Experiment set30IT056 for Pseudomonas putida KT2440

Dictyostellum sp.mixed 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 26 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	3
Cobalt-zinc-cadmium resistance	2
High affinity phosphate transporter and control of PHO regulon	2
Lysine degradation	2
Phosphate 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
Glycogen metabolism	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Ribosome biogenesis bacterial	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:

• Histidine metabolism
• Phenylalanine metabolism
• Glycerophospholipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Biosynthesis of terpenoids and steroids
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Tyrosine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Toluene and xylene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Propanoate metabolism
• Ethylbenzene degradation
• Styrene degradation
• Butanoate metabolism
• Methane metabolism
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis II
• 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
β-alanine degradation I	2	1	1
L-glutamate and L-glutamine biosynthesis	7	6	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
propanoyl-CoA degradation II	5	3	1
astaxanthin biosynthesis (bacteria, fungi, algae)	10	2	2
2,4-dinitrotoluene degradation	7	1	1
myo-inositol degradation I	7	1	1
L-citrulline biosynthesis	8	7	1
L-valine degradation I	8	6	1
L-lysine degradation V	9	9	1
L-lysine degradation II (L-pipecolate pathway)	9	5	1
starch biosynthesis	10	5	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
superpathway of L-lysine degradation	43	23	1