Experiment set2H17 for Pseudomonas stutzeri RCH2

L-Arginine nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + L-Arginine (5 mM), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Kelly on 6/20/2013
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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)
Growth plate: 552 A1,A2

Specific Phenotypes

For 7 genes in this experiment

For nitrogen source L-Arginine in Pseudomonas stutzeri RCH2

For nitrogen source L-Arginine across organisms

SEED Subsystems

Subsystem	#Specific
Urea decomposition	4
Acid resistance mechanisms	1
Arginine and Ornithine Degradation	1
Glutamine, Glutamate, Aspartate and Asparagine 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
• Nitrogen metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• One carbon pool by folate
• Atrazine degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
urea degradation I	3	3	3
arginine dependent acid resistance	1	1	1
L-glutamine biosynthesis I	1	1	1
ammonia assimilation cycle I	2	2	1
superpathway of allantoin degradation in yeast	6	5	3
putrescine biosynthesis I	2	1	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	1	1
ammonia assimilation cycle II	2	1	1
cyanuric acid degradation II	5	4	2
cyanuric acid degradation I	5	2	2
glycine cleavage	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
L-citrulline degradation	3	3	1
ammonia assimilation cycle III	3	3	1
putrescine biosynthesis II	3	3	1
cyanate degradation	3	3	1
glycine biosynthesis II	3	3	1
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-arginine degradation V (arginine deiminase pathway)	4	4	1
putrescine degradation II	4	3	1
superpathway of atrazine degradation	8	4	2
superpathway of putrescine biosynthesis	4	2	1
spermidine biosynthesis III	4	1	1
uracil degradation III	5	2	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	2
superpathway of L-arginine and L-ornithine degradation	13	8	2
L-glutamate and L-glutamine biosynthesis	7	5	1
superpathway of ornithine degradation	8	6	1
superpathway of polyamine biosynthesis II	8	5	1
superpathway of polyamine biosynthesis I	8	5	1
allantoin degradation IV (anaerobic)	9	2	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of arginine and polyamine biosynthesis	17	14	1