Experiment set1IT072 for Variovorax sp. OAS795

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4-Hydroxybenzoic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 4-Hydroxybenzoic Acid (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 4-Hydroxybenzoic Acid in Variovorax sp. OAS795

For carbon source 4-Hydroxybenzoic Acid across organisms

SEED Subsystems

Subsystem #Specific
Protocatechuate branch of beta-ketoadipate pathway 5
Glycerol and Glycerol-3-phosphate Uptake and Utilization 3
Catechol branch of beta-ketoadipate pathway 2
Chloroaromatic degradation pathway 2
Alanine biosynthesis 1
Branched-Chain Amino Acid Biosynthesis 1
Cobalt-zinc-cadmium resistance 1
Conserved gene cluster associated with Met-tRNA formyltransferase 1
Histidine Biosynthesis 1
Hydantoin metabolism 1
Isoleucine degradation 1
Leucine Biosynthesis 1
Leucine Degradation and HMG-CoA Metabolism 1
Polyhydroxybutyrate metabolism 1
Protein degradation 1
Pyruvate Alanine Serine Interconversions 1
Valine degradation 1
p-Hydroxybenzoate degradation 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
cis-cyclopropane fatty acid (CFA) biosynthesis 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
protocatechuate degradation II (ortho-cleavage pathway) 4 4 2
L-alanine biosynthesis I 2 2 1
3-oxoadipate degradation 2 2 1
atromentin biosynthesis 2 1 1
sterculate biosynthesis 2 1 1
L-tyrosine degradation II 2 1 1
toluene degradation III (aerobic) (via p-cresol) 11 7 4
L-tyrosine biosynthesis I 3 3 1
L-phenylalanine biosynthesis I 3 3 1
aromatic compounds degradation via β-ketoadipate 9 8 3
L-isoleucine degradation II 3 2 1
L-valine degradation II 3 2 1
L-isoleucine biosynthesis V 3 2 1
L-leucine degradation III 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
L-leucine degradation V (oxidative Stickland reaction) 3 1 1
L-valine degradation III (oxidative Stickland reaction) 3 1 1
L-isoleucine degradation III (oxidative Stickland reaction) 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
L-valine biosynthesis 4 4 1
superpathway of L-alanine biosynthesis 4 4 1
L-tyrosine degradation III 4 2 1
4-chlorobenzoate degradation 4 2 1
L-phenylalanine degradation III 4 2 1
4-sulfocatechol degradation 4 2 1
4-methylphenol degradation to protocatechuate 4 1 1
4-coumarate degradation (aerobic) 5 5 1
adipate degradation 5 5 1
L-tyrosine degradation I 5 5 1
adipate biosynthesis 5 5 1
gallate degradation II 5 3 1
superpathway of plastoquinol biosynthesis 5 2 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
bisphenol A degradation 5 1 1
L-leucine degradation IV (reductive Stickland reaction) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
superpathway of branched chain amino acid biosynthesis 17 17 3
L-leucine biosynthesis 6 6 1
catechol degradation III (ortho-cleavage pathway) 6 5 1
L-leucine degradation I 6 5 1
L-isoleucine biosynthesis IV 6 4 1
L-isoleucine degradation I 6 4 1
4-hydroxymandelate degradation 6 4 1
L-isoleucine biosynthesis I (from threonine) 7 7 1
superpathway of salicylate degradation 7 6 1
L-isoleucine biosynthesis III 7 4 1
4-methylcatechol degradation (ortho cleavage) 7 4 1
spongiadioxin C biosynthesis 7 1 1
superpathway of aerobic toluene degradation 30 16 4
L-isoleucine biosynthesis II 8 6 1
L-valine degradation I 8 6 1
polybrominated dihydroxylated diphenyl ethers biosynthesis 8 1 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 25 4
superpathway of aromatic amino acid biosynthesis 18 18 2
L-phenylalanine degradation IV (mammalian, via side chain) 9 4 1
L-histidine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 3 1
(S)-reticuline biosynthesis I 11 1 1
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of rosmarinic acid biosynthesis 14 4 1
superpathway of L-threonine metabolism 18 15 1
mandelate degradation to acetyl-CoA 18 14 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 7 1
superpathway of chorismate metabolism 59 40 2
even iso-branched-chain fatty acid biosynthesis 34 31 1
odd iso-branched-chain fatty acid biosynthesis 34 31 1
anteiso-branched-chain fatty acid biosynthesis 34 31 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 22 1
superpathway of histidine, purine, and pyrimidine biosynthesis 46 43 1
mycolate biosynthesis 205 26 3
superpathway of mycolate biosynthesis 239 27 3