Experiment set2IT073 for Pseudomonas simiae WCS417

L-Arginine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Arginine (20 mM), pH=7
Culturing: fluoroDangl_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 2/18/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium 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 7 genes in this experiment

For carbon source L-Arginine in Pseudomonas simiae WCS417

For carbon source L-Arginine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	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
• Glycolysis / Gluconeogenesis
• Glutamate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• Butanoate metabolism
• Methane metabolism
• Nitrogen metabolism
• 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
ammonia assimilation cycle I	2	2	1
ammonia assimilation cycle II	2	2	1
L-arginine degradation I (arginase pathway)	3	3	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
superpathway of ammonia assimilation (plants)	3	3	1
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
L-arginine degradation VI (arginase 2 pathway)	4	4	1
putrescine degradation II	4	3	1
L-arginine biosynthesis II (acetyl cycle)	10	10	2
L-ornithine biosynthesis I	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
L-Nδ-acetylornithine biosynthesis	7	6	1
L-glutamate and L-glutamine biosynthesis	7	6	1
L-citrulline biosynthesis	8	8	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	8	1
superpathway of L-citrulline metabolism	12	10	1
superpathway of L-arginine and L-ornithine degradation	13	10	1
superpathway of arginine and polyamine biosynthesis	17	15	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1