Experiment set5IT044 for Klebsiella michiganensis M5al

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Trisodium citrate dihydrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Trisodium citrate dihydrate (20 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.6 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: 1764 C6

Specific Phenotypes

For 8 genes in this experiment

For carbon source Trisodium citrate dihydrate in Klebsiella michiganensis M5al

For carbon source Trisodium citrate dihydrate across organisms

SEED Subsystems

Subsystem #Specific
Orphan regulatory proteins 2
Pyruvate metabolism I: anaplerotic reactions, PEP 2
Acetoin, butanediol metabolism 1
Branched-Chain Amino Acid Biosynthesis 1
DNA-binding regulatory proteins, strays 1
Glycolysis and Gluconeogenesis 1
Glycolysis and Gluconeogenesis, including Archaeal enzymes 1
Murein hydrolase regulation and cell death 1
Proteolysis in bacteria, ATP-dependent 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
pyruvate fermentation to (R)-acetoin II 2 2 1
pyruvate fermentation to (R)-acetoin I 3 3 1
pyruvate fermentation to (S)-acetoin 3 3 1
L-valine biosynthesis 4 4 1
superpathway of (R,R)-butanediol biosynthesis 5 5 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
superpathway of 2,3-butanediol biosynthesis 6 5 1
L-isoleucine biosynthesis IV 6 4 1
L-isoleucine biosynthesis I (from threonine) 7 7 1
L-isoleucine biosynthesis III 7 5 1
L-isoleucine biosynthesis II 8 4 1
superpathway of branched chain amino acid biosynthesis 17 17 2
glycolysis V (Pyrococcus) 10 7 1
glycolysis II (from fructose 6-phosphate) 11 11 1
glycolysis I (from glucose 6-phosphate) 13 13 1
superpathway of L-isoleucine biosynthesis I 13 13 1
gluconeogenesis I 13 13 1
superpathway of glycolysis and the Entner-Doudoroff pathway 17 17 1
superpathway of hexitol degradation (bacteria) 18 18 1
superpathway of L-threonine metabolism 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 glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 25 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 23 1