Experiment set28IT036 for Pseudomonas putida KT2440

Uracil nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + Uracil (5 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Mitchell Thompson on 11/16/20
Media components: 10 mM D-Glucose, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 7 genes in this experiment

For nitrogen source Uracil in Pseudomonas putida KT2440

For nitrogen source Uracil across organisms

SEED Subsystems

Subsystem	#Specific
Pyrimidine utilization	3
2-Ketogluconate Utilization	1
DNA-binding regulatory proteins, strays	1
Hydantoin metabolism	1
Isobutyryl-CoA to Propionyl-CoA Module	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
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Propanoate metabolism
• Pantothenate and CoA biosynthesis
• Nitrogen metabolism
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• 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
β-alanine degradation II	2	2	2
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
L-glutamate biosynthesis IV	1	1	1
ammonia assimilation cycle III	3	3	2
uracil degradation I (reductive)	3	3	2
thymine degradation	3	3	2
ammonia assimilation cycle I	2	2	1
β-alanine degradation I	2	1	1
L-glutamate and L-glutamine biosynthesis	7	6	3
superpathway of pyrimidine ribonucleosides degradation	5	3	2
superpathway of ammonia assimilation (plants)	3	3	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
propanoyl-CoA degradation II	5	3	1
acrylate degradation I	5	3	1
β-alanine biosynthesis II	6	5	1
myo-inositol degradation I	7	1	1
2,4-dinitrotoluene degradation	7	1	1
L-citrulline biosynthesis	8	7	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	1	1
superpathway of L-citrulline metabolism	12	9	1