Experiment set25S44 for Pseudomonas fluorescens SBW25-INTG

L-Valine carbon source

Group: carbon source
Media: MME_noCarbon + L-Valine (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 1/31/23
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 32 genes in this experiment

For carbon source L-Valine in Pseudomonas fluorescens SBW25-INTG

For carbon source L-Valine across organisms

SEED Subsystems

Subsystem	#Specific
Valine degradation	8
Isoleucine degradation	6
Isobutyryl-CoA to Propionyl-CoA Module	4
Leucine Degradation and HMG-CoA Metabolism	4
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	3
Acetyl-CoA fermentation to Butyrate	2
Anaerobic respiratory reductases	2
Butanol Biosynthesis	2
Methylcitrate cycle	2
Propionate-CoA to Succinate Module	2
Arginine and Ornithine Degradation	1
Aromatic amino acid degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Histidine Degradation	1
Orphan regulatory proteins	1
Phosphate metabolism	1
Pyruvate Alanine Serine Interconversions	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
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Lysine biosynthesis
• Arginine and proline metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Glycolysis / Gluconeogenesis
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Histidine metabolism
• beta-Alanine metabolism
• Inositol phosphate metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Brassinosteroid biosynthesis
• Nitrogen metabolism
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	3
2-methylcitrate cycle I	5	5	3
β-alanine degradation II	2	2	1
2-methylcitrate cycle II	6	5	3
β-alanine degradation I	2	1	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
L-ornithine biosynthesis II	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
L-arginine degradation I (arginase pathway)	3	3	1
glyoxylate cycle	6	5	2
partial TCA cycle (obligate autotrophs)	8	8	2
L-histidine degradation I	4	4	1
L-arginine degradation VI (arginase 2 pathway)	4	4	1
nitrogen remobilization from senescing leaves	8	6	2
L-valine degradation I	8	6	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
L-histidine degradation II	5	5	1
L-ornithine biosynthesis I	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
TCA cycle I (prokaryotic)	10	9	2
propanoyl-CoA degradation II	5	4	1
TCA cycle III (animals)	10	7	2
reductive TCA cycle I	11	6	2
superpathway of glyoxylate bypass and TCA	12	11	2
pyruvate fermentation to butanol II (engineered)	6	4	1
L-histidine degradation III	6	4	1
reductive TCA cycle II	12	5	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
L-Nδ-acetylornithine biosynthesis	7	6	1
myo-inositol degradation I	7	6	1
2-methyl-branched fatty acid β-oxidation	14	11	2
2,4-dinitrotoluene degradation	7	3	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	3
L-citrulline biosynthesis	8	8	1
L-histidine degradation VI	8	7	1
mixed acid fermentation	16	11	2
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
methylaspartate cycle	19	9	2
L-arginine biosynthesis II (acetyl cycle)	10	10	1
myo-, chiro- and scyllo-inositol degradation	10	6	1
pyruvate fermentation to hexanol (engineered)	11	7	1
superpathway of L-citrulline metabolism	12	10	1
ethene biosynthesis V (engineered)	25	18	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
superpathway of arginine and polyamine biosynthesis	17	15	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1