Experiment set4S50 for Pseudomonas sp. RS175

L-Lysine carbon source 10 mM

Group: carbon source
Media: MME_noCarbon + L-Lysine (10 mM)
Culturing: Pseudomonas_RS175_ML2, 96 deep well, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 31-January-23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 10 genes in this experiment

For carbon source L-Lysine in Pseudomonas sp. RS175

For carbon source L-Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	2
Lysine degradation	2
Orphan regulatory proteins	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine degradation
• Arginine and proline metabolism
• Lysine biosynthesis
• Tryptophan metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• Benzoate degradation via CoA ligation
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Nitrogen metabolism
• 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
L-glutamine biosynthesis I	1	1	1
L-lysine degradation IV	5	4	3
indole-3-acetate biosynthesis III (bacteria)	2	2	1
ammonia assimilation cycle I	2	2	1
ammonia assimilation cycle II	2	1	1
L-ornithine biosynthesis II	3	3	1
ammonia assimilation cycle III	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
L-arginine degradation VI (arginase 2 pathway)	4	3	1
putrescine degradation II	4	2	1
L-arginine biosynthesis II (acetyl cycle)	10	10	2
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
L-Nδ-acetylornithine biosynthesis	7	5	1
L-glutamate and L-glutamine biosynthesis	7	5	1
L-citrulline biosynthesis	8	7	1
superpathway of ornithine degradation	8	6	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
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
superpathway of L-lysine degradation	43	18	3
superpathway of arginine and polyamine biosynthesis	17	14	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1