Experiment set9S310 for Enterobacter sp. TBS_079

Sodium Fumarate dibasic carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium Fumarate dibasic (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 33 genes in this experiment

For carbon source Sodium Fumarate dibasic in Enterobacter sp. TBS_079

For carbon source Sodium Fumarate dibasic across organisms

SEED Subsystems

Subsystem	#Specific
Pyruvate metabolism I: anaplerotic reactions, PEP	4
Lactose and Galactose Uptake and Utilization	3
Entner-Doudoroff Pathway	2
Glycolysis and Gluconeogenesis	2
Glycolysis and Gluconeogenesis, including Archaeal enzymes	2
Phosphate metabolism	2
ATP-dependent RNA helicases, bacterial	1
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Copper homeostasis: copper tolerance	1
DNA-replication	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Biosynthesis and gamma-glutamyl cycle	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Homogentisate pathway of aromatic compound degradation	1
Maltose and Maltodextrin Utilization	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Orphan regulatory proteins	1
Photorespiration (oxidative C2 cycle)	1
PnuC-like transporters	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	1
Serine-glyoxylate cycle	1
Transcription factors bacterial	1
Utilization of glutathione as a sulphur source	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glycolysis / Gluconeogenesis
• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• 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
• Glutamate metabolism
• Arginine and proline metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Glycine, serine and threonine metabolism
• gamma-Hexachlorocyclohexane degradation
• Fluorobenzoate degradation
• Taurine and hypotaurine metabolism
• Selenoamino acid metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Lipopolysaccharide biosynthesis
• Arachidonic acid metabolism
• 1,4-Dichlorobenzene degradation
• Folate biosynthesis
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NAD salvage pathway IV (from nicotinamide riboside)	2	2	2
L-glutamate biosynthesis I	2	2	2
L-malate degradation I	1	1	1
L-glutamine degradation I	1	1	1
cellulose biosynthesis	1	1	1
L-glutamine degradation II	1	1	1
ammonia assimilation cycle III	3	3	2
L-proline degradation I	3	3	2
glutathione degradation (DUG pathway)	2	2	1
polyphosphate metabolism	2	2	1
NAD biosynthesis from nicotinamide	2	1	1
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
L-arginine degradation I (arginase pathway)	3	1	1
L-glutamate and L-glutamine biosynthesis	7	5	2
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
L-citrulline biosynthesis	8	6	2
L-asparagine biosynthesis III (tRNA-dependent)	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
ethene biosynthesis II (microbes)	4	1	1
gluconeogenesis I	13	13	3
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	3
Rubisco shunt	10	9	2
glycolysis IV	10	8	2
glycolysis V (Pyrococcus)	10	7	2
4-chlorocatechol degradation	5	2	1
3-chlorocatechol degradation II (ortho)	5	1	1
3-chlorocatechol degradation I (ortho)	5	1	1
glycolysis III (from glucose)	11	11	2
glycolysis II (from fructose 6-phosphate)	11	11	2
glycolysis VI (from fructose)	11	8	2
peptido-conjugates in tissue regeneration biosynthesis	17	5	3
ppGpp metabolism	6	6	1
homolactic fermentation	12	11	2
γ-glutamyl cycle	6	5	1
superpathway of L-citrulline metabolism	12	8	2
methylgallate degradation	6	3	1
leukotriene biosynthesis	6	1	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
glycolysis I (from glucose 6-phosphate)	13	13	2
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
L-Nδ-acetylornithine biosynthesis	7	4	1
superpathway of NAD biosynthesis in eukaryotes	14	7	2
4,5-dichlorocatechol degradation	7	3	1
Bifidobacterium shunt	15	12	2
glycerol degradation to butanol	16	12	2
protocatechuate degradation I (meta-cleavage pathway)	8	4	1
3,5-dichlorocatechol degradation	8	3	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	2
superpathway of glucose and xylose degradation	17	16	2
Entner-Doudoroff pathway I	9	9	1
superpathway of hexitol degradation (bacteria)	18	16	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	8	1
3,4,6-trichlorocatechol degradation	9	4	1
1,4-dichlorobenzene degradation	9	3	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	18	2
superpathway of anaerobic sucrose degradation	19	17	2
photorespiration II	10	6	1
superpathway of vanillin and vanillate degradation	10	4	1
superpathway of N-acetylneuraminate degradation	22	19	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
peptidoglycan maturation (meso-diaminopimelate containing)	12	6	1
syringate degradation	12	4	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
1-butanol autotrophic biosynthesis (engineered)	27	19	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
hypoglycin biosynthesis	14	4	1
mixed acid fermentation	16	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
heterolactic fermentation	18	15	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
ethene biosynthesis V (engineered)	25	18	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1