Experiment set10IT013 for Pseudomonas putida KT2440

L-Lysine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Lysine (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.7 generations
By: Mitchell Thompson on 10/1/18
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	3
Arginine and Ornithine Degradation	2
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
• Tryptophan metabolism
• Glyoxylate and dicarboxylate metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Nitrogen metabolism
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
indole-3-acetate biosynthesis III (bacteria)	2	2	1
glycolate and glyoxylate degradation II	2	2	1
glutarate degradation	2	2	1
L-lysine degradation V	9	9	4
L-lysine degradation IV	5	5	2
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
histamine degradation	3	1	1
glycolate and glyoxylate degradation III	3	1	1
glycolate and glyoxylate degradation I	4	4	1
putrescine degradation III	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	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
superpathway of glycol metabolism and degradation	7	6	1
serotonin degradation	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of L-lysine degradation	43	23	6
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 CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
photorespiration I	9	6	1
photorespiration III	9	6	1
L-lysine degradation II (L-pipecolate pathway)	9	5	1
photorespiration II	10	7	1