Experiment set5IT002 for Pseudomonas fluorescens FW300-N2E3

L-Valine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Valine (20 mM), pH=7
Culturing: pseudo3_N2E3_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2015
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 21 genes in this experiment

For carbon source L-Valine in Pseudomonas fluorescens FW300-N2E3

For carbon source L-Valine across organisms

SEED Subsystems

Subsystem	#Specific
Valine degradation	5
Isobutyryl-CoA to Propionyl-CoA Module	4
Isoleucine degradation	2
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Branched-Chain Amino Acid Biosynthesis	1
Butanol Biosynthesis	1
Conserved gene cluster possibly involved in RNA metabolism	1
Cysteine Biosynthesis	1
Fermentations: Mixed acid	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Lipoic acid metabolism	1
Methionine Biosynthesis	1
Methylcitrate cycle	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Propionate-CoA to Succinate Module	1
Pyruvate metabolism I: anaplerotic reactions, PEP	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
• Glycine, serine and threonine metabolism
• Lysine degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Glycolysis / Gluconeogenesis
• Fatty acid elongation in mitochondria
• Cysteine metabolism
• Geraniol degradation
• Valine, leucine and isoleucine biosynthesis
• Inositol phosphate metabolism
• alpha-Linolenic acid metabolism
• One carbon pool by folate
• Carbon fixation in photosynthetic organisms
• Limonene and pinene degradation
• Nitrogen metabolism
• Sulfur metabolism
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
L-methionine degradation II	3	2	2
β-alanine degradation II	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
L-cysteine biosynthesis I	2	2	1
L-valine degradation I	8	6	4
L-threonine degradation I	6	4	3
L-threonine degradation V	2	1	1
β-alanine degradation I	2	1	1
lipoate salvage I	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
propanoyl-CoA degradation II	5	3	2
glycine biosynthesis II	3	3	1
superpathway of acetate utilization and formation	3	3	1
glycine cleavage	3	3	1
benzoyl-CoA biosynthesis	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
glycine degradation	3	3	1
L-isoleucine biosynthesis V	3	2	1
ethanol degradation III	3	2	1
2-methyl-branched fatty acid β-oxidation	14	11	4
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
chitin deacetylation	4	2	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
lipoate salvage II	4	1	1
superpathway of L-isoleucine biosynthesis I	13	13	3
valproate β-oxidation	9	7	2
reductive glycine pathway of autotrophic CO2 fixation	9	5	2
hypoglycin biosynthesis	14	4	3
L-lysine degradation IV	5	5	1
adipate degradation	5	5	1
2-methylcitrate cycle I	5	5	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
acrylate degradation I	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
seleno-amino acid biosynthesis (plants)	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
superpathway of branched chain amino acid biosynthesis	17	17	3
L-lysine degradation X	6	6	1
L-isoleucine degradation I	6	5	1
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	5	1
L-leucine degradation I	6	5	1
superpathway of L-threonine metabolism	18	12	3
propanoate fermentation to 2-methylbutanoate	6	4	1
pyruvate fermentation to butanol II (engineered)	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
D-cycloserine biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
myo-inositol degradation I	7	7	1
fatty acid β-oxidation I (generic)	7	5	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
2,4-dinitrotoluene degradation	7	1	1
partial TCA cycle (obligate autotrophs)	8	8	1
nitrogen remobilization from senescing leaves	8	6	1
folate transformations III (E. coli)	9	9	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
photorespiration I	9	5	1
photorespiration III	9	5	1
cis-geranyl-CoA degradation	9	4	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
phenylacetate degradation I (aerobic)	9	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
myo-, chiro- and scyllo-inositol degradation	10	7	1
photorespiration II	10	6	1
3-phenylpropanoate degradation	10	4	1
folate transformations II (plants)	11	10	1
pyruvate fermentation to hexanol (engineered)	11	7	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
superpathway of phenylethylamine degradation	11	4	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	30	3
folate transformations I	13	9	1
formaldehyde assimilation I (serine pathway)	13	6	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	3	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	3	1
cyclosporin A biosynthesis	15	2	1
mixed acid fermentation	16	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of seleno-compound metabolism	19	6	1
ethene biosynthesis V (engineered)	25	19	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of L-lysine degradation	43	18	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1