Experiment set10S423 for Enterobacter sp. TBS_079

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Thymine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Thymine (1.25 mM)
Culturing: Enterobacter_TBS_079_ML3, microplate, Aerobic, at 30 (C)
By: Robin on 6/19/24
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 21 genes in this experiment

For nitrogen source Thymine in Enterobacter sp. TBS_079

For nitrogen source Thymine across organisms

SEED Subsystems

Subsystem #Specific
Pyrimidine utilization 5
Phosphate metabolism 2
Trehalose Biosynthesis 2
CBSS-562.2.peg.5158 SK3 including 1
Chorismate Synthesis 1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 1
Glutathione: Biosynthesis and gamma-glutamyl cycle 1
Hydantoin metabolism 1
KDO2-Lipid A biosynthesis 1
Nitrate and nitrite ammonification 1
Stringent Response, (p)ppGpp metabolism 1
Trehalose Uptake and Utilization 1
Urea decomposition 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
trehalose biosynthesis I 2 2 2
glutathione degradation (DUG pathway) 2 2 1
trehalose degradation II (cytosolic) 2 2 1
trehalose degradation VI (periplasmic) 2 2 1
polyphosphate metabolism 2 2 1
trehalose biosynthesis II 2 1 1
trehalose biosynthesis III 2 1 1
uracil degradation III 5 5 2
allantoin degradation to ureidoglycolate II (ammonia producing) 4 1 1
chorismate biosynthesis from 3-dehydroquinate 5 5 1
CMP-3-deoxy-D-manno-octulosonate biosynthesis 5 5 1
allantoin degradation to glyoxylate III 5 1 1
allantoin degradation to glyoxylate II 5 1 1
dibenzothiophene desulfurization 5 1 1
peptido-conjugates in tissue regeneration biosynthesis 17 5 3
ppGpp metabolism 6 6 1
γ-glutamyl cycle 6 5 1
leukotriene biosynthesis 6 1 1
chorismate biosynthesis I 7 7 1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis 7 4 1
glycogen biosynthesis III (from α-maltose 1-phosphate) 8 4 1
bacterial bioluminescence 8 4 1
superpathway of allantoin degradation in plants 8 2 1
chitin biosynthesis 9 6 1
allantoin degradation IV (anaerobic) 9 3 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
chorismate biosynthesis II (archaea) 12 8 1
superpathway of L-tryptophan biosynthesis 13 13 1
hypoglycin biosynthesis 14 4 1
superpathway of (Kdo)2-lipid A biosynthesis 17 17 1
superpathway of aromatic amino acid biosynthesis 18 18 1
superpathway of Kdo2-lipid A biosynthesis 25 17 1
mycolate biosynthesis 205 25 5
superpathway of mycolate biosynthesis 239 26 5
superpathway of chorismate metabolism 59 54 1