Experiment setAIT088 for Pseudomonas fluorescens FW300-N2E2

Uridine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Uridine (20 mM)
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
Growth: about 4.5 generations
By: Mark on 1/21/2016
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 12 genes in this experiment

For nitrogen source Uridine in Pseudomonas fluorescens FW300-N2E2

For nitrogen source Uridine across organisms

SEED Subsystems

Subsystem	#Specific
Pyrimidine utilization	3
DNA-binding regulatory proteins, strays	1
Hydantoin metabolism	1
Maltose and Maltodextrin Utilization	1
Pyruvate Alanine Serine Interconversions	1
Trehalose Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• beta-Alanine metabolism
• Nitrogen metabolism
• Pyrimidine metabolism
• Arginine and proline metabolism
• Pantothenate and CoA biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Urea cycle and metabolism of amino groups
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Starch and sucrose metabolism
• Propanoate 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
ammonia assimilation cycle III	3	3	3
L-glutamate biosynthesis I	2	2	2
ammonia assimilation cycle I	2	2	2
L-glutamine degradation I	1	1	1
L-glutamate biosynthesis IV	1	1	1
L-glutamine biosynthesis I	1	1	1
L-glutamine degradation II	1	1	1
thymine degradation	3	3	2
uracil degradation I (reductive)	3	3	2
superpathway of ammonia assimilation (plants)	3	3	2
L-glutamate and L-glutamine biosynthesis	7	6	4
β-alanine degradation II	2	2	1
ammonia assimilation cycle II	2	2	1
superpathway of pyrimidine ribonucleosides degradation	5	3	2
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
putrescine degradation II	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
β-alanine biosynthesis II	6	5	1
superpathway of ornithine degradation	8	7	1
L-citrulline biosynthesis	8	6	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of L-arginine and L-ornithine degradation	13	11	1