Experiment set1IT041 for Variovorax sp. OAS795

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L-tyrosine disodium salt carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-tyrosine disodium salt (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 10 genes in this experiment

For carbon source L-tyrosine disodium salt in Variovorax sp. OAS795

For carbon source L-tyrosine disodium salt across organisms

SEED Subsystems

Subsystem #Specific
Choline and Betaine Uptake and Betaine Biosynthesis 2
CO Dehydrogenase 1
Carbon monoxide dehydrogenase maturation factors 1
DNA-binding regulatory proteins, strays 1
Maltose and Maltodextrin Utilization 1
Oxidative stress 1
Purine Utilization 1
Thioredoxin-disulfide reductase 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
choline degradation I 2 2 1
glycine betaine biosynthesis II (Gram-positive bacteria) 2 2 1
glycine betaine biosynthesis I (Gram-negative bacteria) 2 2 1
trehalose degradation II (cytosolic) 2 1 1
trehalose degradation I (low osmolarity) 2 1 1
adenosine nucleotides degradation II 5 4 2
choline-O-sulfate degradation 3 3 1
trehalose degradation V 3 2 1
oxalate degradation II 3 2 1
GDP-α-D-glucose biosynthesis 3 2 1
trehalose degradation IV 3 2 1
guanosine nucleotides degradation II 4 4 1
adenosine nucleotides degradation I 8 7 2
sucrose degradation III (sucrose invertase) 4 3 1
inosine 5'-phosphate degradation 4 3 1
guanosine nucleotides degradation I 4 3 1
guanosine nucleotides degradation III 4 3 1
acrylate degradation I 5 5 1
octane oxidation 5 4 1
propanoyl-CoA degradation II 5 4 1
glucose and glucose-1-phosphate degradation 5 4 1
purine nucleotides degradation II (aerobic) 11 8 2
purine nucleotides degradation I (plants) 12 10 2
superpathway of guanosine nucleotides degradation (plants) 6 5 1
glycogen degradation II 6 5 1
β-alanine biosynthesis II 6 5 1
UDP-N-acetyl-D-glucosamine biosynthesis II 6 4 1
purine nucleobases degradation II (anaerobic) 24 15 4
6-gingerol analog biosynthesis (engineered) 6 3 1
ureide biosynthesis 7 5 1
UDP-N-acetyl-D-galactosamine biosynthesis II 7 4 1
caffeine degradation III (bacteria, via demethylation) 7 2 1
glycogen degradation I 8 7 1
sucrose biosynthesis II 8 6 1
superpathway of purines degradation in plants 18 12 2
chitin biosynthesis 9 5 1
1,3-propanediol biosynthesis (engineered) 9 5 1
theophylline degradation 9 1 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 1
caffeine degradation IV (bacteria, via demethylation and oxidation) 10 2 1
glycolysis III (from glucose) 11 11 1
homolactic fermentation 12 11 1
Bifidobacterium shunt 15 14 1
heterolactic fermentation 18 15 1