Experiment set2IT079 for Pseudomonas simiae WCS417

L-Valine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Valine (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 20 genes in this experiment

For carbon source L-Valine in Pseudomonas simiae WCS417

For carbon source L-Valine across organisms

SEED Subsystems

Subsystem	#Specific
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Aromatic amino acid degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Histidine Degradation	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Lysine degradation	1
Methionine Degradation	1
Phosphate metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Ribosome biogenesis bacterial	1
Threonine and Homoserine Biosynthesis	1
Valine degradation	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of plant hormones
• Tryptophan metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• beta-Alanine metabolism
• Propanoate metabolism
• Butanoate metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of phenylpropanoids
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Geraniol degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Carbon fixation in photosynthetic organisms
• Thiamine metabolism
• Riboflavin metabolism
• Limonene and pinene degradation
• Nitrogen metabolism
• Caprolactam degradation
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate biosynthesis	1	1	1
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
L-methionine degradation II	3	3	2
ammonia assimilation cycle III	3	3	2
L-glutamate degradation II	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
L-threonine degradation I	6	4	3
L-threonine degradation V	2	1	1
atromentin biosynthesis	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine degradation II	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
L-phenylalanine biosynthesis I	3	3	1
benzoyl-CoA biosynthesis	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
sulfolactate degradation III	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
superpathway of L-isoleucine biosynthesis I	13	13	4
L-glutamate and L-glutamine biosynthesis	7	6	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
2-methyl-branched fatty acid β-oxidation	14	11	3
hypoglycin biosynthesis	14	4	3
adipate degradation	5	5	1
L-tyrosine degradation I	5	5	1
L-histidine degradation II	5	5	1
L-lysine degradation IV	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
trans-4-hydroxy-L-proline degradation I	5	3	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
superpathway of branched chain amino acid biosynthesis	17	17	3
superpathway of L-threonine biosynthesis	6	6	1
β-alanine biosynthesis II	6	5	1
TCA cycle VIII (Chlamydia)	6	5	1
superpathway of L-threonine metabolism	18	12	3
NAD(P)/NADPH interconversion	6	3	1
methyl ketone biosynthesis (engineered)	6	3	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
fatty acid β-oxidation I (generic)	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
benzoyl-CoA degradation I (aerobic)	7	3	1
L-citrulline biosynthesis	8	8	1
L-valine degradation I	8	6	1
superpathway of aromatic amino acid biosynthesis	18	18	2
valproate β-oxidation	9	7	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
phenylacetate degradation I (aerobic)	9	3	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
3-phenylpropanoate degradation	10	3	1
rosmarinic acid biosynthesis I	10	2	1
superpathway of phenylethylamine degradation	11	4	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
(S)-reticuline biosynthesis I	11	1	1
oleate β-oxidation	35	30	3
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of L-citrulline metabolism	12	10	1
indole-3-acetate biosynthesis II	12	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
superpathway of rosmarinic acid biosynthesis	14	3	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
cyclosporin A biosynthesis	15	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
aspartate superpathway	25	22	1
platensimycin biosynthesis	26	6	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	44	2
superpathway of L-lysine degradation	43	17	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1