Experiment set12IT055 for Paraburkholderia graminis OAS925

RCH2_defined_glucose_5mM with Adenine 2 mM

Group: stress
Media: RCH2_defined_glucose_5mM + Adenine hydrochloride hydrate (2 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 21 genes in this experiment

For stress Adenine hydrochloride hydrate in Paraburkholderia graminis OAS925

For stress Adenine hydrochloride hydrate across organisms

SEED Subsystems

Subsystem	#Specific
Allantoin Utilization	2
Molybdenum cofactor biosynthesis	2
Photorespiration (oxidative C2 cycle)	2
Purine Utilization	2
Transport of Molybdenum	2
Bacterial hemoglobins	1
Carboxysome	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Lysine Biosynthesis DAP Pathway	1
Pentose phosphate pathway	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Respiratory dehydrogenases 1	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 histidine and purine
• Pentose phosphate pathway
• Oxidative phosphorylation
• Purine metabolism
• Lysine biosynthesis
• Glutathione metabolism
• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-malate degradation I	1	1	1
NADH to cytochrome bo oxidase electron transfer I	2	2	1
glycolate and glyoxylate degradation I	4	3	2
NADH to cytochrome bd oxidase electron transfer I	2	1	1
adenosine nucleotides degradation II	5	4	2
pentose phosphate pathway (oxidative branch) I	3	3	1
aerobic respiration III (alternative oxidase pathway)	3	3	1
molybdenum cofactor biosynthesis	3	3	1
superpathway of glycol metabolism and degradation	7	5	2
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
guanosine nucleotides degradation II	4	4	1
adenosine nucleotides degradation I	8	7	2
D-glucarate degradation I	4	3	1
guanosine nucleotides degradation I	4	3	1
D-galactarate degradation I	4	3	1
guanosine nucleotides degradation III	4	3	1
inosine 5'-phosphate degradation	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
superpathway of D-glucarate and D-galactarate degradation	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
methylgallate degradation	6	5	1
purine nucleobases degradation II (anaerobic)	24	16	4
NAD(P)/NADPH interconversion	6	3	1
Fe(II) oxidation	6	2	1
ureide biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
caffeine degradation III (bacteria, via demethylation)	7	1	1
pentose phosphate pathway	8	8	1
protocatechuate degradation I (meta-cleavage pathway)	8	6	1
L-lysine biosynthesis I	9	9	1
superpathway of purines degradation in plants	18	14	2
theophylline degradation	9	1	1
superpathway of vanillin and vanillate degradation	10	6	1
caffeine degradation IV (bacteria, via demethylation and oxidation)	10	1	1
syringate degradation	12	7	1
gluconeogenesis I	13	11	1
superpathway of glucose and xylose degradation	17	16	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