Experiment set17IT018 for Klebsiella michiganensis M5al

RCH2_defined_1percent_glucose with Sodium Chloride 600 mM

Group: stress
Media: RCH2_defined_1percent_glucose + Sodium Chloride (600 mM)
Culturing: Koxy_ML2a, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Robin Herbert on 3/21/19
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 55.5 mM D-Glucose, 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 24 genes in this experiment

For stress Sodium Chloride in Klebsiella michiganensis M5al

For stress Sodium Chloride across organisms

SEED Subsystems

Subsystem	#Specific
Entner-Doudoroff Pathway	2
Glycine Biosynthesis	2
Glycolysis and Gluconeogenesis	2
Glycolysis and Gluconeogenesis, including Archaeal enzymes	2
Phosphate metabolism	2
Trehalose Uptake and Utilization	2
Calvin-Benson cycle	1
Flavodoxin	1
Glycine and Serine Utilization	1
Heat shock dnaK gene cluster extended	1
Na(+) H(+) antiporter	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Thioredoxin-disulfide reductase	1
Threonine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Glycine, serine and threonine metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Methionine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Aminoacyl-tRNA biosynthesis
• Insect hormone biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-threonine degradation II	2	2	2
L-threonine degradation III (to methylglyoxal)	3	3	2
NAD phosphorylation and transhydrogenation	2	2	1
aminopropanol phosphate biosynthesis II	4	3	2
NAD phosphorylation and dephosphorylation	3	3	1
Rubisco shunt	10	9	3
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	2
glycolysis IV	10	8	2
glycolysis V (Pyrococcus)	10	7	2
glycolysis II (from fructose 6-phosphate)	11	11	2
glycolysis III (from glucose)	11	11	2
glycolysis VI (from fructose)	11	8	2
superpathway of L-threonine metabolism	18	18	3
homolactic fermentation	12	12	2
NAD(P)/NADPH interconversion	6	4	1
glycolysis I (from glucose 6-phosphate)	13	13	2
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
Bifidobacterium shunt	15	13	2
glycerol degradation to butanol	16	12	2
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	2
superpathway of glucose and xylose degradation	17	17	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	3
superpathway of hexitol degradation (bacteria)	18	18	2
Entner-Doudoroff pathway I	9	9	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	7	1
1-butanol autotrophic biosynthesis (engineered)	27	19	3
myxochelin A and B biosynthesis	9	2	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	2
superpathway of anaerobic sucrose degradation	19	18	2
photorespiration II	10	6	1
superpathway of N-acetylneuraminate degradation	22	22	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
ethene biosynthesis V (engineered)	25	18	2
gluconeogenesis I	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	2
Calvin-Benson-Bassham cycle	13	10	1
mixed acid fermentation	16	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
oxygenic photosynthesis	17	11	1
heterolactic fermentation	18	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
tRNA charging	21	21	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1