Experiment set12IT031 for Paraburkholderia graminis OAS925

RCH2_defined_glucose_5mM with Indole-3-pyruvic acid 1 mM

Group: stress
Media: RCH2_defined_glucose_5mM + Indole-3-pyruvic 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 Indole-3-pyruvic acid in Paraburkholderia graminis OAS925

For stress Indole-3-pyruvic acid across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
TCA Cycle	2
Copper homeostasis: copper tolerance	1
Methylcitrate cycle	1
Oxidative stress	1
Pentose phosphate pathway	1
Phosphate metabolism	1
Phosphonate metabolism	1
Phosphorylcholine incorporation in LPS	1
Photorespiration (oxidative C2 cycle)	1
Propionate-CoA to Succinate Module	1
Transport of Manganese	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Aminophosphonate metabolism
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Lysine degradation
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Pentose phosphate pathway
• Methionine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Glutathione metabolism
• High-mannose type N-glycan biosynthesis
• Sphingolipid metabolism
• Propanoate metabolism
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Caprolactam degradation
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-aminoethylphosphonate biosynthesis	3	3	3
cardiolipin biosynthesis II	3	3	2
superoxide radicals degradation	2	2	1
2-aminoethylphosphonate degradation II	2	2	1
methylphosphonate biosynthesis	4	2	2
methanol oxidation to formaldehyde IV	2	1	1
ethanol degradation IV	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
cardiolipin biosynthesis I	3	2	1
2-aminoethylphosphonate degradation I	3	2	1
cardiolipin biosynthesis III	3	2	1
fosfomycin biosynthesis	7	2	2
reactive oxygen species degradation	4	4	1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
2-methylcitrate cycle I	5	5	1
phosphatidylglycerol biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
2-methylcitrate cycle II	6	5	1
rhizocticin A and B biosynthesis	12	2	2
superpathway of cardiolipin biosynthesis (bacteria)	13	9	2
dehydrophos biosynthesis	13	2	2
pyruvate fermentation to propanoate I	7	3	1
incomplete reductive TCA cycle	7	3	1
pentose phosphate pathway	8	8	1
partial TCA cycle (obligate autotrophs)	8	7	1
TCA cycle V (2-oxoglutarate synthase)	9	8	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle II (plants and fungi)	9	7	1
TCA cycle VII (acetate-producers)	9	6	1
TCA cycle VI (Helicobacter)	9	6	1
nicotinate degradation III	9	3	1
TCA cycle I (prokaryotic)	10	8	1
TCA cycle III (animals)	10	7	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
FR-900098 and FR-33289 antibiotics biosynthesis	10	1	1
reductive TCA cycle I	11	6	1
L-glutamate degradation VIII (to propanoate)	11	3	1
superpathway of glyoxylate bypass and TCA	12	10	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	1
reductive TCA cycle II	12	6	1
phosalacine biosynthesis	25	6	2
phosphinothricin tripeptide biosynthesis	25	6	2
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
mixed acid fermentation	16	12	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
superpathway of nicotinate degradation	18	4	1
methylaspartate cycle	19	11	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of phospholipid biosynthesis II (plants)	28	10	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1