Experiment set6IT085 for Pseudomonas fluorescens FW300-N2C3

Minimal media pH9

Group: pH
Media: RCH2_defined_glucose_TAPS, pH=9
Culturing: pseudo5_N2-C3_1_ML2, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Jayashree on 10/28/2014
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 10 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Fructose utilization	2
Carboxysome	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Cyanate hydrolysis	1
Fructose and Mannose Inducible PTS	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Mannitol Utilization	1
Photorespiration (oxidative C2 cycle)	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
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Tyrosine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Limonene and pinene degradation
• Nitrogen metabolism
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
glycine cleavage	3	3	1
cyanate degradation	3	3	1
glycine biosynthesis II	3	3	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
chorismate biosynthesis I	7	7	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of thiamine diphosphate biosynthesis I	10	7	1
superpathway of thiamine diphosphate biosynthesis II	11	8	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-tryptophan biosynthesis	13	13	1
3-hydroxypropanoate cycle	13	5	1
glyoxylate assimilation	13	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
superpathway of aromatic amino acid biosynthesis	18	18	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
superpathway of the 3-hydroxypropanoate cycle	18	5	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1
superpathway of chorismate metabolism	59	44	1