation to acetyl-CoA 18 12 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 9 1
toluene degradation VI (anaerobic) 18 3 1
sitosterol degradation to androstenedione 18 1 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 3 1
superpathway of cholesterol degradation III (oxidase) 49 5 2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 18 1
superpathway of ergosterol biosynthesis I 26 5 1
1-butanol autotrophic biosynthesis (engineered) 27 19 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 5 1
superpathway of aerobic toluene degradation 30 14 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 21 1
superpathway of cholesterol biosynthesis 38 5 1
superpathway of L-lysine degradation 43 11 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 1