Experiment set30IT057 for Pseudomonas putida KT2440

C.elegans, mixed culture-1

Group: micoeukaryotes
Media: LB (0.1x) + Pelleted after growth overnight in LB+Kan50 + CaCl2, MgSO4 (10mM ), pH=7
Culturing: Putida_ML5, 48-well_plate, Aerobic, at 30 (C), shaken=700 rpm
By: VM on 6/23/21
Media components: 1 g/L Tryptone, 0.5 g/L Yeast Extract, 0.5 g/L Sodium Chloride (final concentrations)

Specific Phenotypes

For 49 genes in this experiment

For micoeukaryotes Pelleted after growth overnight in LB+Kan50 in Pseudomonas putida KT2440

For micoeukaryotes Pelleted after growth overnight in LB+Kan50 across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	6
Lysine degradation	3
Phosphate metabolism	3
Biogenesis of cbb3-type cytochrome c oxidases	2
Cobalt-zinc-cadmium resistance	2
High affinity phosphate transporter and control of PHO regulon	2
Polyhydroxybutyrate metabolism	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Ammonia assimilation	1
Bacterial Chemotaxis	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Biogenesis of cytochrome c oxidases	1
Carotenoids	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Redox cycle	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycogen metabolism	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
Polyamine Metabolism	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1
Rhamnolipids in Pseudomonas	1
Ribosome biogenesis bacterial	1
Rrf2 family transcriptional regulators	1
Terminal cytochrome C oxidases	1
Triacylglycerol metabolism	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Carotenoid biosynthesis - General
• Lysine degradation
• Histidine metabolism
• Phenylalanine metabolism
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Limonene and pinene degradation
• Alkaloid biosynthesis I
• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Glutathione metabolism
• Lipopolysaccharide biosynthesis
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Styrene degradation
• Butanoate metabolism
• Nitrogen metabolism
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of terpenoids and steroids
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Glutamate metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• beta-Alanine metabolism
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Nucleotide sugars metabolism
• Keratan sulfate biosynthesis
• Peptidoglycan biosynthesis
• Inositol phosphate metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Pyruvate metabolism
• Toluene and xylene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• 1,2-Dichloroethane degradation
• Trinitrotoluene degradation
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Methane metabolism
• Porphyrin and chlorophyll metabolism
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Zeatin biosynthesis
• Phenylpropanoid biosynthesis
• Isoflavonoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis II
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
zeaxanthin biosynthesis	2	2	2
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
β-alanine degradation II	2	2	1
echinenone and zeaxanthin biosynthesis (Synechocystis)	4	2	2
phospholipid remodeling (phosphatidate, yeast)	2	1	1
β-alanine degradation I	2	1	1
palmitoleate biosynthesis III (cyanobacteria)	2	1	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
glutathione-peroxide redox reactions	3	2	1
polyhydroxydecanoate biosynthesis	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
oleate biosynthesis III (cyanobacteria)	3	2	1
gentisate degradation I	3	1	1
histamine degradation	3	1	1
glycine betaine degradation III	7	7	2
L-glutamate and L-glutamine biosynthesis	7	6	2
Arg/N-end rule pathway (eukaryotic)	14	8	4
CDP-diacylglycerol biosynthesis I	4	4	1
queuosine biosynthesis I (de novo)	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
phytol degradation	4	3	1
putrescine degradation III	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
4-hydroxy-2-nonenal detoxification	4	1	1
L-lysine degradation V	9	9	2
L-tyrosine degradation I	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
octane oxidation	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
queuosine biosynthesis III (queuosine salvage)	5	3	1
propanoyl-CoA degradation II	5	3	1
phosphatidate biosynthesis (yeast)	5	3	1
CDP-diacylglycerol biosynthesis III	5	3	1
pentachlorophenol degradation	10	4	2
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
astaxanthin biosynthesis (bacteria, fungi, algae)	10	2	2
phosphatidylglycerol biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	2
3-methyl-branched fatty acid α-oxidation	6	3	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
5-nitroanthranilate degradation	6	2	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
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-citrulline biosynthesis	8	7	1
L-valine degradation I	8	6	1
glutathione-mediated detoxification I	8	3	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
L-lysine degradation II (L-pipecolate pathway)	9	5	1
gliotoxin biosynthesis	9	2	1
glutathione-mediated detoxification II	9	1	1
starch biosynthesis	10	5	1
3-phenylpropanoate degradation	10	4	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
superpathway of carotenoid biosynthesis in plants	22	3	2
superpathway of L-citrulline metabolism	12	9	1
anandamide biosynthesis I	12	3	1
indole glucosinolate activation (intact plant cell)	12	3	1
camalexin biosynthesis	12	2	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 L-lysine degradation	43	23	2