Experiment set2IT083 for Rahnella sp. WP5

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casamino acids carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + casamino acids (5 mg/mL)
Culturing: RahnellaWP5_ML7, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Robert Tournay on December 7, 2021
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 10 genes in this experiment

For carbon source casamino acids in Rahnella sp. WP5

For carbon source casamino acids across organisms

SEED Subsystems

Subsystem #Specific
Glycolysis and Gluconeogenesis 2
Glycolysis and Gluconeogenesis, including Archaeal enzymes 2
Calvin-Benson cycle 1
Fructose utilization 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Multidrug Resistance Efflux Pumps 1
Phosphate metabolism 1
Proteolysis in bacteria, ATP-dependent 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1
Serine-glyoxylate cycle 1
Succinate dehydrogenase 1
TCA Cycle 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
succinate to cytochrome bd oxidase electron transfer 2 2 1
L-glutamate degradation II 2 2 1
succinate to cytochrome bo oxidase electron transfer 2 1 1
L-aspartate degradation III (anaerobic) 3 3 1
aerobic respiration III (alternative oxidase pathway) 3 3 1
L-aspartate degradation II (aerobic) 3 3 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 4 1
aerobic respiration I (cytochrome c) 4 2 1
aerobic respiration II (cytochrome c) (yeast) 4 2 1
glycolysis II (from fructose 6-phosphate) 11 11 2
NAD(P)/NADPH interconversion 6 4 1
L-canavanine degradation II 6 1 1
glycolysis I (from glucose 6-phosphate) 13 13 2
gluconeogenesis I 13 13 2
superpathway of glycolysis and the Entner-Doudoroff pathway 17 17 2
superpathway of hexitol degradation (bacteria) 18 18 2
sucrose biosynthesis I (from photosynthesis) 9 7 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 19 2
superpathway of anaerobic sucrose degradation 19 18 2
TCA cycle III (animals) 10 8 1
glycolysis V (Pyrococcus) 10 7 1
superpathway of N-acetylneuraminate degradation 22 20 2
formaldehyde assimilation III (dihydroxyacetone cycle) 12 11 1
gluconeogenesis III 12 9 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 25 2
Calvin-Benson-Bassham cycle 13 10 1
oxygenic photosynthesis 17 11 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 9 1
ethene biosynthesis V (engineered) 25 18 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 19 1
1-butanol autotrophic biosynthesis (engineered) 27 19 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 23 1