Experiment set12IT017 for Paraburkholderia graminis OAS925

Compare to:

RCH2_defined_glucose_5mM with caffeic acid 1 mM

Group: stress
Media: RCH2_defined_glucose_5mM + caffeic acid (1 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 21 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
ATP-dependent RNA helicases, bacterial 1
Fatty Acid Biosynthesis FASII 1
Glycerol and Glycerol-3-phosphate Uptake and Utilization 1
Glycerol fermenation to 1,3-propanediol 1
Ketoisovalerate oxidoreductase 1
Oxidative stress 1
Photorespiration (oxidative C2 cycle) 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Rhamnose containing glycans 1
Transport of Manganese 1
dTDP-rhamnose synthesis 1
linker unit-arabinogalactan 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
S-adenosyl-L-methionine biosynthesis 1 1 1
acetate and ATP formation from acetyl-CoA III 1 1 1
acetate conversion to acetyl-CoA 1 1 1
ethanol degradation IV 3 3 2
superoxide radicals degradation 2 2 1
methanol oxidation to formaldehyde IV 2 1 1
ferulate degradation 3 3 1
ethanol degradation II 3 3 1
superpathway of acetate utilization and formation 3 3 1
L-isoleucine biosynthesis V 3 2 1
umbelliferone biosynthesis 3 2 1
L-methionine degradation I (to L-homocysteine) 3 2 1
S-adenosyl-L-methionine salvage II 3 2 1
ethanol degradation III 3 2 1
ethene biosynthesis I (plants) 3 1 1
reactive oxygen species degradation 4 4 1
S-adenosyl-L-methionine salvage I 4 2 1
chitin deacetylation 4 2 1
xanthohumol biosynthesis 4 1 1
2'-deoxymugineic acid phytosiderophore biosynthesis 4 1 1
naringenin biosynthesis (engineered) 4 1 1
dTDP-β-L-rhamnose biosynthesis 5 5 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
4-coumarate degradation (aerobic) 5 2 1
superpathway of L-cysteine biosynthesis (mammalian) 5 2 1
phaselate biosynthesis 5 1 1
chlorogenic acid biosynthesis II 5 1 1
flavonoid biosynthesis 5 1 1
6-gingerol analog biosynthesis (engineered) 6 3 1
superpathway of bitter acids biosynthesis 18 3 3
adlupulone and adhumulone biosynthesis 6 1 1
lupulone and humulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
4-coumarate degradation (anaerobic) 6 1 1
L-cysteine biosynthesis VI (reverse transsulfuration) 7 3 1
chlorogenic acid biosynthesis I 8 1 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 6 1
reductive glycine pathway of autotrophic CO2 fixation 9 4 1
cis-geranyl-CoA degradation 9 2 1
avenanthramide biosynthesis 9 1 1
rosmarinic acid biosynthesis I 10 2 1
curcuminoid biosynthesis 10 1 1
O-antigen building blocks biosynthesis (E. coli) 11 10 1
L-methionine salvage cycle II (plants) 11 4 1
L-methionine salvage cycle III 11 3 1
L-methionine salvage cycle I (bacteria and plants) 12 5 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
superpathway of L-methionine salvage and degradation 16 7 1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis 19 5 1
suberin monomers biosynthesis 20 5 1
aspartate superpathway 25 22 1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 33 12 1