Experiment set6IT015 for Paraburkholderia bryophila 376MFSha3.1

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p-Coumaric acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + p-Coumaric acid (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Burk376_ML3, 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 7 genes in this experiment

For carbon source p-Coumaric acid in Paraburkholderia bryophila 376MFSha3.1

For carbon source p-Coumaric acid across organisms

SEED Subsystems

Subsystem #Specific
Phenylpropanoid compound degradation 2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
N-heterocyclic aromatic compound 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
vanillin and vanillate degradation II 2 2 1
vanillin and vanillate degradation I 2 1 1
4-coumarate degradation (aerobic) 5 2 2
ferulate degradation 3 3 1
cardiolipin biosynthesis II 3 3 1
umbelliferone biosynthesis 3 2 1
cardiolipin biosynthesis I 3 2 1
cardiolipin biosynthesis III 3 2 1
4-chlorobenzoate degradation 4 2 1
xanthohumol biosynthesis 4 1 1
4-methylphenol degradation to protocatechuate 4 1 1
naringenin biosynthesis (engineered) 4 1 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
bisphenol A degradation 5 1 1
chlorogenic acid biosynthesis II 5 1 1
phaselate biosynthesis 5 1 1
flavonoid biosynthesis 5 1 1
phosphatidylglycerol biosynthesis II 6 6 1
phosphatidylglycerol biosynthesis I 6 6 1
6-gingerol analog biosynthesis (engineered) 6 3 1
4-hydroxymandelate degradation 6 2 1
4-coumarate degradation (anaerobic) 6 2 1
spongiadioxin C biosynthesis 7 2 1
polybrominated dihydroxylated diphenyl ethers biosynthesis 8 2 1
chlorogenic acid biosynthesis I 8 1 1
avenanthramide biosynthesis 9 1 1
superpathway of vanillin and vanillate degradation 10 7 1
pinoresinol degradation 10 2 1
rosmarinic acid biosynthesis I 10 2 1
curcuminoid biosynthesis 10 1 1
toluene degradation III (aerobic) (via p-cresol) 11 7 1
superpathway of phospholipid biosynthesis III (E. coli) 12 10 1
superpathway of cardiolipin biosynthesis (bacteria) 13 9 1
coumarins biosynthesis (engineered) 13 5 1
superpathway of rosmarinic acid biosynthesis 14 3 1
flavonoid di-C-glucosylation 15 3 1
monolignol biosynthesis 15 1 1
type I lipoteichoic acid biosynthesis (S. aureus) 17 5 1
suberin monomers biosynthesis 20 3 1
superpathway of phospholipid biosynthesis II (plants) 28 10 1
superpathway of aerobic toluene degradation 30 16 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 22 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 18 1