Experiment set5IT004 for Pseudomonas fluorescens FW300-N2E3

L-Leucine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Leucine (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 19 genes in this experiment

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

For carbon source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	6
Fermentations: Mixed acid	1
Isoleucine degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Methylcitrate cycle	1
Multidrug Resistance Efflux Pumps	1
Propionate-CoA to Succinate Module	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Ton and Tol transport systems	1
Valine 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
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Glutathione metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
2-methylcitrate cycle I	5	5	1
L-leucine degradation I	6	5	1
2-methylcitrate cycle II	6	5	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
partial TCA cycle (obligate autotrophs)	8	8	1
nitrogen remobilization from senescing leaves	8	6	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
formaldehyde assimilation I (serine pathway)	13	6	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
mixed acid fermentation	16	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
ethene biosynthesis V (engineered)	25	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1