Experiment set27IT032 for Pseudomonas putida KT2440

D-Lysine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + D-Lysine (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 10 genes in this experiment

For nitrogen source D-Lysine in Pseudomonas putida KT2440

For nitrogen source D-Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Lysine degradation	3
Arginine and Ornithine Degradation	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine degradation
• Arginine and proline metabolism
• Alkaloid biosynthesis II
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Histidine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
trans-3-hydroxy-L-proline degradation	2	1	1
L-proline biosynthesis IV	2	1	1
L-lysine degradation V	9	9	4
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
histamine degradation	3	1	1
putrescine degradation III	4	3	1
phytol degradation	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
N-hydroxy-L-pipecolate biosynthesis	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-lysine degradation II (L-pipecolate pathway)	9	5	2
octane oxidation	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
serotonin degradation	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of L-lysine degradation	43	23	4