Experiment set7IT056 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 4/26/18
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 12 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	2
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
• beta-Alanine metabolism
• Propanoate metabolism
• Butanoate metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Limonene and pinene degradation
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-lysine degradation V	9	9	5
glycolate and glyoxylate degradation II	2	2	1
4-aminobutanoate degradation III	2	2	1
4-aminobutanoate degradation I	2	2	1
4-aminobutanoate degradation II	2	2	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
superpathway of 4-aminobutanoate degradation	3	3	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
glycolate and glyoxylate degradation III	3	1	1
histamine degradation	3	1	1
glycolate and glyoxylate degradation I	4	4	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
GABA shunt II	4	3	1
phytol degradation	4	3	1
putrescine degradation III	4	3	1
GABA shunt I	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
L-lysine degradation XI	5	2	1
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
4-aminobutanoate degradation V	7	2	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	5
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
superpathway of L-arginine and L-ornithine degradation	13	11	1
nicotine degradation I (pyridine pathway)	17	5	1