Experiment set2IT090 for Rahnella sp. WP5

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 12 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
Serine-glyoxylate cycle	2
Succinate dehydrogenase	2
TCA Cycle	2
Calvin-Benson cycle	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Fructose utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Phosphate metabolism	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of phenylpropanoids
• Reductive carboxylate cycle (CO2 fixation)
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Oxidative phosphorylation
• Purine metabolism
• Alanine and aspartate metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Nicotinate and nicotinamide metabolism
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation II	2	2	1
succinate to cytochrome bd oxidase electron transfer	2	2	1
3-dehydroquinate biosynthesis I	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 II (cytochrome c) (yeast)	4	2	1
aerobic respiration I (cytochrome c)	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
gluconeogenesis I	13	13	2
glycolysis I (from glucose 6-phosphate)	13	13	2
chorismate biosynthesis I	7	7	1
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
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
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 L-tryptophan biosynthesis	13	13	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
superpathway of aromatic amino acid biosynthesis	18	18	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
superpathway of chorismate metabolism	59	52	1