Experiment set1IT088 for Variovorax sp. OAS795

L-Phenylalanine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Phenylalanine (20 mM)
Culturing: Variovorax_OAS795_ML2, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Marta on 10-Apr-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 21 genes in this experiment

For carbon source L-Phenylalanine in Variovorax sp. OAS795

For carbon source L-Phenylalanine across organisms

SEED Subsystems

Subsystem	#Specific
Homogentisate pathway of aromatic compound degradation	3
Aromatic amino acid degradation	2
Folate Biosynthesis	2
Heat shock dnaK gene cluster extended	2
Queuosine-Archaeosine Biosynthesis	2
Salicylate and gentisate catabolism	2
Heme and Siroheme Biosynthesis	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Phosphate metabolism	1
Plastoquinone Biosynthesis	1
Pterin biosynthesis	1
Salicylate ester degradation	1
Tocopherol Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Styrene degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Biosynthesis of plant hormones
• Bile acid biosynthesis
• Histidine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Lipopolysaccharide biosynthesis
• Toluene and xylene degradation
• 2,4-Dichlorobenzoate degradation
• 1,4-Dichlorobenzene degradation
• Fluorene degradation
• Benzoate degradation via CoA ligation
• Methane metabolism
• Thiamine metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
methylsalicylate degradation	2	2	2
L-tyrosine biosynthesis IV	1	1	1
salicylate degradation I	1	1	1
L-phenylalanine degradation I (aerobic)	1	1	1
L-tyrosine degradation I	5	5	3
vanillin and vanillate degradation II	2	2	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
tetrahydrofolate biosynthesis I	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-phenylalanine degradation V	3	2	1
plastoquinol-9 biosynthesis I	3	1	1
UTP and CTP dephosphorylation I	7	5	2
chlorosalicylate degradation	7	3	2
L-phenylalanine biosynthesis II	4	2	1
superpathway of tetrahydrofolate biosynthesis	10	8	2
6-hydroxymethyl-dihydropterin diphosphate biosynthesis I	5	4	1
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	2
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	6	1
superpathway of salicylate degradation	7	6	1
vitamin E biosynthesis (tocopherols)	7	1	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	6	1
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	9	1
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	8	1
folate transformations III (E. coli)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
superpathway of L-phenylalanine biosynthesis	10	10	1
folate transformations II (plants)	11	8	1
naphthalene degradation to acetyl-CoA	12	6	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	12	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	17	1
superpathway of chorismate metabolism	59	40	3
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	22	1