Experiment set5IT093 for Pseudomonas simiae WCS417

Urea nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Urea (20 mM), pH=7
Culturing: fluoroDangl_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/2/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 10 genes in this experiment

For nitrogen source Urea in Pseudomonas simiae WCS417

For nitrogen source Urea across organisms

SEED Subsystems

Subsystem	#Specific
2-Ketogluconate Utilization	2
Urea decomposition	2
Carboxysome	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Cyanate hydrolysis	1
D-gluconate and ketogluconates metabolism	1
Peptidyl-prolyl cis-trans isomerase	1
Potassium homeostasis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Arginine and proline metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Glutathione metabolism
• Atrazine degradation
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
urea degradation II	1	1	1
3-dehydroquinate biosynthesis I	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
cyanate degradation	3	3	1
glucose degradation (oxidative)	5	5	1
chorismate biosynthesis I	7	7	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
superpathway of allantoin degradation in plants	8	4	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
NiFe(CO)(CN)2 cofactor biosynthesis	10	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
superpathway of L-tryptophan biosynthesis	13	13	1
3-hydroxypropanoate cycle	13	6	1
glyoxylate assimilation	13	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
superpathway of aromatic amino acid biosynthesis	18	18	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
superpathway of the 3-hydroxypropanoate cycle	18	6	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1
superpathway of chorismate metabolism	59	44	1