Experiment set2IT047 for Ralstonia sp. UNC404CL21Col

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4-Hydroxybenzoic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 4-Hydroxybenzoic Acid (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: CL21_ML4, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: RobinH_and_TrentonO on 13-Feb-19
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 4-Hydroxybenzoic Acid in Ralstonia sp. UNC404CL21Col

For carbon source 4-Hydroxybenzoic Acid across organisms

SEED Subsystems

Subsystem #Specific
Protocatechuate branch of beta-ketoadipate pathway 3
Catechol branch of beta-ketoadipate pathway 1
Chloroaromatic degradation pathway 1
NAD and NADP cofactor biosynthesis global 1
NAD regulation 1
Redox-dependent regulation of nucleus processes 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
protocatechuate degradation II (ortho-cleavage pathway) 4 4 3
toluene degradation III (aerobic) (via p-cresol) 11 7 4
aromatic compounds degradation via β-ketoadipate 9 9 3
catechol degradation to β-ketoadipate 4 4 1
4-chlorobenzoate degradation 4 2 1
4-sulfocatechol degradation 4 1 1
4-methylphenol degradation to protocatechuate 4 1 1
NAD salvage pathway V (PNC V cycle) 5 4 1
gallate degradation II 5 2 1
4-coumarate degradation (aerobic) 5 2 1
bisphenol A degradation 5 1 1
catechol degradation III (ortho-cleavage pathway) 6 6 1
4-hydroxymandelate degradation 6 2 1
superpathway of salicylate degradation 7 7 1
NAD salvage pathway I (PNC VI cycle) 7 6 1
4-methylcatechol degradation (ortho cleavage) 7 4 1
spongiadioxin C biosynthesis 7 2 1
superpathway of aerobic toluene degradation 30 9 4
polybrominated dihydroxylated diphenyl ethers biosynthesis 8 2 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 18 4
NAD salvage (plants) 11 6 1
superpathway of NAD biosynthesis in eukaryotes 14 9 1
mandelate degradation to acetyl-CoA 18 9 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 11 1