Experiment set8IT032 for Pseudomonas fluorescens FW300-N2E2

L-Leucine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Leucine (20 mM), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
Growth: about 4.1 generations
By: Mark on 1/21/2016
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 30 genes in this experiment

For carbon source L-Leucine in Pseudomonas fluorescens FW300-N2E2

For carbon source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	9
Leucine Degradation and HMG-CoA Metabolism	5
HMG CoA Synthesis	3
Isoleucine degradation	2
Serine-glyoxylate cycle	2
Valine degradation	2
Benzoate transport and degradation cluster	1
Ethanolamine utilization	1
Fermentations: Lactate	1
Fermentations: Mixed acid	1
Folate Biosynthesis	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
L-rhamnose utilization	1
MLST	1
Proline, 4-hydroxyproline uptake and utilization	1
Propanediol utilization	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Threonine anaerobic catabolism gene cluster	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
• Arginine and proline metabolism
• Propanoate metabolism
• Methane metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Tryptophan metabolism
• Taurine and hypotaurine metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Butanoate metabolism
• One carbon pool by folate
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Folate biosynthesis
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation I	1	1	1
acetate and ATP formation from acetyl-CoA I	2	2	1
L-leucine degradation I	6	5	3
sulfoacetaldehyde degradation I	2	1	1
superpathway of acetate utilization and formation	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
pyruvate fermentation to acetate II	3	3	1
pyruvate fermentation to acetate I	3	2	1
pyruvate fermentation to acetate IV	3	2	1
pyruvate fermentation to acetate VII	3	2	1
ethene biosynthesis IV (engineered)	3	1	1
putrescine degradation II	4	4	1
tetrahydromonapterin biosynthesis	4	3	1
pyruvate fermentation to acetate and (S)-lactate I	4	3	1
pyruvate fermentation to acetate and lactate II	4	2	1
sulfolactate degradation II	4	1	1
ethanolamine utilization	5	5	1
acetylene degradation (anaerobic)	5	4	1
ferrichrome A biosynthesis	5	3	1
(S)-propane-1,2-diol degradation	5	2	1
L-threonine degradation I	6	4	1
methanogenesis from acetate	6	2	1
superpathway of taurine degradation	6	2	1
superpathway of sulfolactate degradation	6	2	1
acetyl-CoA fermentation to butanoate	7	3	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	2	1
superpathway of ornithine degradation	8	7	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	3	1
folate transformations III (E. coli)	9	9	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
L-lysine fermentation to acetate and butanoate	10	4	1
folate transformations II (plants)	11	10	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
gallate degradation III (anaerobic)	11	3	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	4	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	15	1
superpathway of L-threonine metabolism	18	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
methylaspartate cycle	19	9	1
superpathway of methanogenesis	21	2	1
superpathway of N-acetylneuraminate degradation	22	13	1
purine nucleobases degradation II (anaerobic)	24	16	1
superpathway of L-lysine degradation	43	19	1
superpathway of chorismate metabolism	59	43	1