Experiment set19IT078 for Pseudomonas simiae WCS417

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Chemotaxis:Motility:: Method=Plug_approach; Chemical=L-Valine; Chemical_conc=5mM; Distance=2cm; Sample=outer; Collection=outgrowth_in_LBkan50

Group: motility_chemotaxis
Media: RCH2_defined_NO_ammonium_with_Glycerol
Culturing: fluoroDangl_ML3, soft agar plate, Aerobic, at 30 (C), shaken=0 rpm, (solid)
By: Peter Kim on 4-Oct-21
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, 2.2 mM Glycerol, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 7 genes in this experiment

SEED Subsystems

Subsystem #Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 3
Ammonia assimilation 1
Isobutyryl-CoA to Propionyl-CoA Module 1
Methionine Degradation 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Valine degradation 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
benzoyl-CoA biosynthesis 3 3 1
pyruvate decarboxylation to acetyl CoA I 3 3 1
2-methyl-branched fatty acid β-oxidation 14 11 3
adipate degradation 5 5 1
adipate biosynthesis 5 4 1
fatty acid β-oxidation IV (unsaturated, even number) 5 4 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
acrylate degradation I 5 3 1
propanoyl-CoA degradation II 5 3 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 2 1
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 2
β-alanine biosynthesis II 6 5 1
methyl ketone biosynthesis (engineered) 6 3 1
fatty acid β-oxidation I (generic) 7 5 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 4 1
benzoyl-CoA degradation I (aerobic) 7 3 1
L-valine degradation I 8 6 1
valproate β-oxidation 9 7 1
phenylacetate degradation I (aerobic) 9 3 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 1
3-phenylpropanoate degradation 10 3 1
superpathway of phenylethylamine degradation 11 4 1
Spodoptera littoralis pheromone biosynthesis 22 4 2
oleate β-oxidation 35 30 3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 18 1
platensimycin biosynthesis 26 6 1