Experiment set2IT068 for Paraburkholderia graminis OAS925

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Sodium butyrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium butyrate (4 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 13 genes in this experiment

For carbon source Sodium butyrate in Paraburkholderia graminis OAS925

For carbon source Sodium butyrate across organisms

SEED Subsystems

Subsystem #Specific
HMG CoA Synthesis 2
Propionyl-CoA to Succinyl-CoA Module 2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 2
Serine-glyoxylate cycle 2
Acetyl-CoA fermentation to Butyrate 1
Biotin biosynthesis 1
Isobutyryl-CoA to Propionyl-CoA Module 1
Ketoisovalerate oxidoreductase 1
Leucine Degradation and HMG-CoA Metabolism 1
Polyhydroxybutyrate metabolism 1
Valine degradation 1
n-Phenylalkanoic acid degradation 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
acetate and ATP formation from acetyl-CoA III 1 1 1
long-chain fatty acid activation 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
acetate conversion to acetyl-CoA 1 1 1
L-phenylalanine biosynthesis III (cytosolic, plants) 2 2 1
γ-linolenate biosynthesis II (animals) 2 1 1
linoleate biosynthesis II (animals) 2 1 1
L-tyrosine degradation II 2 1 1
atromentin biosynthesis 2 1 1
L-tyrosine biosynthesis I 3 3 1
ketolysis 3 3 1
ethanol degradation IV 3 3 1
benzoyl-CoA biosynthesis 3 3 1
L-phenylalanine biosynthesis I 3 3 1
ethanol degradation II 3 3 1
superpathway of acetate utilization and formation 3 3 1
propanoyl CoA degradation I 3 2 1
L-isoleucine biosynthesis V 3 2 1
ethanol degradation III 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
L-phenylalanine degradation II (anaerobic) 3 1 1
oleate biosynthesis I (plants) 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
conversion of succinate to propanoate 3 1 1
D-threitol degradation 3 1 1
alkane biosynthesis II 3 1 1
phytol degradation 4 3 1
2-oxobutanoate degradation I 4 2 1
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
chitin deacetylation 4 2 1
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
sporopollenin precursors biosynthesis 18 8 4
2-methyl-branched fatty acid β-oxidation 14 9 3
adipate degradation 5 5 1
L-tyrosine degradation I 5 5 1
ketogenesis 5 4 1
adipate biosynthesis 5 4 1
fatty acid β-oxidation IV (unsaturated, even number) 5 3 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
propanoyl-CoA degradation II 5 3 1
octane oxidation 5 3 1
acrylate degradation I 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 2 1
superpathway of plastoquinol biosynthesis 5 2 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 2
stearate biosynthesis II (bacteria and plants) 6 5 1
β-alanine biosynthesis II 6 5 1
fatty acid salvage 6 5 1
stearate biosynthesis IV 6 4 1
methyl ketone biosynthesis (engineered) 6 3 1
6-gingerol analog biosynthesis (engineered) 6 3 1
stearate biosynthesis I (animals) 6 2 1
methylthiopropanoate degradation I (cleavage) 6 2 1
superpathway of bitter acids biosynthesis 18 3 3
lupulone and humulone biosynthesis 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
fatty acid β-oxidation I (generic) 7 5 1
benzoyl-CoA degradation I (aerobic) 7 5 1
pyruvate fermentation to propanoate I 7 3 1
capsaicin biosynthesis 7 3 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 1
ceramide degradation by α-oxidation 7 2 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
L-valine degradation I 8 5 1
2-deoxy-D-ribose degradation II 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
superpathway of dimethylsulfoniopropanoate degradation 8 2 1
oleate β-oxidation 35 29 4
superpathway of aromatic amino acid biosynthesis 18 18 2
phenylacetate degradation I (aerobic) 9 7 1
valproate β-oxidation 9 6 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 5 1
reductive glycine pathway of autotrophic CO2 fixation 9 4 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 3 1
cis-geranyl-CoA degradation 9 2 1
L-histidine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 1
anaerobic energy metabolism (invertebrates, mitochondrial) 10 5 1
3-phenylpropanoate degradation 10 5 1
suberin monomers biosynthesis 20 5 2
rosmarinic acid biosynthesis I 10 2 1
superpathway of fatty acid biosynthesis II (plant) 43 38 4
superpathway of phenylethylamine degradation 11 7 1
L-glutamate degradation VIII (to propanoate) 11 3 1
Spodoptera littoralis pheromone biosynthesis 22 4 2
tropane alkaloids biosynthesis 11 1 1
(S)-reticuline biosynthesis I 11 1 1
3-hydroxypropanoate cycle 13 8 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 5 1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered) 14 2 1
superpathway of rosmarinic acid biosynthesis 14 2 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
superpathway of L-methionine salvage and degradation 16 7 1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis 16 3 1
cutin biosynthesis 16 3 1
superpathway of anaerobic energy metabolism (invertebrates) 17 12 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 10 1
superpathway of the 3-hydroxypropanoate cycle 18 8 1
methylaspartate cycle 19 11 1
platensimycin biosynthesis 26 6 1
superpathway of fatty acids biosynthesis (E. coli) 53 48 2
anaerobic aromatic compound degradation (Thauera aromatica) 27 5 1
palmitate biosynthesis III 29 28 1
superpathway of chorismate metabolism 59 42 2
superpathway of histidine, purine, and pyrimidine biosynthesis 46 44 1