Experiment set13H6 for Pseudomonas stutzeri RCH2

L-Valine nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + L-Valine (5 mM), pH=7.2
Culturing: psRCH2_ML7c, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.8 generations
By: Kelly on 2/27/2014
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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 17 genes in this experiment

For nitrogen source L-Valine in Pseudomonas stutzeri RCH2

For nitrogen source L-Valine across organisms

SEED Subsystems

Subsystem	#Specific
Isobutyryl-CoA to Propionyl-CoA Module	4
Valine degradation	4
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Aromatic amino acid interconversions with aryl acids	1
Bacterial hemoglobins	1
Butanol Biosynthesis	1
Curli production	1
DNA repair, bacterial	1
Glycogen metabolism	1
HMG CoA Synthesis	1
Isoleucine degradation	1
Lactate utilization	1
Leucine Degradation and HMG-CoA Metabolism	1
Serine-glyoxylate cycle	1
Trehalose Biosynthesis	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
• Fatty acid metabolism
• Propanoate metabolism
• Butanoate metabolism
• Fatty acid elongation in mitochondria
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• Starch and sucrose metabolism
• Inositol phosphate metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine degradation II	2	2	1
L-valine degradation I	8	6	4
β-alanine degradation I	2	1	1
2-oxobutanoate degradation II	2	1	1
propanoyl-CoA degradation II	5	3	2
L-isoleucine biosynthesis V	3	3	1
benzoyl-CoA biosynthesis	3	3	1
L-leucine degradation I	6	5	2
acrylate degradation II	3	2	1
L-valine degradation III (oxidative Stickland reaction)	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	2	1
L-leucine degradation V (oxidative Stickland reaction)	3	2	1
2-methyl-branched fatty acid β-oxidation	14	10	4
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
glycogen biosynthesis II (from UDP-D-Glucose)	4	1	1
valproate β-oxidation	9	7	2
adipate degradation	5	5	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
acrylate degradation I	5	3	1
starch biosynthesis	10	5	2
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	5	2
L-isoleucine biosynthesis IV	6	5	1
β-alanine biosynthesis II	6	5	1
L-isoleucine degradation I	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
propanoate fermentation to 2-methylbutanoate	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
benzoyl-CoA degradation I (aerobic)	7	3	1
2,4-dinitrotoluene degradation	7	1	1
myo-inositol degradation I	7	1	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	4	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
phenylacetate degradation I (aerobic)	9	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
3-phenylpropanoate degradation	10	3	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
pyruvate fermentation to hexanol (engineered)	11	7	1
superpathway of phenylethylamine degradation	11	4	1
Spodoptera littoralis pheromone biosynthesis	22	3	2
oleate β-oxidation	35	30	3
3-hydroxypropanoate cycle	13	6	1
glyoxylate assimilation	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
superpathway of the 3-hydroxypropanoate cycle	18	6	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1