Experiment set2IT039 for Pseudomonas fluorescens FW300-N2E3

L-Arginine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Arginine (10 mM), pH=7.2
Culturing: pseudo3_N2E3_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.8 generations
By: Jayashree on 6/11/2014
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 5 genes in this experiment

For carbon source L-Arginine in Pseudomonas fluorescens FW300-N2E3

For carbon source L-Arginine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	2
Transport of Zinc	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
• Glutamate metabolism
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Tyrosine metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Nitrogen metabolism

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
4-aminobutanoate degradation III	2	2	1
ammonia assimilation cycle II	2	2	1
ammonia assimilation cycle III	3	3	1
superpathway of ammonia assimilation (plants)	3	3	1
L-aspartate degradation II (aerobic)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
putrescine degradation II	4	3	1
L-lysine degradation IV	5	5	1
L-lysine degradation X	6	6	1
L-lysine degradation III	6	2	1
L-glutamate and L-glutamine biosynthesis	7	6	1
L-lysine degradation I	7	5	1
lipoprotein posttranslational modification (Gram-negative bacteria)	7	2	1
superpathway of ornithine degradation	8	7	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
superpathway of L-lysine degradation	43	18	1