Experiment set6IT063 for Pseudomonas fluorescens FW300-N2E3

Minimal media pH9

Group: pH
Media: RCH2_defined_glucose_TAPS, pH=9
Culturing: pseudo3_N2E3_ML2, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Jayashree on 10/28/2015
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, 20 mM TAPS sodium 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 35 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	4
Glycine and Serine Utilization	2
Glycine cleavage system	2
Photorespiration (oxidative C2 cycle)	2
Sodium Hydrogen Antiporter	2
Biogenesis of c-type cytochromes	1
De Novo Pyrimidine Synthesis	1
Fructose utilization	1
Hemin transport system	1
LMPTP YwlE cluster	1
Periplasmic disulfide interchange	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Queuosine-Archaeosine Biosynthesis	1
Thiamin biosynthesis	1
Ubiquinone Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Thiamine metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Pyrimidine metabolism
• Glutamate metabolism
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Tyrosine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Propanoate metabolism
• Butanoate metabolism
• One carbon pool by folate
• Limonene and pinene degradation
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
hydroxymethylpyrimidine salvage	2	2	2
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	2
glyphosate degradation II	1	1	1
pyrimidine nucleobases salvage I	1	1	1
4-hydroxybenzoate biosynthesis II (bacteria)	1	1	1
glycine biosynthesis II	3	3	2
glycine cleavage	3	3	2
pyrimidine nucleobases salvage II	2	2	1
4-aminobutanoate degradation III	2	2	1
spermidine biosynthesis I	2	2	1
spermine biosynthesis	2	1	1
thiamine diphosphate salvage II	5	4	2
glycine degradation	3	3	1
aminopropylcadaverine biosynthesis	3	3	1
thiamine diphosphate salvage IV (yeast)	7	3	2
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	2
superpathway of thiamine diphosphate biosynthesis II	11	9	3
superpathway of pyrimidine nucleobases salvage	4	4	1
spermidine biosynthesis III	4	2	1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	3	2
polybrominated phenols biosynthesis	4	1	1
L-lysine degradation IV	5	5	1
superpathway of thiamine diphosphate biosynthesis I	10	8	2
L-lysine degradation X	6	6	1
L-leucine degradation I	6	5	1
L-lysine degradation III	6	2	1
L-lysine degradation I	7	5	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
spongiadioxin C biosynthesis	7	2	1
superpathway of polyamine biosynthesis I	8	7	1
superpathway of polyamine biosynthesis II	8	6	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
polybrominated dihydroxylated diphenyl ethers biosynthesis	8	2	1
folate transformations III (E. coli)	9	9	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
photorespiration I	9	5	1
photorespiration III	9	5	1
ubiquinol-8 biosynthesis (late decarboxylation)	9	4	1
p-HBAD biosynthesis	9	1	1
superpathway of pyrimidine ribonucleosides salvage	10	7	1
photorespiration II	10	6	1
folate transformations II (plants)	11	10	1
L-methionine salvage cycle III	11	10	1
superpathway of ubiquinol-8 biosynthesis (early decarboxylation)	12	10	1
L-methionine salvage cycle I (bacteria and plants)	12	9	1
folate transformations I	13	9	1
tetrahydromethanopterin biosynthesis	14	3	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of polybrominated aromatic compound biosynthesis	20	2	1
phenolphthiocerol biosynthesis	23	1	1
superpathway of L-lysine degradation	43	18	1
superpathway of chorismate metabolism	59	43	1