Experiment set12IT054 for Paraburkholderia graminis OAS925

RCH2_defined_glucose_5mM with Adenine 4 mM

Group: stress
Media: RCH2_defined_glucose_5mM + Adenine hydrochloride hydrate (4 mM) + Potassium hydroxide (1 mM)
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 40 genes in this experiment

For stress Adenine hydrochloride hydrate in Paraburkholderia graminis OAS925

For stress Adenine hydrochloride hydrate across organisms

SEED Subsystems

Subsystem	#Specific
Purine Utilization	4
Photorespiration (oxidative C2 cycle)	3
Allantoin Utilization	2
Purine conversions	2
ATP-dependent RNA helicases, bacterial	1
Anaerobic respiratory reductases	1
Bacterial hemoglobins	1
Carboxysome	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Lysine Biosynthesis DAP Pathway	1
Methylcitrate cycle	1
Molybdenum cofactor biosynthesis	1
Pentose phosphate pathway	1
Peptidyl-prolyl cis-trans isomerase	1
Potassium homeostasis	1
Propionate-CoA to Succinate Module	1
Protein degradation	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Respiratory dehydrogenases 1	1
Transport of Molybdenum	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glyoxylate and dicarboxylate metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones
• Purine metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Citrate cycle (TCA cycle)
• Pentose phosphate pathway
• Oxidative phosphorylation
• Lysine biosynthesis
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Glutathione metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-malate degradation I	1	1	1
adenosine nucleotides degradation II	5	4	3
glyoxylate cycle	6	6	3
NADH to cytochrome bo oxidase electron transfer I	2	2	1
glycolate and glyoxylate degradation II	2	2	1
glycolate and glyoxylate degradation I	4	3	2
NADH to cytochrome bd oxidase electron transfer I	2	1	1
superpathway of glycol metabolism and degradation	7	5	3
2-methylcitrate cycle I	5	5	2
aerobic respiration III (alternative oxidase pathway)	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
2-methylcitrate cycle II	6	5	2
purine deoxyribonucleosides degradation II	3	1	1
microcin B17 biosynthesis	3	1	1
adenine and adenosine salvage V	3	1	1
Arg/N-end rule pathway (eukaryotic)	14	8	4
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
purine nucleotides degradation II (aerobic)	11	8	3
guanosine nucleotides degradation II	4	4	1
partial TCA cycle (obligate autotrophs)	8	7	2
adenosine nucleotides degradation I	8	7	2
superpathway of glyoxylate bypass and TCA	12	10	3
nitrogen remobilization from senescing leaves	8	6	2
D-galactarate degradation I	4	3	1
D-glucarate degradation I	4	3	1
guanosine nucleotides degradation III	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
inosine 5'-phosphate degradation	4	3	1
guanosine nucleotides degradation I	4	3	1
adenine and adenosine salvage III	4	2	1
chitin deacetylation	4	2	1
purine deoxyribonucleosides degradation I	4	1	1
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle VI (Helicobacter)	9	6	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	3
TCA cycle I (prokaryotic)	10	8	2
superpathway of D-glucarate and D-galactarate degradation	5	4	1
TCA cycle III (animals)	10	7	2
reductive TCA cycle I	11	6	2
L-tryptophan biosynthesis	6	6	1
purine nucleotides degradation I (plants)	12	10	2
methylgallate degradation	6	5	1
superpathway of guanosine nucleotides degradation (plants)	6	5	1
purine nucleobases degradation II (anaerobic)	24	16	4
reductive TCA cycle II	12	6	2
NAD(P)/NADPH interconversion	6	3	1
Fe(II) oxidation	6	2	1
purine ribonucleosides degradation	6	1	1
ureide biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
D-xylose degradation IV	7	4	1
superpathway of purine deoxyribonucleosides degradation	7	2	1
caffeine degradation III (bacteria, via demethylation)	7	1	1
pentose phosphate pathway	8	8	1
mixed acid fermentation	16	12	2
protocatechuate degradation I (meta-cleavage pathway)	8	6	1
L-arabinose degradation IV	8	6	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	3
L-lysine biosynthesis I	9	9	1
superpathway of purines degradation in plants	18	14	2
theophylline degradation	9	1	1
methylaspartate cycle	19	11	2
superpathway of vanillin and vanillate degradation	10	6	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	2
syringate degradation	12	7	1
ethene biosynthesis V (engineered)	25	19	2
superpathway of L-tryptophan biosynthesis	13	13	1
gluconeogenesis I	13	11	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	1
aspartate superpathway	25	22	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	19	1
superpathway of pentose and pentitol degradation	42	21	1
superpathway of chorismate metabolism	59	42	1