Experiment set4IT075 for Pseudomonas fluorescens FW300-N1B4

L-Leucine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Leucine (20 mM), pH=7
Culturing: pseudo1_N1B4_ML1, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/16/2014
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)
Growth plate: Cplate1 D3

Specific Phenotypes

For 16 genes in this experiment

For carbon source L-Leucine in Pseudomonas fluorescens FW300-N1B4

For carbon source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	7
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Proline, 4-hydroxyproline uptake and utilization	2
Arginine and Ornithine Degradation	1
Fermentations: Mixed acid	1
Glutamate dehydrogenases	1
HMG CoA Synthesis	1
Ketoisovalerate oxidoreductase	1
Leucine Degradation and HMG-CoA Metabolism	1
Phosphate metabolism	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Respiratory dehydrogenases 1	1
Serine-glyoxylate cycle	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Glutamate metabolism
• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Alanine and aspartate metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Limonene and pinene degradation
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate biosynthesis	1	1	1
L-glutamate degradation I	1	1	1
L-aspartate degradation I	1	1	1
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-proline degradation I	3	3	2
L-glutamate degradation II	2	2	1
oleate β-oxidation (thioesterase-dependent, yeast)	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
malate/L-aspartate shuttle pathway	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	2
L-tyrosine biosynthesis I	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
ethanol degradation IV	3	3	1
superpathway of acetate utilization and formation	3	3	1
L-phenylalanine biosynthesis I	3	3	1
ethanol degradation II	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
ethene biosynthesis IV (engineered)	3	2	1
ethanol degradation III	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	3
ethene biosynthesis II (microbes)	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
chitin deacetylation	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	3
2-methylcitrate cycle I	5	5	1
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
superpathway of L-threonine biosynthesis	6	6	1
β-alanine biosynthesis II	6	5	1
2-methylcitrate cycle II	6	5	1
L-leucine degradation I	6	5	1
L-isoleucine biosynthesis IV	6	4	1
TCA cycle VIII (Chlamydia)	6	4	1
superpathway of sulfolactate degradation	6	3	1
coenzyme M biosynthesis II	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
(5R)-carbapenem carboxylate biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
L-Nδ-acetylornithine biosynthesis	7	5	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	2	1
partial TCA cycle (obligate autotrophs)	8	8	1
L-citrulline biosynthesis	8	7	1
nitrogen remobilization from senescing leaves	8	5	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	4	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
rosmarinic acid biosynthesis I	10	2	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of L-citrulline metabolism	12	9	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
formaldehyde assimilation I (serine pathway)	13	6	1
superpathway of rosmarinic acid biosynthesis	14	2	1
mixed acid fermentation	16	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
methylaspartate cycle	19	9	1
aspartate superpathway	25	21	1
ethene biosynthesis V (engineered)	25	19	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	2
superpathway of chorismate metabolism	59	42	2
oleate β-oxidation	35	30	1