Experiment set2IT062 for Pseudomonas sp. RS175

L-Arginine carbon source 10 mM

Group: carbon source
Media: MME_noCarbon + L-Arginine (10 mM), pH=7
Culturing: Pseudomonas_RS175_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 1-Jul-22
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 11 genes in this experiment

For carbon source L-Arginine in Pseudomonas sp. RS175

For carbon source L-Arginine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	8
Acid resistance mechanisms	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Folate Biosynthesis	1
Polyamine Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Lysine biosynthesis
• Glutamate metabolism
• Folate biosynthesis
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine biosynthesis I	1	1	1
arginine dependent acid resistance	1	1	1
L-arginine degradation II (AST pathway)	5	5	3
4-aminobenzoate biosynthesis II	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
ammonia assimilation cycle I	2	2	1
putrescine biosynthesis I	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
putrescine degradation II	4	2	2
ammonia assimilation cycle II	2	1	1
putrescine biosynthesis II	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
ammonia assimilation cycle III	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
L-ornithine biosynthesis II	3	3	1
L-aspartate degradation II (aerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	3
superpathway of ornithine degradation	8	6	2
superpathway of putrescine biosynthesis	4	3	1
L-arginine degradation VI (arginase 2 pathway)	4	3	1
spermidine biosynthesis III	4	1	1
superpathway of L-arginine and L-ornithine degradation	13	9	3
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-glutamate and L-glutamine biosynthesis	7	5	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-citrulline biosynthesis	8	7	1
superpathway of polyamine biosynthesis II	8	5	1
superpathway of polyamine biosynthesis I	8	5	1
superpathway of arginine and polyamine biosynthesis	17	14	2
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 tetrahydrofolate biosynthesis	10	8	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
superpathway of chorismate metabolism	59	43	1