Experiment set12IT023 for Pseudomonas putida KT2440

L-Lysine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Lysine (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Putida_ML5_JBEI, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: Matthew Incha on 12-Feb-19
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 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 16 genes in this experiment

For carbon source L-Lysine in Pseudomonas putida KT2440

For carbon source L-Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Lysine degradation	4
Arginine and Ornithine Degradation	1
Glycolate, glyoxylate interconversions	1
Photorespiration (oxidative C2 cycle)	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
• Tryptophan metabolism
• Urea cycle and metabolism of amino groups
• Glyoxylate and dicarboxylate metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Alkaloid biosynthesis II
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Nitrogen metabolism
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-lysine degradation IV	5	5	3
L-lysine degradation V	9	9	5
indole-3-acetate biosynthesis III (bacteria)	2	2	1
4-aminobutanoate degradation III	2	2	1
glycolate and glyoxylate degradation II	2	2	1
glutarate degradation	2	2	1
L-proline biosynthesis IV	2	1	1
trans-3-hydroxy-L-proline degradation	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
histamine degradation	3	1	1
glycolate and glyoxylate degradation III	3	1	1
glycolate and glyoxylate degradation I	4	4	1
phytol degradation	4	3	1
putrescine degradation III	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
superpathway of L-lysine degradation	43	23	8
L-lysine degradation X	6	5	1
3-methyl-branched fatty acid α-oxidation	6	3	1
L-lysine degradation III	6	2	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
superpathway of glycol metabolism and degradation	7	6	1
L-lysine degradation I	7	5	1
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
photorespiration I	9	6	1
photorespiration III	9	6	1
photorespiration II	10	7	1