Experiment set12IT059 for Cupriavidus basilensis FW507-4G11

Carbon source Phenylacetic acid 2.5 mM

Group: carbon source
Media: RCH2_defined_noCarbon + Phenylacetic acid (2.5 mM), pH=7
Culturing: cupriavidus_4G11_ML11, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 4-Aug-21
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)

Specific Phenotypes

For 8 genes in this experiment

For carbon source Phenylacetic acid in Cupriavidus basilensis FW507-4G11

For carbon source Phenylacetic acid across organisms

SEED Subsystems

Subsystem	#Specific
Polyhydroxybutyrate metabolism	3
Acetyl-CoA fermentation to Butyrate	2
Isoleucine degradation	2
Valine degradation	2
n-Phenylalkanoic acid degradation	2
Aromatic Amin Catabolism	1
Aromatic amino acid interconversions with aryl acids	1
Butanol Biosynthesis	1
Purine conversions	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Butanoate metabolism
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Tryptophan metabolism
• Benzoate degradation via CoA ligation
• Ascorbate and aldarate metabolism
• Fatty acid elongation in mitochondria
• Geraniol degradation
• beta-Alanine metabolism
• Propanoate metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Bile acid biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• 2,4-Dichlorobenzoate degradation
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Retinol metabolism
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
benzoyl-CoA biosynthesis	3	3	2
phenylacetate degradation I (aerobic)	9	7	4
adipate biosynthesis	5	5	2
adipate degradation	5	5	2
oleate β-oxidation	35	29	14
fatty acid β-oxidation II (plant peroxisome)	5	3	2
glutaryl-CoA degradation	5	3	2
superpathway of phenylethylamine degradation	11	9	4
pyruvate fermentation to hexanol (engineered)	11	7	4
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	4
2-methyl-branched fatty acid β-oxidation	14	10	5
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
fatty acid salvage	6	5	2
valproate β-oxidation	9	6	3
L-isoleucine degradation I	6	4	2
propanoate fermentation to 2-methylbutanoate	6	4	2
pyruvate fermentation to butanol II (engineered)	6	4	2
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
methyl ketone biosynthesis (engineered)	6	3	2
histamine degradation	3	1	1
benzoyl-CoA degradation I (aerobic)	7	6	2
fatty acid β-oxidation I (generic)	7	5	2
pyruvate fermentation to butanoate	7	4	2
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	2
L-valine degradation I	8	6	2
phytol degradation	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
putrescine degradation III	4	2	1
pyruvate fermentation to butanol I	8	3	2
phenylacetate degradation II (anaerobic)	4	1	1
penicillin G and penicillin V biosynthesis	4	1	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	6	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	2
mitochondrial NADPH production (yeast)	5	4	1
4-hydroxybenzoate biosynthesis III (plants)	5	4	1
octane oxidation	5	4	1
L-glutamate degradation V (via hydroxyglutarate)	10	7	2
3-phenylpropanoate degradation	10	6	2
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	3	1
fatty acid β-oxidation IV (unsaturated, even number)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
6-gingerol analog biosynthesis (engineered)	6	3	1
L-glutamate degradation VII (to butanoate)	12	4	2
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	7	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
serotonin degradation	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
Spodoptera littoralis pheromone biosynthesis	22	4	3
L-tryptophan degradation III (eukaryotic)	15	10	2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
glycerol degradation to butanol	16	9	2
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	6	2
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-methylpropene degradation	8	2	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	10	2
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	7	2
benzoyl-CoA degradation III (anaerobic)	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	2
toluene degradation VI (anaerobic)	18	5	2
methyl tert-butyl ether degradation	10	3	1
gallate degradation III (anaerobic)	11	5	1
androstenedione degradation I (aerobic)	25	16	2
platensimycin biosynthesis	26	7	2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
1-butanol autotrophic biosynthesis (engineered)	27	18	2
androstenedione degradation II (anaerobic)	27	10	2
superpathway of testosterone and androsterone degradation	28	17	2
superpathway of cholesterol degradation I (cholesterol oxidase)	42	20	3
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	20	3
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	4	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	4	1
superpathway of cholesterol degradation III (oxidase)	49	12	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	17	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	7	1