Experiment set4IT080 for Paraburkholderia bryophila 376MFSha3.1

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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: Burk376_ML3, 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: Burk376_deoxyribosePlus_plate C1

Specific Phenotypes

For 12 genes in this experiment

For carbon source 2-Deoxyadenosine 5-monophosphate in Paraburkholderia bryophila 376MFSha3.1

For carbon source 2-Deoxyadenosine 5-monophosphate across organisms

SEED Subsystems

Subsystem #Specific
Purine Utilization 2
Ammonia assimilation 1
DNA structural proteins, bacterial 1
Glutathione: Non-redox reactions 1
Lysine degradation 1
Methylglyoxal Metabolism 1
Purine conversions 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 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
L-malate degradation I 1 1 1
adenine and adenosine salvage II 2 2 1
guanine and guanosine salvage II 2 2 1
adenine and adenosine salvage I 2 1 1
guanine and guanosine salvage I 2 1 1
adenosine nucleotides degradation II 5 4 2
methylglyoxal degradation VIII 3 3 1
adenine salvage 3 3 1
methylglyoxal degradation I 3 2 1
superpathway of guanine and guanosine salvage 3 1 1
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
guanosine nucleotides degradation III 4 3 1
inosine 5'-phosphate degradation 4 3 1
guanosine nucleotides degradation I 4 3 1
purine nucleotides degradation II (aerobic) 11 8 2
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
superpathway of purine nucleotide salvage 14 12 2
ureide biosynthesis 7 5 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 8 2
glyphosate degradation III 7 3 1
caffeine degradation III (bacteria, via demethylation) 7 1 1
protocatechuate degradation I (meta-cleavage pathway) 8 6 1
superpathway of methylglyoxal degradation 8 4 1
(aminomethyl)phosphonate degradation 8 3 1
superpathway of purines degradation in plants 18 14 2
theophylline degradation 9 1 1
superpathway of vanillin and vanillate degradation 10 7 1
caffeine degradation IV (bacteria, via demethylation and oxidation) 10 1 1
syringate degradation 12 7 1
gluconeogenesis I 13 12 1