Experiment set27IT069 for Pseudomonas putida KT2440

L-Leucine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + L-Leucine (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Mitchell Thompson on 11/8/20
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 17 genes in this experiment

For nitrogen source L-Leucine in Pseudomonas putida KT2440

For nitrogen source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	2
Respiratory dehydrogenases 1	2
Ammonia assimilation	1
Bacterial Chemotaxis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
HMG CoA Synthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Peptidoglycan Biosynthesis	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate Alanine Serine Interconversions	1
Serine-glyoxylate cycle	1
Type IV pilus	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
• Glutamate metabolism
• Lysine degradation
• Peptidoglycan biosynthesis
• Nitrogen metabolism
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Phenylalanine metabolism
• Aminophosphonate metabolism
• Nucleotide sugars metabolism
• Biotin metabolism
• Caprolactam degradation
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-alanine biosynthesis II	1	1	1
L-glutamine degradation I	1	1	1
L-alanine degradation III	1	1	1
L-glutamine degradation II	1	1	1
L-proline degradation I	3	3	2
ammonia assimilation cycle III	3	3	2
L-alanine degradation V (oxidative Stickland reaction)	2	1	1
L-alanine degradation II (to D-lactate)	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
pyruvate fermentation to acetate and alanine	3	1	1
L-glutamate and L-glutamine biosynthesis	7	6	2
superpathway of L-alanine biosynthesis	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
L-citrulline biosynthesis	8	7	2
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
ethene biosynthesis II (microbes)	4	1	1
L-arginine degradation II (AST pathway)	5	5	1
L-leucine degradation I	6	5	1
superpathway of L-citrulline metabolism	12	9	2
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
L-Nδ-acetylornithine biosynthesis	7	5	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
L-lysine degradation V	9	9	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of L-lysine degradation	43	23	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1