Experiment set39IT025 for Pseudomonas putida KT2440

D-2-Aminobutyric acid nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + D-2-Aminobutyric acid (10 mM)
Culturing: Putida_ML5_JBEI, 24-well plate, Aerobic, at 30 (C), shaken=200 rpm
By: Allie Pearson on 28-Sep
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 53 genes in this experiment

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

For nitrogen source D-2-Aminobutyric acid across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	8
Valine degradation	6
Isoleucine degradation	5
Leucine Degradation and HMG-CoA Metabolism	4
Glycine and Serine Utilization	3
Pyruvate Alanine Serine Interconversions	3
Acetyl-CoA fermentation to Butyrate	2
Isobutyryl-CoA to Propionyl-CoA Module	2
Proteolysis in bacteria, ATP-dependent	2
2-Ketogluconate Utilization	1
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Ammonia assimilation	1
Anaerobic respiratory reductases	1
Bacterial Chemotaxis	1
Biotin biosynthesis	1
Butanol Biosynthesis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
D-gluconate and ketogluconates metabolism	1
Fermentations: Mixed acid	1
Folate Biosynthesis	1
Glycine Biosynthesis	1
Ketoisovalerate oxidoreductase	1
LMPTP YwlE cluster	1
Photorespiration (oxidative C2 cycle)	1
Proline, 4-hydroxyproline uptake and utilization	1
Proteasome bacterial	1
Protein chaperones	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Respiratory dehydrogenases 1	1
Serine-glyoxylate cycle	1
Serine Biosynthesis	1
n-Phenylalkanoic acid degradation	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
• Fatty acid metabolism
• Pyruvate metabolism
• Glycolysis / Gluconeogenesis
• Glycine, serine and threonine metabolism
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Geraniol degradation
• Phenylalanine metabolism
• Cyanoamino acid metabolism
• Inositol phosphate metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Brassinosteroid biosynthesis
• Nitrogen metabolism
• Caprolactam degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	3
acetate and ATP formation from acetyl-CoA III	1	1	1
glycine biosynthesis I	1	1	1
long-chain fatty acid activation	1	1	1
acetate conversion to acetyl-CoA	1	1	1
β-alanine degradation II	2	2	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
L-alanine degradation I	2	2	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
β-alanine degradation I	2	1	1
glycine betaine degradation III	7	7	3
pyruvate decarboxylation to acetyl CoA I	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
ethanol degradation IV	3	3	1
glycine degradation	3	3	1
ethanol degradation II	3	3	1
superpathway of acetate utilization and formation	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
ethanol degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
phytol degradation	4	3	1
chitin deacetylation	4	2	1
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
glycine betaine degradation II (mammalian)	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
sporopollenin precursors biosynthesis	18	4	4
2-methylcitrate cycle I	5	5	1
octane oxidation	5	4	1
folate polyglutamylation	5	4	1
propanoyl-CoA degradation II	5	3	1
acrylate degradation I	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
fatty acid salvage	6	6	1
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
L-isoleucine biosynthesis IV	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
superpathway of bitter acids biosynthesis	18	3	3
adlupulone and adhumulone biosynthesis	6	1	1
stearate biosynthesis I (animals)	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
formaldehyde assimilation I (serine pathway)	13	7	2
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
capsaicin biosynthesis	7	3	1
ceramide degradation by α-oxidation	7	2	1
myo-inositol degradation I	7	1	1
2,4-dinitrotoluene degradation	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
partial TCA cycle (obligate autotrophs)	8	8	1
glycine betaine degradation I	8	6	1
L-valine degradation I	8	6	1
nitrogen remobilization from senescing leaves	8	6	1
2-deoxy-D-ribose degradation II	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
folate transformations III (E. coli)	9	9	1
photorespiration I	9	6	1
photorespiration III	9	6	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	2	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
photorespiration II	10	7	1
suberin monomers biosynthesis	20	4	2
myo-, chiro- and scyllo-inositol degradation	10	1	1
superpathway of fatty acid biosynthesis II (plant)	43	38	4
folate transformations II (plants)	11	10	1
pyruvate fermentation to hexanol (engineered)	11	8	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	1
folate transformations I	13	9	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
mixed acid fermentation	16	12	1
cutin biosynthesis	16	1	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
purine nucleobases degradation II (anaerobic)	24	16	1
ethene biosynthesis V (engineered)	25	18	1
superpathway of fatty acids biosynthesis (E. coli)	53	51	2
1-butanol autotrophic biosynthesis (engineered)	27	19	1
palmitate biosynthesis III	29	28	1
oleate β-oxidation	35	30	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1