Experiment set7IT055 for Pseudomonas putida KT2440

L-Lysine 10 mM 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 6.3 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 23 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	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Cobalt-zinc-cadmium resistance	1
Glycine cleavage system	1
Glycolate, glyoxylate interconversions	1
Orphan regulatory proteins	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1
Universal stress protein family	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine degradation
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• Glyoxylate and dicarboxylate metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Atrazine degradation
• Nitrogen metabolism
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
urea degradation I	3	2	2
L-lysine degradation IV	5	5	3
glycolate and glyoxylate degradation II	2	2	1
4-aminobutanoate degradation III	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
glutarate degradation	2	2	1
L-lysine degradation V	9	9	4
cyanuric acid degradation II	5	3	2
cyanuric acid degradation I	5	2	2
ethanol degradation IV	3	3	1
L-citrulline degradation	3	3	1
ethanol degradation II	3	3	1
ethanol degradation III	3	2	1
cyanate degradation	3	2	1
hypotaurine degradation	3	2	1
superpathway of allantoin degradation in yeast	6	3	2
histamine degradation	3	1	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
glycolate and glyoxylate degradation III	3	1	1
glycolate and glyoxylate degradation I	4	4	1
L-arginine degradation V (arginine deiminase pathway)	4	4	1
glycine betaine degradation I	8	6	2
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
creatinine degradation I	4	2	1
superpathway of atrazine degradation	8	3	2
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	5	4	1
uracil degradation III	5	3	1
creatinine degradation II	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
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
superpathway of L-lysine degradation	43	23	7
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
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
allantoin degradation IV (anaerobic)	9	2	1
photorespiration II	10	7	1