Experiment set1IT028 for Sinorhizobium meliloti 1021

L-Leucine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Leucine (20 mM), pH=7
Culturing: Smeli_ML6, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.5 generations
By: Mark on 6/2/2015
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)
Growth plate: Smeli_carbon_plate2 B3

Specific Phenotypes

For 15 genes in this experiment

For carbon source L-Leucine in Sinorhizobium meliloti 1021

For carbon source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
Leucine Degradation and HMG-CoA Metabolism	8
HMG CoA Synthesis	4
Isoleucine degradation	4
Serine-glyoxylate cycle	4
Valine degradation	4
D-gluconate and ketogluconates metabolism	1
Entner-Doudoroff Pathway	1
Polyhydroxybutyrate metabolism	1
Propionyl-CoA to Succinyl-CoA Module	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
• Butanoate metabolism
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Pentose phosphate pathway
• Synthesis and degradation of ketone bodies
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate 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	3
D-gluconate degradation	1	1	1
L-leucine degradation I	6	5	3
mevalonate degradation	2	1	1
glycine biosynthesis II	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
L-idonate degradation	3	3	1
glycine cleavage	3	3	1
sorbitol biosynthesis II	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
propanoyl CoA degradation I	3	3	1
L-proline degradation I	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
conversion of succinate to propanoate	3	1	1
2-oxobutanoate degradation I	4	3	1
ethene biosynthesis II (microbes)	4	1	1
ketogenesis	5	3	1
glyoxylate cycle	6	6	1
pyruvate fermentation to propanoate I	7	4	1
ketogluconate metabolism	8	5	1
2-deoxy-D-ribose degradation II	8	3	1
cis-geranyl-CoA degradation	9	2	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
L-glutamate degradation VIII (to propanoate)	11	4	1
superpathway of glyoxylate bypass and TCA	12	11	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
3-hydroxypropanoate cycle	13	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	3	1
superpathway of L-methionine salvage and degradation	16	9	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
superpathway of the 3-hydroxypropanoate cycle	18	7	1
methylaspartate cycle	19	12	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1