Experiment set10S420 for Enterobacter sp. TBS_079

Thymidine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Thymidine (10 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 16 genes in this experiment

For nitrogen source Thymidine in Enterobacter sp. TBS_079

For nitrogen source Thymidine across organisms

SEED Subsystems

Subsystem	#Specific
Pyrimidine utilization	4
Phosphate metabolism	2
Deoxyribose and Deoxynucleoside Catabolism	1
Hydantoin metabolism	1
Nitrate and nitrite ammonification	1
RNA processing and degradation, bacterial	1
Stringent Response, (p)ppGpp metabolism	1
Trehalose Uptake and Utilization	1
Urea decomposition	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Pyrimidine metabolism
• Tryptophan metabolism
• Carotenoid biosynthesis - General
• Ascorbate and aldarate metabolism
• Biosynthesis of steroids
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• gamma-Hexachlorocyclohexane degradation
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Trinitrotoluene degradation
• Methane metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Phenylpropanoid biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyrimidine deoxyribonucleosides degradation	3	3	2
trehalose degradation II (cytosolic)	2	2	1
trehalose degradation VI (periplasmic)	2	2	1
pyrimidine ribonucleosides degradation	2	2	1
polyphosphate metabolism	2	2	1
β-alanine degradation III	2	1	1
uracil degradation III	5	5	2
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	2
allantoin degradation to ureidoglycolate II (ammonia producing)	4	1	1
tRNA processing	10	10	2
superpathway of pyrimidine ribonucleosides degradation	5	2	1
allantoin degradation to glyoxylate II	5	1	1
dibenzothiophene desulfurization	5	1	1
allantoin degradation to glyoxylate III	5	1	1
ppGpp metabolism	6	6	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
nucleoside and nucleotide degradation (archaea)	10	4	1
3-hydroxypropanoate cycle	13	6	1
glyoxylate assimilation	13	5	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
superpathway of the 3-hydroxypropanoate cycle	18	6	1