Experiment set12IT036 for Paraburkholderia graminis OAS925

Compare to:

RCH2_defined_glucose_5mM with Lumazine 5 mM

Group: stress
Media: RCH2_defined_glucose_5mM + Lumazine (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 24 genes in this experiment

For stress Lumazine in Paraburkholderia graminis OAS925

For stress Lumazine across organisms

SEED Subsystems

Subsystem #Specific
Purine Utilization 3
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 2
Bacterial Chemotaxis 1
D-ribose utilization 1
Glycine reductase, sarcosine reductase and betaine reductase 1
Glycolate, glyoxylate interconversions 1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 1
Photorespiration (oxidative C2 cycle) 1
Ribosome biogenesis bacterial 1
TCA Cycle 1
Thioredoxin-disulfide reductase 1
Wyeosine-MimG Biosynthesis 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
glycolate and glyoxylate degradation II 2 2 1
pseudouridine degradation 2 1 1
thioredoxin pathway 2 1 1
adenosine nucleotides degradation II 5 4 2
glycolate and glyoxylate degradation III 3 1 1
Ac/N-end rule pathway 21 6 6
guanosine nucleotides degradation II 4 4 1
adenosine nucleotides degradation I 8 7 2
glycolate and glyoxylate degradation I 4 3 1
inosine 5'-phosphate degradation 4 3 1
guanosine nucleotides degradation I 4 3 1
guanosine nucleotides degradation III 4 3 1
cytosolic NADPH production (yeast) 5 4 1
purine nucleotides degradation II (aerobic) 11 8 2
purine nucleotides degradation I (plants) 12 10 2
superpathway of guanosine nucleotides degradation (plants) 6 5 1
purine nucleobases degradation II (anaerobic) 24 16 4
ureide biosynthesis 7 5 1
superpathway of glycol metabolism and degradation 7 5 1
caffeine degradation III (bacteria, via demethylation) 7 1 1
partial TCA cycle (obligate autotrophs) 8 7 1
nitrogen remobilization from senescing leaves 8 6 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 6 1
TCA cycle V (2-oxoglutarate synthase) 9 8 1
superpathway of purines degradation in plants 18 14 2
TCA cycle IV (2-oxoglutarate decarboxylase) 9 7 1
photorespiration I 9 6 1
TCA cycle VII (acetate-producers) 9 6 1
TCA cycle VI (Helicobacter) 9 6 1
photorespiration III 9 6 1
theophylline degradation 9 1 1
TCA cycle I (prokaryotic) 10 8 1
photorespiration II 10 6 1
caffeine degradation IV (bacteria, via demethylation and oxidation) 10 1 1
reductive TCA cycle I 11 6 1
superpathway of glyoxylate bypass and TCA 12 10 1
Arg/N-end rule pathway (eukaryotic) 14 8 1
mixed acid fermentation 16 12 1
methylaspartate cycle 19 11 1
ethene biosynthesis V (engineered) 25 19 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 1