Experiment set4IT096 for Klebsiella michiganensis M5al

Potassium acetate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Potassium acetate (20 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.5 generations
By: Adam on 27-Mar-17
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)
Growth plate: 1763 C4

Specific Phenotypes

For 10 genes in this experiment

For carbon source Potassium acetate in Klebsiella michiganensis M5al

For carbon source Potassium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Acetoin, butanediol metabolism	1
Branched-Chain Amino Acid Biosynthesis	1
Flavodoxin	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Ketoisovalerate oxidoreductase	1
Photorespiration (oxidative C2 cycle)	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Redox-dependent regulation of nucleus processes	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Lipopolysaccharide biosynthesis
• Sphingolipid metabolism
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine biosynthesis
• Glutathione metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Ether lipid metabolism
• 1,4-Dichlorobenzene degradation
• Propanoate metabolism
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Thiamine metabolism
• Riboflavin metabolism
• Pantothenate and CoA biosynthesis
• Caprolactam degradation
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
glycolate and glyoxylate degradation II	2	2	1
pyruvate fermentation to (R)-acetoin II	2	2	1
chitin deacetylation	4	3	2
glyoxylate cycle	6	6	2
ethanol degradation II	3	3	1
superpathway of acetate utilization and formation	3	3	1
ethanol degradation IV	3	3	1
pyruvate fermentation to (R)-acetoin I	3	3	1
pyruvate fermentation to (S)-acetoin	3	3	1
L-isoleucine biosynthesis IV	6	4	2
L-isoleucine biosynthesis V	3	2	1
ethanol degradation III	3	2	1
L-valine biosynthesis	4	4	1
superpathway of (R,R)-butanediol biosynthesis	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
2-methylcitrate cycle I	5	2	1
superpathway of glyoxylate bypass and TCA	12	11	2
superpathway of 2,3-butanediol biosynthesis	6	5	1
2-methylcitrate cycle II	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
β-alanine biosynthesis II	6	1	1
lupulone and humulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
superpathway of glycol metabolism and degradation	7	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
L-isoleucine biosynthesis III	7	5	1
D-xylose degradation IV	7	3	1
L-isoleucine biosynthesis II	8	4	1
L-arabinose degradation IV	8	4	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	3
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
cis-geranyl-CoA degradation	9	1	1
glycolysis V (Pyrococcus)	10	7	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1
glycolysis II (from fructose 6-phosphate)	11	11	1
gluconeogenesis I	13	13	1
glycolysis I (from glucose 6-phosphate)	13	13	1
superpathway of L-isoleucine biosynthesis I	13	13	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of L-threonine metabolism	18	18	1
superpathway of hexitol degradation (bacteria)	18	18	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	18	1
superpathway of N-acetylneuraminate degradation	22	22	1
superpathway of pentose and pentitol degradation	42	21	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1