Experiment set30IT060 for Pseudomonas putida KT2440

Acanthamoeba sp., muxed culture-2

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 36 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	5
Polyamine Metabolism	5
Isoleucine degradation	3
Leucine Degradation and HMG-CoA Metabolism	3
Valine degradation	3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Lysine degradation	2
Acetyl-CoA fermentation to Butyrate	1
Ammonia assimilation	1
Biogenesis of cytochrome c oxidases	1
Carotenoids	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Cobalt-zinc-cadmium resistance	1
Folate Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycogen metabolism	1
Phosphate metabolism	1
Polyhydroxybutyrate metabolism	1
Rrf2 family transcriptional regulators	1
Triacylglycerol metabolism	1
Tryptophan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycerophospholipid metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Histidine metabolism
• Phenylalanine metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Lysine degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Toluene and xylene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Ethylbenzene degradation
• Styrene degradation
• Butanoate metabolism
• Methane metabolism
• Folate biosynthesis
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• 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
ammonia assimilation cycle III	3	3	3
zeaxanthin biosynthesis	2	2	2
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
L-glutamine biosynthesis I	1	1	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	2
4-aminobenzoate biosynthesis I	2	2	1
ammonia assimilation cycle II	2	2	1
ammonia assimilation cycle I	2	2	1
echinenone and zeaxanthin biosynthesis (Synechocystis)	4	2	2
phospholipid remodeling (phosphatidate, yeast)	2	1	1
palmitoleate biosynthesis III (cyanobacteria)	2	1	1
L-glutamate and L-glutamine biosynthesis	7	6	3
superpathway of ammonia assimilation (plants)	3	3	1
oleate biosynthesis III (cyanobacteria)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
polyhydroxydecanoate biosynthesis	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
glycine betaine degradation III	7	7	2
Arg/N-end rule pathway (eukaryotic)	14	8	4
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
creatinine degradation I	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
CDP-diacylglycerol biosynthesis III	5	3	1
phosphatidate biosynthesis (yeast)	5	3	1
creatinine degradation II	5	3	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
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
stigma estolide biosynthesis	7	2	1
L-citrulline biosynthesis	8	7	1
glycine betaine degradation I	8	6	1
anandamide biosynthesis II	8	2	1
L-lysine degradation V	9	9	1
L-lysine degradation II (L-pipecolate pathway)	9	5	1
chloramphenicol biosynthesis	9	1	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
starch biosynthesis	10	5	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of carotenoid biosynthesis in plants	22	3	2
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-citrulline metabolism	12	9	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 L-lysine degradation	43	23	1
superpathway of chorismate metabolism	59	42	1