Experiment set3IT008 for Pseudomonas simiae WCS417

L-Leucine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Leucine (20 mM), pH=7
Culturing: fluoroDangl_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 2/18/2015
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 6 genes in this experiment

For carbon source L-Leucine in Pseudomonas simiae WCS417

For carbon source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
Isoleucine degradation	2
Leucine Degradation and HMG-CoA Metabolism	2
Valine degradation	2
Ethanolamine utilization	1
Fermentations: Lactate	1
Fermentations: Mixed acid	1
Lactate utilization	1
MLST	1
Propanediol utilization	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
RNA processing and degradation, bacterial	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
• Pyruvate metabolism
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Glycine, serine and threonine metabolism
• Taurine and hypotaurine metabolism
• Propanoate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	2
acetate and ATP formation from acetyl-CoA I	2	2	1
sulfoacetaldehyde degradation I	2	1	1
pyruvate fermentation to acetate II	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
glycine biosynthesis II	3	3	1
superpathway of acetate utilization and formation	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
glycine cleavage	3	3	1
pyruvate fermentation to acetate VII	3	2	1
pyruvate fermentation to acetate IV	3	2	1
pyruvate fermentation to acetate I	3	2	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
(S)-propane-1,2-diol degradation	5	2	1
L-leucine degradation I	6	5	1
L-threonine degradation I	6	4	1
methanogenesis from acetate	6	2	1
superpathway of sulfolactate degradation	6	2	1
superpathway of taurine degradation	6	2	1
acetyl-CoA fermentation to butanoate	7	3	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	4	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
L-lysine fermentation to acetate and butanoate	10	3	1
gallate degradation III (anaerobic)	11	3	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	14	1
superpathway of L-threonine metabolism	18	12	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of methanogenesis	21	2	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of N-acetylneuraminate degradation	22	15	1
purine nucleobases degradation II (anaerobic)	24	16	1
superpathway of L-lysine degradation	43	17	1