Experiment set2S428 for Bacteroides ovatus ATCC 8483

D-Galactose 10 mM carbon source

Group: carbon source
Media: Varel_Bryant_medium + D-Galactose (10 mM)
Culturing: Bovatus_ATCC8483_ML6, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 10/30/24
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 8.25 mM L-Cysteine, 23.8 mM Sodium bicarbonate, Mineral 3B solution (6.6 mM Potassium phosphate monobasic, 15.4 mM Sodium Chloride, 98 uM Magnesium chloride hexahydrate, 176.5 uM Calcium chloride dihydrate, 4.2 uM Cobalt chloride hexahydrate, 50.5 uM Manganese (II) chloride tetrahydrate, 9.3 mM Ammonium chloride, 1.75 mM Sodium sulfate)

Specific Phenotypes

For 21 genes in this experiment

For carbon source D-Galactose in Bacteroides ovatus ATCC 8483

For carbon source D-Galactose across organisms

SEED Subsystems

Subsystem	#Specific
Phosphate metabolism	3
Campylobacter Iron Metabolism	1
Copper homeostasis: copper tolerance	1
De Novo Pyrimidine Synthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycine reductase, sarcosine reductase and betaine reductase	1
LMPTP YwlE cluster	1
Serine-glyoxylate cycle	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Propanoate metabolism
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Fatty acid metabolism
• Pyrimidine metabolism
• Geraniol degradation
• Tyrosine metabolism
• Glycerophospholipid metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• C5-Branched dibasic acid metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyrimidine nucleobases salvage I	1	1	1
long-chain fatty acid activation	1	1	1
phosphatidylcholine resynthesis via glycerophosphocholine	2	1	1
pyrimidine nucleobases salvage II	2	1	1
linoleate biosynthesis II (animals)	2	1	1
glycerophosphodiester degradation	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
pyruvate fermentation to acetate VI	3	2	1
3-methyl-branched fatty acid α-oxidation	6	2	2
pyruvate fermentation to acetate V	3	1	1
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
superpathway of pyrimidine nucleobases salvage	4	4	1
phytol degradation	4	2	1
wax esters biosynthesis II	4	1	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
glycerol and glycerophosphodiester degradation	4	1	1
sporopollenin precursors biosynthesis	18	4	4
adipate degradation	5	2	1
sphingosine and sphingosine-1-phosphate metabolism	10	2	2
octane oxidation	5	1	1
adipate biosynthesis	5	1	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
TCA cycle VIII (Chlamydia)	6	4	1
fatty acid salvage	6	2	1
6-gingerol analog biosynthesis (engineered)	6	1	1
stearate biosynthesis I (animals)	6	1	1
incomplete reductive TCA cycle	7	6	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
ceramide degradation by α-oxidation	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
ceramide and sphingolipid recycling and degradation (yeast)	16	2	2
TCA cycle V (2-oxoglutarate synthase)	9	8	1
TCA cycle II (plants and fungi)	9	6	1
superpathway of pyrimidine ribonucleosides salvage	10	9	1
TCA cycle III (animals)	10	7	1
TCA cycle I (prokaryotic)	10	7	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	6	1
suberin monomers biosynthesis	20	2	2
superpathway of fatty acid biosynthesis II (plant)	43	37	4
reductive TCA cycle I	11	9	1
reductive TCA cycle II	12	8	1
superpathway of glyoxylate bypass and TCA	12	7	1
anandamide biosynthesis I	12	2	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
methylaspartate cycle	19	11	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	1
superpathway of fatty acids biosynthesis (E. coli)	53	47	2
palmitate biosynthesis III	29	21	1
oleate β-oxidation	35	4	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1