Experiment set12IT018 for Paraburkholderia graminis OAS925

Compare to:

RCH2_defined_glucose_5mM with caffeic acid 0.5 mM

Group: stress
Media: RCH2_defined_glucose_5mM + caffeic acid (0.5 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Burkholderia_OAS925_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Albina on 15-Mar-22
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 5 mM D-Glucose, 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 12 genes in this experiment

For stress caffeic acid in Paraburkholderia graminis OAS925

For stress caffeic acid across organisms

SEED Subsystems

Subsystem #Specific
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 2
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 1
Copper homeostasis: copper tolerance 1
Folate Biosynthesis 1
Glycerol and Glycerol-3-phosphate Uptake and Utilization 1
Glycerol fermenation to 1,3-propanediol 1
Oxidative stress 1
Phosphate metabolism 1
Photorespiration (oxidative C2 cycle) 1
Transport of Manganese 1
Tryptophan synthesis 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
L-glutamine degradation I 1 1 1
L-glutamate biosynthesis I 2 2 1
4-aminobenzoate biosynthesis I 2 2 1
superoxide radicals degradation 2 2 1
methanol oxidation to formaldehyde IV 2 1 1
ethanol degradation IV 3 3 1
ferulate degradation 3 3 1
ammonia assimilation cycle III 3 3 1
umbelliferone biosynthesis 3 2 1
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
reactive oxygen species degradation 4 4 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
naringenin biosynthesis (engineered) 4 1 1
xanthohumol biosynthesis 4 1 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
4-coumarate degradation (aerobic) 5 2 1
flavonoid biosynthesis 5 1 1
phaselate biosynthesis 5 1 1
chlorogenic acid biosynthesis II 5 1 1
6-gingerol analog biosynthesis (engineered) 6 3 1
4-coumarate degradation (anaerobic) 6 1 1
L-glutamate and L-glutamine biosynthesis 7 7 1
L-citrulline biosynthesis 8 7 1
chlorogenic acid biosynthesis I 8 1 1
chloramphenicol biosynthesis 9 1 1
avenanthramide biosynthesis 9 1 1
superpathway of tetrahydrofolate biosynthesis 10 9 1
rosmarinic acid biosynthesis I 10 2 1
curcuminoid biosynthesis 10 1 1
superpathway of candicidin biosynthesis 11 4 1
superpathway of tetrahydrofolate biosynthesis and salvage 12 11 1
superpathway of L-citrulline metabolism 12 9 1
coumarins biosynthesis (engineered) 13 5 1
superpathway of rosmarinic acid biosynthesis 14 2 1
flavonoid di-C-glucosylation 15 3 1
monolignol biosynthesis 15 1 1
suberin monomers biosynthesis 20 5 1
superpathway of chorismate metabolism 59 42 1