Experiment set5IT028 for Pseudomonas fluorescens FW300-N1B4

Minimal media pH9

Group: pH
Media: RCH2_defined_glucose_TAPS, pH=9
Culturing: pseudo1_N1B4_ML1, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Jayashree on 10/18/2014_or_07/22/16
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, 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 34 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	5
Biogenesis of c-type cytochromes	2
Lysine degradation	2
Arginine Biosynthesis extended	1
Arginine Deiminase Pathway	1
Biogenesis of cytochrome c oxidases	1
Branched-Chain Amino Acid Biosynthesis	1
DNA Repair Base Excision	1
De Novo Pyrimidine Synthesis	1
Fructose utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Hemin transport system	1
LMPTP YwlE cluster	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Periplasmic disulfide interchange	1
Photorespiration (oxidative C2 cycle)	1
Rhamnose containing glycans	1
Thiamin biosynthesis	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Propanoate metabolism
• Thiamine metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Tyrosine metabolism
• beta-Alanine metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Folate biosynthesis
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

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
pyrimidine nucleobases salvage I	1	1	1
pyrimidine nucleobases salvage II	2	2	1
4-aminobutanoate degradation I	2	2	1
4-aminobutanoate degradation II	2	2	1
4-aminobutanoate degradation III	2	2	1
L-lysine degradation IV	5	5	2
thiamine diphosphate salvage II	5	4	2
glycine biosynthesis II	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
L-ornithine biosynthesis II	3	3	1
glycine cleavage	3	3	1
superpathway of 4-aminobutanoate degradation	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
superpathway of thiamine diphosphate biosynthesis I	10	8	3
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	2
thiamine diphosphate salvage IV (yeast)	7	3	2
superpathway of thiamine diphosphate biosynthesis II	11	9	3
superpathway of pyrimidine nucleobases salvage	4	4	1
L-arginine degradation VI (arginase 2 pathway)	4	3	1
GABA shunt I	4	2	1
GABA shunt II	4	2	1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	3	2
dTDP-β-L-rhamnose biosynthesis	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
L-ornithine biosynthesis I	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
L-lysine degradation X	6	5	1
thiazole component of thiamine diphosphate biosynthesis I	6	4	1
L-lysine degradation III	6	2	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-lysine degradation I	7	4	1
4-aminobutanoate degradation V	7	2	1
L-citrulline biosynthesis	8	7	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	4	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of pyrimidine ribonucleosides salvage	10	7	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
superpathway of arginine and polyamine biosynthesis	17	14	1
nicotine degradation I (pyridine pathway)	17	5	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of L-lysine degradation	43	19	2
aspartate superpathway	25	21	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1