Experiment set2S391 for Bacteroides ovatus ATCC 8483

Rhamnogalacturonan from soy bean pectic fibre 2.5 mg/ml carbon source

Group: carbon source
Media: Varel_Bryant_medium + Rhamnogalacturonan from soy bean pectic fibre (2.5 mg/mL)
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 3 genes in this experiment

For carbon source Rhamnogalacturonan from soy bean pectic fibre in Bacteroides ovatus ATCC 8483

For carbon source Rhamnogalacturonan from soy bean pectic fibre across organisms

SEED Subsystems

Subsystem	#Specific
D-Galacturonate and D-Glucuronate Utilization	1
Fermentations: Mixed acid	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	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
• Starch and sucrose metabolism
• Retinol metabolism
• Glycolysis / Gluconeogenesis
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• C21-Steroid hormone metabolism
• Tyrosine metabolism
• Bisphenol A degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Alkaloid biosynthesis I
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
L-galactonate degradation	1	1	1
ethanol degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
pyruvate fermentation to ethanol I	3	2	1
L-valine degradation II	3	2	1
pyruvate fermentation to ethanol III	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
ethanol degradation II	3	2	1
L-methionine degradation III	3	1	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
phytol degradation	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
salidroside biosynthesis	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
ethanolamine utilization	5	3	1
acetylene degradation (anaerobic)	5	3	1
(S)-propane-1,2-diol degradation	5	3	1
phenylethanol biosynthesis	5	1	1
noradrenaline and adrenaline degradation	13	2	2
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	2	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	3	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	14	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of N-acetylneuraminate degradation	22	17	1