Experiment set9S342 for Enterobacter sp. TBS_079

L-Serine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Serine (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 6 genes in this experiment

For carbon source L-Serine in Enterobacter sp. TBS_079

For carbon source L-Serine across organisms

SEED Subsystems

Subsystem	#Specific
Glycine and Serine Utilization	4
Glycine cleavage system	2
Photorespiration (oxidative C2 cycle)	2
Pyruvate Alanine Serine Interconversions	2
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Pyruvate metabolism
• One carbon pool by folate
• Reductive carboxylate cycle (CO2 fixation)
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-serine degradation	3	3	3
L-serine degradation	3	3	3
L-cysteine degradation II	3	3	2
glycine biosynthesis II	3	3	2
glycine degradation	3	3	2
glycine cleavage	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	4	3
L-methionine biosynthesis II	6	5	2
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	13	3
folate transformations III (E. coli)	9	9	1
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
photorespiration I	9	5	1
photorespiration III	9	5	1
glycolysis V (Pyrococcus)	10	7	1
photorespiration II	10	6	1
glycolysis II (from fructose 6-phosphate)	11	11	1
folate transformations II (plants)	11	10	1
glycolysis I (from glucose 6-phosphate)	13	13	1
gluconeogenesis I	13	13	1
folate transformations I	13	9	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of hexitol degradation (bacteria)	18	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	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 glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1