Experiment set7IT061 for Pseudomonas putida KT2440

DL-2-Aminoadipic acid 10 mM carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + DL-2-Aminoadipic acid (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.3 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 12 genes in this experiment

For carbon source DL-2-Aminoadipic acid in Pseudomonas putida KT2440

For carbon source DL-2-Aminoadipic acid across organisms

SEED Subsystems

Subsystem	#Specific
Fermentations: Mixed acid	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycolate, glyoxylate interconversions	1
Ketoisovalerate oxidoreductase	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Propanoate metabolism
• Fatty acid metabolism
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
ethanol degradation II	3	3	2
glycolate and glyoxylate degradation II	2	2	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation I	2	1	1
superpathway of acetate utilization and formation	3	3	1
ethanol degradation IV	3	3	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-valine degradation II	3	2	1
ethanol degradation III	3	2	1
L-methionine degradation III	3	1	1
pyruvate fermentation to ethanol III	3	1	1
glycolate and glyoxylate degradation III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
glycolate and glyoxylate degradation I	4	4	1
phytol degradation	4	3	1
salidroside biosynthesis	4	3	1
chitin deacetylation	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
2-methylcitrate cycle I	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
ethanolamine utilization	5	4	1
acetylene degradation (anaerobic)	5	3	1
phenylethanol biosynthesis	5	3	1
(S)-propane-1,2-diol degradation	5	2	1
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	5	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of bitter acids biosynthesis	18	3	3
lupulone and humulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
noradrenaline and adrenaline degradation	13	8	2
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glycol metabolism and degradation	7	6	1
serotonin degradation	7	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
L-lysine degradation V	9	9	1
photorespiration I	9	6	1
photorespiration III	9	6	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	1
cis-geranyl-CoA degradation	9	2	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
photorespiration II	10	7	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	1
heterolactic fermentation	18	12	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of anaerobic sucrose degradation	19	13	1
superpathway of N-acetylneuraminate degradation	22	12	1
superpathway of L-lysine degradation	43	23	1