Experiment set30IT058 for Pseudomonas putida KT2440

C.elegans, 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 29 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	4
Lysine degradation	3
Cobalt-zinc-cadmium resistance	2
High affinity phosphate transporter and control of PHO regulon	2
Phosphate metabolism	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Acetoin, butanediol metabolism	1
Ammonia assimilation	1
Bacterial Chemotaxis	1
Biogenesis of cbb3-type cytochrome c oxidases	1
Branched-Chain Amino Acid Biosynthesis	1
Carotenoids	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Redox cycle	1
Glycogen metabolism	1
Polyamine Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tryptophan metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Biosynthesis of plant hormones
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Cyanoamino acid metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Toluene and xylene degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• Styrene degradation
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Methane metabolism
• Pantothenate and CoA biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Isoflavonoid biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• 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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
zeaxanthin biosynthesis	2	2	2
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
indole-3-acetate biosynthesis III (bacteria)	2	2	1
echinenone and zeaxanthin biosynthesis (Synechocystis)	4	2	2
pyruvate fermentation to (R)-acetoin II	2	1	1
pyruvate fermentation to (S)-acetoin	3	2	1
pyruvate fermentation to (R)-acetoin I	3	2	1
glutathione-peroxide redox reactions	3	2	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
L-valine biosynthesis	4	4	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
queuosine biosynthesis I (de novo)	4	4	1
L-arginine degradation VIII (arginine oxidase pathway)	4	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
L-arginine degradation XII	4	2	1
creatinine degradation I	4	2	1
L-lysine degradation IV	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
superpathway of (R,R)-butanediol biosynthesis	5	3	1
queuosine biosynthesis III (queuosine salvage)	5	3	1
creatinine degradation II	5	3	1
astaxanthin biosynthesis (bacteria, fungi, algae)	10	2	2
L-isoleucine biosynthesis IV	6	4	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-citrulline biosynthesis	8	7	1
glycine betaine degradation I	8	6	1
L-isoleucine biosynthesis II	8	5	1
superpathway of branched chain amino acid biosynthesis	17	17	2
L-lysine degradation V	9	9	1
L-lysine degradation II (L-pipecolate pathway)	9	5	1
starch biosynthesis	10	5	1
superpathway of carotenoid biosynthesis in plants	22	3	2
superpathway of L-citrulline metabolism	12	9	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	12	1
superpathway of L-lysine degradation	43	23	2