Experiment set6IT006 for Paraburkholderia bryophila 376MFSha3.1

4-Methyl-2-oxopentanoic acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 4-Methyl-2-oxovaleric acid (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Burk376_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: RobinH_and_TrentonO on 13-Feb-19
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 6 genes in this experiment

For carbon source 4-Methyl-2-oxovaleric acid in Paraburkholderia bryophila 376MFSha3.1

For carbon source 4-Methyl-2-oxovaleric acid across organisms

SEED Subsystems

Subsystem	#Specific
Isobutyryl-CoA to Propionyl-CoA Module	2
Valine degradation	2
HMG CoA Synthesis	1
Ketoisovalerate oxidoreductase	1
Leucine Degradation and HMG-CoA Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Serine-glyoxylate cycle	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Propanoate metabolism
• beta-Alanine metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• Pyruvate metabolism
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acyl-CoA hydrolysis	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
palmitoleate biosynthesis IV (fungi and animals)	2	2	1
superpathway of acetate utilization and formation	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
benzoyl-CoA biosynthesis	3	3	1
ethanol degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
chitin deacetylation	4	3	1
L-valine degradation I	8	5	2
2-methyl-branched fatty acid β-oxidation	14	9	3
adipate degradation	5	5	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
fatty acid β-oxidation IV (unsaturated, even number)	5	3	1
acrylate degradation I	5	2	1
propanoyl-CoA degradation II	5	2	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
L-leucine degradation I	6	5	1
β-alanine biosynthesis II	6	4	1
methyl ketone biosynthesis (engineered)	6	3	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
benzoyl-CoA degradation I (aerobic)	7	5	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
phenylacetate degradation I (aerobic)	9	9	1
valproate β-oxidation	9	6	1
reductive glycine pathway of autotrophic CO2 fixation	9	4	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	1
cis-geranyl-CoA degradation	9	2	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
3-phenylpropanoate degradation	10	5	1
superpathway of phenylethylamine degradation	11	9	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	29	3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	10	1
firefly bioluminescence	14	3	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
jasmonic acid biosynthesis	19	5	1
platensimycin biosynthesis	26	6	1