Experiment set2IT014 for Paraburkholderia graminis OAS925

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Uridine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Uridine (20 mM)
Culturing: Burkholderia_OAS925_ML2, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Marta on 10-Apr-21
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)

Specific Phenotypes

For 8 genes in this experiment

For carbon source Uridine in Paraburkholderia graminis OAS925

For carbon source Uridine across organisms

SEED Subsystems

Subsystem #Specific
Coenzyme A Biosynthesis 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Homogentisate pathway of aromatic compound degradation 1
Hydantoin metabolism 1
Lactose and Galactose Uptake and Utilization 1
Maltose and Maltodextrin Utilization 1
Purine conversions 1
Pyrimidine utilization 1
Pyruvate Alanine Serine Interconversions 1
Queuosine-Archaeosine Biosynthesis 1
Threonine and Homoserine Biosynthesis 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
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
L-aspartate biosynthesis 1 1 1
L-aspartate degradation I 1 1 1
guanine and guanosine salvage II 2 2 1
malate/L-aspartate shuttle pathway 2 2 1
β-alanine degradation II 2 2 1
adenine and adenosine salvage II 2 2 1
trehalose degradation VI (periplasmic) 2 2 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
atromentin biosynthesis 2 1 1
L-glutamate degradation II 2 1 1
L-tyrosine degradation II 2 1 1
uracil degradation I (reductive) 3 3 1
thymine degradation 3 3 1
L-tyrosine biosynthesis I 3 3 1
L-phenylalanine biosynthesis I 3 3 1
superpathway of guanosine nucleotides degradation (plants) 6 5 2
L-asparagine degradation III (mammalian) 3 2 1
sulfolactate degradation III 3 2 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 1
(R)-cysteate degradation 3 1 1
L-phenylalanine degradation II (anaerobic) 3 1 1
phosphopantothenate biosynthesis I 4 4 1
guanosine nucleotides degradation II 4 4 1
adenosine nucleotides degradation I 8 7 2
purine nucleotides degradation I (plants) 12 10 3
guanosine nucleotides degradation I 4 3 1
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
phosphopantothenate biosynthesis III (archaea) 4 2 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 2 1
L-tryptophan degradation VIII (to tryptophol) 4 1 1
L-tyrosine degradation I 5 5 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 2
superpathway of pyrimidine ribonucleosides degradation 5 4 1
trans-4-hydroxy-L-proline degradation I 5 3 1
D-galactose degradation I (Leloir pathway) 5 3 1
superpathway of plastoquinol biosynthesis 5 2 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 7 2
superpathway of L-threonine biosynthesis 6 6 1
TCA cycle VIII (Chlamydia) 6 5 1
β-alanine biosynthesis II 6 5 1
superpathway of purines degradation in plants 18 14 3
superpathway of sulfolactate degradation 6 3 1
coenzyme M biosynthesis II 6 1 1
anaerobic energy metabolism (invertebrates, cytosol) 7 7 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 8 2
superpathway of aromatic amino acid biosynthesis 18 18 2
superpathway of coenzyme A biosynthesis I (bacteria) 9 9 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 6 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 3 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 2 1
(S)-reticuline biosynthesis I 11 1 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 11 1
indole-3-acetate biosynthesis II 12 4 1
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of rosmarinic acid biosynthesis 14 2 1
superpathway of anaerobic energy metabolism (invertebrates) 17 12 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 15 1
aspartate superpathway 25 22 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 5 1
superpathway of chorismate metabolism 59 42 2
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 23 1