Experiment set7IT062 for Pseudomonas putida KT2440

D-Lysine 10 mM carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + D-Lysine (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.6 generations
By: Mitchell Thompson on 5/3/18
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 19 genes in this experiment

For carbon source D-Lysine in Pseudomonas putida KT2440

For carbon source D-Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Lysine degradation	3
Alginate metabolism	1
Arginine and Ornithine Degradation	1
Glycolate, glyoxylate interconversions	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Mannose Metabolism	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine degradation
• Valine, leucine and isoleucine degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• Propanoate metabolism
• Butanoate metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Alanine and aspartate metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Nicotinate and nicotinamide metabolism
• Limonene and pinene degradation
• Nitrogen metabolism
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-lysine degradation V	9	9	5
indole-3-acetate biosynthesis III (bacteria)	2	2	1
4-aminobutanoate degradation I	2	2	1
4-aminobutanoate degradation II	2	2	1
4-aminobutanoate degradation III	2	2	1
glycolate and glyoxylate degradation II	2	2	1
D-mannose degradation I	2	1	1
D-mannose degradation II	2	1	1
L-lysine degradation IV	5	5	2
superpathway of 4-aminobutanoate degradation	3	3	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation	3	2	1
glycolate and glyoxylate degradation III	3	1	1
mannitol biosynthesis	3	1	1
histamine degradation	3	1	1
glycolate and glyoxylate degradation I	4	4	1
GDP-mannose biosynthesis	4	4	1
phytol degradation	4	3	1
putrescine degradation III	4	3	1
GABA shunt II	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
GABA shunt I	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
mannitol degradation II	4	2	1
L-lysine degradation II (L-pipecolate pathway)	9	5	2
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
1,5-anhydrofructose degradation	5	2	1
L-lysine degradation XI	5	2	1
dopamine degradation	5	2	1
3-methyl-branched fatty acid α-oxidation	6	3	1
NAD(P)/NADPH interconversion	6	3	1
alkane oxidation	6	1	1
superpathway of L-lysine degradation	43	23	7
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
β-(1,4)-mannan degradation	7	2	1
4-aminobutanoate degradation V	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
L-valine degradation I	8	6	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
photorespiration III	9	6	1
photorespiration I	9	6	1
L-lysine biosynthesis IV	9	2	1
photorespiration II	10	7	1
L-lysine biosynthesis V	10	2	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
colanic acid building blocks biosynthesis	11	9	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	7	1
nicotine degradation I (pyridine pathway)	17	5	1