Experiment set12H18 for Pseudomonas stutzeri RCH2

L-Leucine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Leucine (20 mM), pH=7.2
Culturing: psRCH2_ML7c, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.2 generations
By: Kelly on 2/25/2014
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)

Specific Phenotypes

For 14 genes in this experiment

For carbon source L-Leucine in Pseudomonas stutzeri RCH2

For carbon source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
Leucine Degradation and HMG-CoA Metabolism	4
Serine-glyoxylate cycle	4
Catechol branch of beta-ketoadipate pathway	2
Protocatechuate branch of beta-ketoadipate pathway	2
Aromatic amino acid interconversions with aryl acids	1
Branched-Chain Amino Acid Biosynthesis	1
HMG CoA Synthesis	1
Photorespiration (oxidative C2 cycle)	1
Type IV pilus	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
• Glyoxylate and dicarboxylate metabolism
• Butanoate metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Synthesis and degradation of ketone bodies
• Geraniol degradation
• Valine, leucine and isoleucine biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycolate and glyoxylate degradation II	2	2	1
2-oxobutanoate degradation II	2	1	1
L-isoleucine biosynthesis V	3	3	1
ketolysis	3	3	1
L-leucine degradation I	6	5	2
glyoxylate cycle	6	5	2
L-leucine degradation V (oxidative Stickland reaction)	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	2	1
L-valine degradation III (oxidative Stickland reaction)	3	2	1
chitin deacetylation	4	2	1
gallate degradation III (anaerobic)	11	5	2
superpathway of glyoxylate bypass and TCA	12	11	2
L-isoleucine biosynthesis IV	6	5	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
superpathway of glycol metabolism and degradation	7	5	1
acetyl-CoA fermentation to butanoate	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	4	1
4-aminobutanoate degradation V	7	3	1
succinate fermentation to butanoate	7	2	1
D-xylose degradation IV	7	2	1
L-arabinose degradation IV	8	3	1
TCA cycle VI (Helicobacter)	9	7	1
L-glutamate degradation V (via hydroxyglutarate)	10	7	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	2
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	1	1
superpathway of pentose and pentitol degradation	42	7	1