Experiment set29IT004 for Pseudomonas putida KT2440

Propandiamine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + Propandiamine (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Matthias Schmidt on 4/13/21
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 55 genes in this experiment

For nitrogen source Propandiamine in Pseudomonas putida KT2440

For nitrogen source Propandiamine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	5
Polyamine Metabolism	4
Cobalt-zinc-cadmium resistance	3
Phosphate metabolism	3
Choline and Betaine Uptake and Betaine Biosynthesis	2
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	2
Folate Biosynthesis	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Acid resistance mechanisms	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Branched-Chain Amino Acid Biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
D-gluconate and ketogluconates metabolism	1
DNA-binding regulatory proteins, strays	1
Entner-Doudoroff Pathway	1
Fructose utilization	1
High affinity phosphate transporter and control of PHO regulon	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Ketoisovalerate oxidoreductase	1
Methionine Biosynthesis	1
Methylglyoxal Metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1
Ribosome biogenesis bacterial	1
Tryptophan synthesis	1
Valine degradation	1
ZZ gjo need homes	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
• Urea cycle and metabolism of amino groups
• Tryptophan metabolism
• Propanoate metabolism
• Glycolysis / Gluconeogenesis
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Nucleotide sugars metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Ascorbate and aldarate metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Anthocyanin biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Fructose and mannose metabolism
• Galactose metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Alanine and aspartate metabolism
• Methionine metabolism
• Cysteine metabolism
• Geraniol degradation
• Lysine biosynthesis
• Benzoxazinone biosynthesis
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1,2-Dichloroethane degradation
• Trinitrotoluene degradation
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Styrene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Diterpenoid biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine biosynthesis II	3	3	3
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	3
4-aminobenzoate biosynthesis I	2	2	2
β-alanine degradation II	2	2	2
acetate conversion to acetyl-CoA	1	1	1
L-glutamine biosynthesis I	1	1	1
L-glutamine degradation I	1	1	1
arginine dependent acid resistance	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
ammonia assimilation cycle III	3	3	2
ethanol degradation II	3	3	2
ethanol degradation IV	3	3	2
L-proline degradation I	3	3	2
ethanol degradation III	3	2	2
putrescine degradation V	2	2	1
4-aminobutanoate degradation III	2	2	1
L-homocysteine biosynthesis	2	2	1
putrescine biosynthesis I	2	2	1
L-glutamate biosynthesis I	2	2	1
ammonia assimilation cycle I	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
ammonia assimilation cycle II	2	2	1
putrescine degradation II	4	3	2
putrescine degradation I	2	1	1
phospholipid remodeling (phosphatidate, yeast)	2	1	1
ethylene glycol degradation	2	1	1
indole-3-acetate biosynthesis IV (bacteria)	2	1	1
acrylonitrile degradation I	2	1	1
4-aminobenzoate biosynthesis II	2	1	1
palmitoleate biosynthesis III (cyanobacteria)	2	1	1
β-alanine degradation I	2	1	1
superpathway of ornithine degradation	8	6	3
superpathway of polyamine biosynthesis II	8	5	3
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	4
superpathway of ammonia assimilation (plants)	3	3	1
superpathway of acetate utilization and formation	3	3	1
β-alanine biosynthesis II	6	5	2
L-isoleucine biosynthesis V	3	2	1
putrescine degradation IV	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
hypotaurine degradation	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
oleate biosynthesis III (cyanobacteria)	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
superpathway of acrylonitrile degradation	3	1	1
histamine degradation	3	1	1
superpathway of L-arginine and L-ornithine degradation	13	11	4
L-glutamate and L-glutamine biosynthesis	7	6	2
L-methionine biosynthesis III	4	4	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
L-citrulline biosynthesis	8	7	2
superpathway of putrescine biosynthesis	4	3	1
phytol degradation	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
L-arginine degradation VIII (arginine oxidase pathway)	4	3	1
putrescine degradation III	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
chitin deacetylation	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
D-arabinose degradation II	4	2	1
ethene biosynthesis II (microbes)	4	1	1
spermidine biosynthesis III	4	1	1
L-arginine degradation II (AST pathway)	5	5	1
L-lysine degradation IV	5	5	1
2-methylcitrate cycle I	5	5	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	2
superpathway of tetrahydrofolate biosynthesis	10	8	2
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	5	4	1
phosphatidate biosynthesis (yeast)	5	3	1
CDP-diacylglycerol biosynthesis III	5	3	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	2	1
dopamine degradation	5	2	1
superpathway of candicidin biosynthesis	11	4	2
phosphatidylglycerol biosynthesis II	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	2
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	2
2-methylcitrate cycle II	6	5	1
L-lysine degradation X	6	5	1
superpathway of L-citrulline metabolism	12	9	2
superpathway of L-cysteine biosynthesis (fungi)	6	4	1
L-isoleucine biosynthesis IV	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
L-lysine degradation III	6	2	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
(5R)-carbapenem carboxylate biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
alkane oxidation	6	1	1
lupulone and humulone biosynthesis	6	1	1
noradrenaline and adrenaline degradation	13	8	2
superpathway of glycol metabolism and degradation	7	6	1
L-lysine degradation I	7	5	1
L-Nδ-acetylornithine biosynthesis	7	5	1
serotonin degradation	7	4	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
stigma estolide biosynthesis	7	2	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
myo-inositol degradation I	7	1	1
2,4-dinitrotoluene degradation	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
L-valine degradation I	8	6	1
superpathway of polyamine biosynthesis I	8	5	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
anandamide biosynthesis II	8	2	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
cis-geranyl-CoA degradation	9	2	1
chloramphenicol biosynthesis	9	1	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	8	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	5	1
anandamide biosynthesis I	12	3	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of phospholipid biosynthesis II (plants)	28	10	2
plasmalogen biosynthesis I (aerobic)	16	1	1
superpathway of arginine and polyamine biosynthesis	17	14	1
superpathway of chorismate metabolism	59	42	2
superpathway of pentose and pentitol degradation	42	10	1
superpathway of L-lysine degradation	43	23	1