Experiment set4IT076 for Paraburkholderia bryophila 376MFSha3.1

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Deoxyribonucleic acid from herring sperm 10 mg/mL carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Deoxyribonucleic acid from herring sperm (10 mg/mL), 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 B2

Specific Phenotypes

For 13 genes in this experiment

For carbon source Deoxyribonucleic acid from herring sperm in Paraburkholderia bryophila 376MFSha3.1

For carbon source Deoxyribonucleic acid from herring sperm across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter dipeptide (TC 3.A.1.5.2) 2
Purine conversions 2
ATP-dependent RNA helicases, bacterial 1
Ammonia assimilation 1
Bacterial Chemotaxis 1
Carboxysome 1
Cyanate hydrolysis 1
Isoprenoid Biosynthesis 1
Lysine degradation 1
Purine Utilization 1
cAMP signaling in bacteria 1
polyprenyl synthesis 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
adenine and adenosine salvage II 2 2 1
guanine and guanosine salvage II 2 2 1
CO2 fixation into oxaloacetate (anaplerotic) 2 2 1
adenine and adenosine salvage I 2 1 1
guanine and guanosine salvage I 2 1 1
adenine salvage 3 3 1
cyanate degradation 3 3 1
adenine and adenosine salvage V 3 1 1
superpathway of guanine and guanosine salvage 3 1 1
purine deoxyribonucleosides degradation II 3 1 1
adenine and adenosine salvage III 4 2 1
purine deoxyribonucleosides degradation I 4 1 1
methylerythritol phosphate pathway II 9 8 2
methylerythritol phosphate pathway I 9 7 2
adenosine nucleotides degradation II 5 4 1
isoprene biosynthesis I 10 7 2
superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) 12 10 2
purine ribonucleosides degradation 6 1 1
taxadiene biosynthesis (engineered) 13 10 2
superpathway of purine nucleotide salvage 14 12 2
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 1
glyphosate degradation III 7 3 1
superpathway of purine deoxyribonucleosides degradation 7 3 1
(aminomethyl)phosphonate degradation 8 3 1
purine nucleotides degradation II (aerobic) 11 8 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 8 1
3-hydroxypropanoate cycle 13 8 1
glyoxylate assimilation 13 6 1
superpathway of ergosterol biosynthesis II 26 11 2
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 8 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 11 1
superpathway of the 3-hydroxypropanoate cycle 18 10 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 9 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 24 1