Experiment set4S45 for Pseudomonas sp. RS175

L-Valine carbon source 10 mM

Group: carbon source
Media: MME_noCarbon + L-Valine (10 mM)
Culturing: Pseudomonas_RS175_ML2, 96 deep well, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 31-January-23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 5 genes in this experiment

For carbon source L-Valine in Pseudomonas sp. RS175

For carbon source L-Valine across organisms

SEED Subsystems

Subsystem	#Specific
Isobutyryl-CoA to Propionyl-CoA Module	3
Valine degradation	3
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Butanol Biosynthesis	1
Flavodoxin	1
Isoleucine degradation	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
• Fatty acid metabolism
• beta-Alanine metabolism
• Butanoate metabolism
• Fatty acid elongation in mitochondria
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• Inositol phosphate metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine degradation II	2	2	1
β-alanine degradation I	2	1	1
propanoyl-CoA degradation II	5	3	2
benzoyl-CoA biosynthesis	3	3	1
L-valine degradation I	8	5	2
2-methyl-branched fatty acid β-oxidation	14	10	3
adipate degradation	5	5	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
acrylate degradation I	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
β-alanine biosynthesis II	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
myo-inositol degradation I	7	6	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
benzoyl-CoA degradation I (aerobic)	7	3	1
2,4-dinitrotoluene degradation	7	1	1
valproate β-oxidation	9	6	1
phenylacetate degradation I (aerobic)	9	4	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
myo-, chiro- and scyllo-inositol degradation	10	6	1
3-phenylpropanoate degradation	10	3	1
pyruvate fermentation to hexanol (engineered)	11	7	1
superpathway of phenylethylamine degradation	11	6	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	30	3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	20	1