Experiment set25S542 for Pseudomonas fluorescens FW300-N2E2

Ying_AminoAcid20 rep C; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_AminoAcid20
Culturing: pseudo6_N2E2_ML5b, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on 1-Sep-23
Media components: 1.5 g/L Ammonium chloride, 0.6 g/L Potassium phosphate monobasic, 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)

Ying_AminoAcid20 1x includes: 128 uM L-Alanine, 128 uM L-Arginine, 128 uM L-Asparagine, 128 uM L-Aspartic Acid, 128 uM L-Cysteine, 128 uM L-Glutamic acid, 128 uM L-Glutamine, 128 uM Glycine, 128 uM L-Histidine, 128 uM L-Isoleucine, 128 uM L-Leucine, 128 uM L-Lysine, 128 uM L-Methionine, 128 uM L-Phenylalanine, 128 uM L-Proline, 128 uM L-Serine, 128 uM L-Threonine, 128 uM L-Tryptophan, 128 uM L-tyrosine, 128 uM L-Valine

Specific Phenotypes

For 5 genes in this experiment

For carbon source Ying_AminoAcid20 in Pseudomonas fluorescens FW300-N2E2

For carbon source Ying_AminoAcid20 across organisms

SEED Subsystems

Subsystem	#Specific
Arginine Biosynthesis extended	1
Flagellum	1
Histidine Degradation	1
Isoleucine degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Methylcitrate cycle	1
Propionate-CoA to Succinate Module	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Histidine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Propanoate metabolism
• Limonene and pinene degradation
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
L-histidine degradation I	4	4	1
L-ornithine biosynthesis I	5	5	1
L-histidine degradation II	5	5	1
2-methylcitrate cycle I	5	5	1
2-methylcitrate cycle II	6	5	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 arginine and polyamine biosynthesis	17	14	1