Experiment set6IT052 for Pseudomonas fluorescens FW300-N2C3

Uridine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Uridine (5 mM), pH=7
Culturing: pseudo5_N2-C3_1_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2014
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 Uridine in Pseudomonas fluorescens FW300-N2C3

For nitrogen source Uridine across organisms

SEED Subsystems

Subsystem	#Specific
Pyrimidine utilization	4
Hydantoin metabolism	2
Ammonia assimilation	1
Bacterial Cell Division	1
DNA-binding regulatory proteins, strays	1
Glycine cleavage system	1
Isobutyryl-CoA to Propionyl-CoA Module	1
L-2-amino-thiazoline-4-carboxylic acid-Lcysteine conversion	1
Orphan regulatory proteins	1
Pyruvate Alanine Serine Interconversions	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• beta-Alanine metabolism
• Pyrimidine metabolism
• Pantothenate and CoA biosynthesis
• Drug metabolism - other enzymes
• Valine, leucine and isoleucine degradation
• Propanoate metabolism
• Alanine and aspartate metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Inositol phosphate metabolism
• Limonene and pinene degradation
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
uracil degradation I (reductive)	3	3	3
thymine degradation	3	3	3
β-alanine degradation II	2	2	2
superpathway of pyrimidine ribonucleosides degradation	5	3	3
β-alanine degradation I	2	1	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
β-alanine biosynthesis II	6	5	1
myo-inositol degradation I	7	7	1
2,4-dinitrotoluene degradation	7	2	1
L-valine degradation I	8	6	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
myo-, chiro- and scyllo-inositol degradation	10	7	1