Experiment set4IT081 for Acidovorax sp. GW101-3H11

L-Leucine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Leucine (20 mM), pH=7
Culturing: acidovorax_3H11_ML3a, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 6.3 generations
By: Mark on 6/10/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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: Nplate1 C4

Specific Phenotypes

For 9 genes in this experiment

For nitrogen source L-Leucine in Acidovorax sp. GW101-3H11

For nitrogen source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
Alanine biosynthesis	1
Biotin biosynthesis	1
Biphenyl Degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Glycolate, glyoxylate interconversions	1
HMG CoA Synthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Polyhydroxybutyrate metabolism	1
Pyruvate Alanine Serine Interconversions	1
Serine-glyoxylate cycle	1
n-Phenylalkanoic acid 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
• Valine, leucine and isoleucine biosynthesis
• Fatty acid metabolism
• Geraniol degradation
• Tyrosine metabolism
• alpha-Linolenic acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Pantothenate and CoA biosynthesis
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine biosynthesis I	2	2	2
long-chain fatty acid activation	1	1	1
superpathway of L-alanine biosynthesis	4	4	2
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
L-leucine degradation I	6	5	2
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
L-valine biosynthesis	4	4	1
phytol degradation	4	3	1
phosphatidylcholine acyl editing	4	2	1
long chain fatty acid ester synthesis (engineered)	4	2	1
wax esters biosynthesis II	4	1	1
sporopollenin precursors biosynthesis	18	4	4
octane oxidation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
superpathway of branched chain amino acid biosynthesis	17	17	3
L-leucine biosynthesis	6	6	1
glyoxylate cycle	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
fatty acid salvage	6	5	1
L-isoleucine degradation I	6	5	1
L-isoleucine biosynthesis IV	6	4	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
stearate biosynthesis I (animals)	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
ceramide degradation by α-oxidation	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
L-valine degradation I	8	6	1
L-isoleucine biosynthesis II	8	5	1
2-deoxy-D-ribose degradation II	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
suberin monomers biosynthesis	20	3	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of glyoxylate bypass and TCA	12	10	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of L-threonine metabolism	18	10	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	28	1
anteiso-branched-chain fatty acid biosynthesis	34	30	1
odd iso-branched-chain fatty acid biosynthesis	34	30	1
even iso-branched-chain fatty acid biosynthesis	34	30	1
oleate β-oxidation	35	29	1