Experiment set9S319 for Enterobacter sp. TBS_079

Sodium succinate dibasic hexahydrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium succinate dibasic hexahydrate (10 mM)
Culturing: Enterobacter_TBS_079_ML3, microplate, Aerobic, at 30 (C)
By: Robin on 6/19/24
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 Sodium succinate dibasic hexahydrate in Enterobacter sp. TBS_079

For carbon source Sodium succinate dibasic hexahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Pyruvate metabolism I: anaplerotic reactions, PEP	4
Lactose and Galactose Uptake and Utilization	2
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glycolysis / Gluconeogenesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Citrate cycle (TCA cycle)
• Purine metabolism
• Alanine and aspartate metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-malate degradation I	1	1	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	3
NAD de novo biosynthesis I	6	5	1
NAD de novo biosynthesis IV (anaerobic)	6	5	1
methylgallate degradation	6	3	1
gluconeogenesis I	13	13	2
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
protocatechuate degradation I (meta-cleavage pathway)	8	4	1
Entner-Doudoroff pathway I	9	9	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	8	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
nicotine biosynthesis	9	3	1
Rubisco shunt	10	9	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
superpathway of vanillin and vanillate degradation	10	4	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	11	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	6	1
superpathway of nicotine biosynthesis	12	4	1
syringate degradation	12	4	1
glycolysis I (from glucose 6-phosphate)	13	13	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
Bifidobacterium shunt	15	12	1
mixed acid fermentation	16	16	1
glycerol degradation to butanol	16	12	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of hexitol degradation (bacteria)	18	16	1
heterolactic fermentation	18	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	18	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of N-acetylneuraminate degradation	22	19	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
aspartate superpathway	25	24	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1