Experiment set27IT028 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 56 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	7
Valine degradation	6
Isoleucine degradation	5
Polyamine Metabolism	4
Leucine Degradation and HMG-CoA Metabolism	3
Respiratory dehydrogenases 1	3
D-gluconate and ketogluconates metabolism	2
Folate Biosynthesis	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Isobutyryl-CoA to Propionyl-CoA Module	2
2-Ketogluconate Utilization	1
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
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
Glycine cleavage system	1
Hfl operon	1
Ketoisovalerate oxidoreductase	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
Pyrroloquinoline Quinone biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Threonine and Homoserine Biosynthesis	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:

• Arginine and proline metabolism
• Valine, leucine and isoleucine degradation
• Urea cycle and metabolism of amino groups
• Biosynthesis of phenylpropanoids
• Fatty acid metabolism
• Glutamate metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Folate biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Geraniol degradation
• Histidine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Starch and sucrose metabolism
• Inositol phosphate metabolism
• Pyruvate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• 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 II
• Insect hormone biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cadaverine biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
trehalose biosynthesis IV	1	1	1
adenosine nucleotides degradation III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
arginine dependent acid resistance	1	1	1
L-aspartate biosynthesis	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
L-glutamine degradation I	1	1	1
L-proline degradation I	3	3	2
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	2
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	2
putrescine biosynthesis II	3	3	2
putrescine biosynthesis I	2	2	1
L-alanine degradation I	2	2	1
L-glutamate biosynthesis I	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
L-glutamate degradation II	2	2	1
β-alanine degradation II	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
superpathway of putrescine biosynthesis	4	3	2
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
β-alanine degradation I	2	1	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
putrescine biosynthesis III	2	1	1
superpathway of polyamine biosynthesis I	8	5	3
superpathway of polyamine biosynthesis II	8	5	3
ethanol degradation IV	3	3	1
L-phenylalanine biosynthesis I	3	3	1
ammonia assimilation cycle III	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
ethanol degradation II	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
superpathway of acetate utilization and formation	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
L-isoleucine biosynthesis V	3	2	1
ethanol degradation III	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
aminopropylcadaverine biosynthesis	3	1	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
sulfolactate degradation III	3	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
L-citrulline biosynthesis	8	7	2
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
chitin deacetylation	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
ethene biosynthesis II (microbes)	4	1	1
spermidine biosynthesis III	4	1	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-tyrosine degradation I	5	5	1
glucose degradation (oxidative)	5	5	1
2-methylcitrate cycle I	5	5	1
superpathway of tetrahydrofolate biosynthesis	10	8	2
glucose and glucose-1-phosphate degradation	5	4	1
propanoyl-CoA degradation II	5	3	1
acrylate degradation I	5	3	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
desferrioxamine E biosynthesis	5	1	1
bisucaberin biosynthesis	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
lupanine biosynthesis	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
desferrioxamine B biosynthesis	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	2
superpathway of arginine and polyamine biosynthesis	17	14	3
superpathway of L-threonine biosynthesis	6	6	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	2
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	5	1
TCA cycle VIII (Chlamydia)	6	5	1
L-lysine degradation X	6	5	1
superpathway of L-citrulline metabolism	12	9	2
L-isoleucine biosynthesis IV	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
superpathway of sulfolactate degradation	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
lupulone and humulone biosynthesis	6	1	1
coenzyme M biosynthesis II	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
adlupulone and adhumulone 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-ascorbate biosynthesis VIII (engineered pathway)	7	5	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-lysine degradation I	7	5	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
myo-inositol degradation I	7	1	1
2,4-dinitrotoluene degradation	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
superpathway of aromatic amino acid biosynthesis	18	18	2
folate transformations III (E. coli)	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	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 L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
rosmarinic acid biosynthesis I	10	2	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
(S)-reticuline biosynthesis I	11	3	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of chorismate metabolism	59	42	4
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of L-lysine degradation	43	23	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1