Experiment set8IT028 for Burkholderia phytofirmans PsJN

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2-Deoxyadenosine 5-monophosphate 5 mM carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 2-Deoxyadenosine 5-monophosphate (5 mM), pH=7
Culturing: BFirm_ML3a, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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)
Growth plate: Bfirm_deoxyribosePlus_plate C1

Specific Phenotypes

For 39 genes in this experiment

For carbon source 2-Deoxyadenosine 5-monophosphate in Burkholderia phytofirmans PsJN

For carbon source 2-Deoxyadenosine 5-monophosphate across organisms

SEED Subsystems

Subsystem #Specific
Purine conversions 4
Allantoin Utilization 2
Ammonia assimilation 2
Purine Utilization 2
Choline and Betaine Uptake and Betaine Biosynthesis 1
Glycogen metabolism 1
Homogentisate pathway of aromatic compound degradation 1
Luciferases 1
Photorespiration (oxidative C2 cycle) 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Stringent Response, (p)ppGpp metabolism 1
cAMP signaling in bacteria 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
adenosine nucleotides degradation III 1 1 1
adenine salvage 3 3 2
adenosine nucleotides degradation II 5 4 3
choline degradation I 2 2 1
sulfoacetaldehyde degradation I 2 2 1
glycine betaine biosynthesis II (Gram-positive bacteria) 2 2 1
adenine and adenosine salvage II 2 2 1
guanine and guanosine salvage II 2 2 1
glycine betaine biosynthesis I (Gram-negative bacteria) 2 2 1
adenine and adenosine salvage III 4 2 2
allantoin degradation to ureidoglycolate I (urea producing) 2 1 1
xanthine and xanthosine salvage 2 1 1
D-mannose degradation II 2 1 1
adenine and adenosine salvage I 2 1 1
D-mannose degradation I 2 1 1
guanine and guanosine salvage I 2 1 1
glyoxylate cycle 6 6 2
ppGpp metabolism 6 6 2
choline-O-sulfate degradation 3 3 1
allantoin degradation to glyoxylate I 3 2 1
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation 3 2 1
superpathway of guanine and guanosine salvage 3 1 1
adenine and adenosine salvage V 3 1 1
purine deoxyribonucleosides degradation II 3 1 1
mannitol biosynthesis 3 1 1
purine nucleotides degradation II (aerobic) 11 8 3
guanosine nucleotides degradation II 4 4 1
glycogen biosynthesis I (from ADP-D-Glucose) 4 4 1
GDP-mannose biosynthesis 4 4 1
partial TCA cycle (obligate autotrophs) 8 7 2
adenosine nucleotides degradation I 8 7 2
nitrogen remobilization from senescing leaves 8 6 2
guanosine nucleotides degradation III 4 3 1
glycolate and glyoxylate degradation I 4 3 1
inosine 5'-phosphate degradation 4 3 1
guanosine nucleotides degradation I 4 3 1
sulfolactate degradation II 4 2 1
mannitol degradation II 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 7 2
TCA cycle VI (Helicobacter) 9 6 2
2-methylcitrate cycle I 5 5 1
NAD salvage pathway II (PNC IV cycle) 5 5 1
TCA cycle I (prokaryotic) 10 8 2
TCA cycle III (animals) 10 7 2
1,5-anhydrofructose degradation 5 2 1
reductive TCA cycle I 11 6 2
purine nucleotides degradation I (plants) 12 10 2
superpathway of glyoxylate bypass and TCA 12 10 2
superpathway of guanosine nucleotides degradation (plants) 6 5 1
superpathway of allantoin degradation in yeast 6 5 1
2-methylcitrate cycle II 6 5 1
superpathway of purines degradation in plants 18 14 3
purine nucleobases degradation II (anaerobic) 24 16 4
reductive TCA cycle II 12 6 2
superpathway of sulfolactate degradation 6 3 1
superpathway of taurine degradation 6 3 1
purine ribonucleosides degradation 6 1 1
superpathway of purine nucleotide salvage 14 12 2
superpathway of glyoxylate cycle and fatty acid degradation 14 11 2
superpathway of glycol metabolism and degradation 7 5 1
ureide biosynthesis 7 5 1
glyphosate degradation III 7 3 1
superpathway of purine deoxyribonucleosides degradation 7 3 1
β-(1,4)-mannan degradation 7 2 1
caffeine degradation III (bacteria, via demethylation) 7 1 1
mixed acid fermentation 16 13 2
(aminomethyl)phosphonate degradation 8 5 1
superpathway of allantoin degradation in plants 8 4 1
theophylline degradation 9 1 1
methylaspartate cycle 19 11 2
starch biosynthesis 10 6 1
caffeine degradation IV (bacteria, via demethylation and oxidation) 10 1 1
colanic acid building blocks biosynthesis 11 11 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 17 2
ethene biosynthesis V (engineered) 25 18 2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 2
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis 14 9 1