Experiment set27IT029 for Pseudomonas putida KT2440

DL-2-Aminobutyric acid nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + DL-2-Aminobutyric acid (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Mitchell Thompson on 11/8/20
Media components: 10 mM D-Glucose, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 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 62 genes in this experiment

For nitrogen source DL-2-Aminobutyric acid in Pseudomonas putida KT2440

For nitrogen source DL-2-Aminobutyric acid across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	6
Valine degradation	6
Isoleucine degradation	5
Leucine Degradation and HMG-CoA Metabolism	3
Respiratory dehydrogenases 1	3
2-Ketogluconate Utilization	2
D-gluconate and ketogluconates metabolism	2
Folate Biosynthesis	2
Isobutyryl-CoA to Propionyl-CoA Module	2
Polyamine Metabolism	2
Acetyl-CoA fermentation to Butyrate	1
Acid resistance mechanisms	1
Ammonia assimilation	1
Anaerobic respiratory reductases	1
Branched-Chain Amino Acid Biosynthesis	1
Butanol Biosynthesis	1
Central meta-cleavage pathway of aromatic compound degradation	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Cobalt-zinc-cadmium resistance	1
Coenzyme PQQ synthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA repair, bacterial MutL-MutS system	1
Entner-Doudoroff Pathway	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine cleavage system	1
Heat shock dnaK gene cluster extended	1
Hfl operon	1
Ketoisovalerate oxidoreductase	1
Lysine degradation	1
Orphan regulatory proteins	1
Phosphate metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Purine conversions	1
Pyrimidine utilization	1
Pyrroloquinoline Quinone biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Transport of Zinc	1
Trehalose Biosynthesis	1
Tryptophan synthesis	1
Universal GTPases	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Folate biosynthesis
• Biosynthesis of phenylpropanoids
• Pentose phosphate pathway
• Ubiquinone and menaquinone biosynthesis
• Pyrimidine metabolism
• Glutamate metabolism
• Geraniol degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Starch and sucrose metabolism
• Inositol phosphate metabolism
• Pyruvate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cadaverine biosynthesis	1	1	1
adenosine nucleotides degradation III	1	1	1
arginine dependent acid resistance	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
L-glutamine degradation I	1	1	1
acetate conversion to acetyl-CoA	1	1	1
trehalose biosynthesis IV	1	1	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	2
L-proline degradation I	3	3	2
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
L-alanine degradation I	2	2	1
putrescine biosynthesis I	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
β-alanine degradation II	2	2	1
L-glutamate biosynthesis I	2	2	1
superpathway of putrescine biosynthesis	4	3	2
putrescine biosynthesis III	2	1	1
β-alanine degradation I	2	1	1
superpathway of polyamine biosynthesis I	8	5	3
ethanol degradation II	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
putrescine biosynthesis II	3	3	1
ethanol degradation IV	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
superpathway of acetate utilization and formation	3	3	1
ammonia assimilation cycle III	3	3	1
L-isoleucine biosynthesis V	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
ethanol degradation III	3	2	1
aminopropylcadaverine biosynthesis	3	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
L-citrulline biosynthesis	8	7	2
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
superpathway of polyamine biosynthesis II	8	5	2
chitin deacetylation	4	2	1
ethene biosynthesis II (microbes)	4	1	1
spermidine biosynthesis III	4	1	1
2-methylcitrate cycle I	5	5	1
glucose degradation (oxidative)	5	5	1
superpathway of tetrahydrofolate biosynthesis	10	8	2
glucose and glucose-1-phosphate degradation	5	4	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
desferrioxamine B biosynthesis	5	1	1
desferrioxamine E biosynthesis	5	1	1
bisucaberin biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
superpathway of arginine and polyamine biosynthesis	17	14	3
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	2
β-alanine biosynthesis II	6	5	1
L-lysine degradation X	6	5	1
2-methylcitrate cycle II	6	5	1
superpathway of L-citrulline metabolism	12	9	2
pyruvate fermentation to butanol II (engineered)	6	4	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of bitter acids biosynthesis	18	3	3
(5R)-carbapenem carboxylate biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
superpathway of L-arginine and L-ornithine degradation	13	11	2
L-glutamate and L-glutamine biosynthesis	7	6	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-ascorbate biosynthesis VIII (engineered pathway)	7	5	1
L-lysine degradation I	7	5	1
2,4-dinitrotoluene degradation	7	1	1
myo-inositol degradation I	7	1	1
L-valine degradation I	8	6	1
superpathway of ornithine degradation	8	6	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
folate transformations III (E. coli)	9	9	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	2	1
chloramphenicol biosynthesis	9	1	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
folate transformations II (plants)	11	10	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
pyruvate fermentation to hexanol (engineered)	11	8	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of chorismate metabolism	59	42	2
superpathway of L-lysine degradation	43	23	1