Experiment set5IT049 for Klebsiella michiganensis M5al

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Sodium succinate dibasic hexahydrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium succinate dibasic hexahydrate (20 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
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: 1764 D5

Specific Phenotypes

For 11 genes in this experiment

For carbon source Sodium succinate dibasic hexahydrate in Klebsiella michiganensis M5al

For carbon source Sodium succinate dibasic hexahydrate across organisms

SEED Subsystems

Subsystem #Specific
Lactose and Galactose Uptake and Utilization 2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 2
ABC transporter oligopeptide (TC 3.A.1.5.1) 1
Entner-Doudoroff Pathway 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Ketoisovalerate oxidoreductase 1
Methylglyoxal Metabolism 1
Pyruvate metabolism I: anaplerotic reactions, PEP 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
acetate and ATP formation from acetyl-CoA III 1 1 1
acetate conversion to acetyl-CoA 1 1 1
ethanol degradation II 3 3 2
ethanol degradation IV 3 3 2
ethanol degradation III 3 2 2
putrescine degradation I 2 2 1
phenylethylamine degradation I 2 2 1
ethylene glycol degradation 2 2 1
phenylethanol degradation 2 1 1
putrescine degradation V 2 1 1
phenylethylamine degradation II 2 1 1
superpathway of acetate utilization and formation 3 3 1
L-isoleucine biosynthesis V 3 2 1
putrescine degradation IV 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
hypotaurine degradation 3 2 1
histamine degradation 3 1 1
styrene degradation 3 1 1
D-arabinose degradation II 4 4 1
chitin deacetylation 4 3 1
phytol degradation 4 3 1
putrescine degradation III 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 1 1
mitochondrial NADPH production (yeast) 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
octane oxidation 5 2 1
2-methylcitrate cycle I 5 2 1
dopamine degradation 5 1 1
L-isoleucine biosynthesis IV 6 4 1
3-methyl-branched fatty acid α-oxidation 6 3 1
2-methylcitrate cycle II 6 2 1
superpathway of bitter acids biosynthesis 18 3 3
alkane oxidation 6 1 1
lupulone and humulone biosynthesis 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
β-alanine biosynthesis II 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
noradrenaline and adrenaline degradation 13 4 2
superpathway of glycol metabolism and degradation 7 7 1
serotonin degradation 7 3 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
superpathway of ornithine degradation 8 8 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 5 1
aromatic biogenic amine degradation (bacteria) 8 3 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
Entner-Doudoroff pathway II (non-phosphorylative) 9 7 1
reductive glycine pathway of autotrophic CO2 fixation 9 6 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 5 1
cis-geranyl-CoA degradation 9 1 1
superpathway of coenzyme A biosynthesis II (plants) 10 5 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 11 1
superpathway of phenylethylamine degradation 11 11 1
superpathway of L-arginine and L-ornithine degradation 13 13 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 3 1
superpathway of pentose and pentitol degradation 42 21 1