Experiment set1IT085 for Pseudomonas putida KT2440

Potassium Acetate Carbon Source (20mM)

Group: carbon source
Media: RCH2_defined_noCarbon + Potassium acetate (20 mM), pH=7
Culturing: Putida_ML5, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.6 generations
By: Kelly on 7/20/20
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, 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 6 genes in this experiment

For carbon source Potassium acetate in Pseudomonas putida KT2440

For carbon source Potassium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Ketoisovalerate oxidoreductase	1
Ribosome biogenesis bacterial	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Glycolysis / Gluconeogenesis
• Geraniol degradation
• 1- and 2-Methylnaphthalene degradation
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate formation from acetyl-CoA (succinate)	1	1	1
acetate conversion to acetyl-CoA	1	1	1
superpathway of acetate utilization and formation	3	3	1
ethanol degradation IV	3	3	1
pyruvate fermentation to acetate V	3	3	1
ethanol degradation II	3	3	1
ethanol degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
pyruvate fermentation to acetate VI	3	2	1
chitin deacetylation	4	2	1
2-methylcitrate cycle I	5	5	1
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	5	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of bitter acids biosynthesis	18	3	3
adlupulone and adhumulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
succinate fermentation to butanoate	7	1	1
TCA cycle VII (acetate-producers)	9	8	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	2	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1