Experiment set19IT030 for Pseudomonas stutzeri RCH2

Defined media with L-tyrosine disodium salt

Group: nutrient
Media: RCH2_defined_glucose + L-tyrosine disodium salt (1 mM)
Culturing: psRCH2_ML7c, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.3 generations
By: Adam on 20-Jun-16
Media components: 0.25 g/L Ammonium chloride, 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)

Specific Phenotypes

For 18 genes in this experiment

For nutrient L-tyrosine disodium salt in Pseudomonas stutzeri RCH2

For nutrient L-tyrosine disodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Flagellum	6
Flagellar motility	4
Bacterial Chemotaxis	3
Aromatic amino acid degradation	1
Bacterial Cytoskeleton	1
Catechol branch of beta-ketoadipate pathway	1
Gentisare degradation	1
Homogentisate pathway of aromatic compound degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Plasmid replication	1
Plastoquinone Biosynthesis	1
Protocatechuate branch of beta-ketoadipate pathway	1
Salicylate and gentisate catabolism	1
Serine-glyoxylate cycle	1
Tocopherol Biosynthesis	1
Two cell division clusters relating to chromosome partitioning	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Styrene degradation
• Butanoate metabolism
• Synthesis and degradation of ketone bodies
• Ubiquinone and menaquinone biosynthesis
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Phenylalanine metabolism
• Glutathione metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
thiosulfate disproportionation IV (rhodanese)	1	1	1
L-tyrosine degradation I	5	5	3
L-cysteine degradation III	2	1	1
ketolysis	3	3	1
plastoquinol-9 biosynthesis I	3	1	1
4-hydroxy-2-nonenal detoxification	4	1	1
superpathway of plastoquinol biosynthesis	5	2	1
sulfide oxidation IV (mitochondria)	5	2	1
pentachlorophenol degradation	10	3	2
gallate degradation III (anaerobic)	11	5	2
acetyl-CoA fermentation to butanoate	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	4	1
4-aminobutanoate degradation V	7	3	1
succinate fermentation to butanoate	7	2	1
vitamin E biosynthesis (tocopherols)	7	1	1
glutathione-mediated detoxification I	8	3	1
TCA cycle VI (Helicobacter)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
gliotoxin biosynthesis	9	1	1
glutathione-mediated detoxification II	9	1	1
L-glutamate degradation V (via hydroxyglutarate)	10	7	1
indole glucosinolate activation (intact plant cell)	12	3	1
camalexin biosynthesis	12	2	1