Experiment set2S559 for Bacteroides stercoris CC31F

D-Galacturonic Acid monohydrate 10 mM carbon source

Group: carbon source
Media: Varel_Bryant_medium + D-Galacturonic Acid monohydrate (10 mM)
Culturing: Bstercoris_CC31F_ML5, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 10/31/24
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 5 genes in this experiment

For carbon source D-Galacturonic Acid monohydrate in Bacteroides stercoris CC31F

For carbon source D-Galacturonic Acid monohydrate across organisms

SEED Subsystems

Subsystem	#Specific
L-rhamnose utilization	1
Phosphate metabolism	1
Propionate-CoA to Succinate Module	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:

• Citrate cycle (TCA cycle)
• Fructose and mannose metabolism
• Oxidative phosphorylation
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• 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
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glyoxylate cycle	6	4	2
partial TCA cycle (obligate autotrophs)	8	5	2
nitrogen remobilization from senescing leaves	8	5	2
L-lyxose degradation	4	1	1
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle VI (Helicobacter)	9	6	2
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	2
TCA cycle II (plants and fungi)	9	6	2
L-rhamnose degradation I	5	4	1
TCA cycle III (animals)	10	7	2
TCA cycle I (prokaryotic)	10	7	2
reductive TCA cycle I	11	8	2
reductive TCA cycle II	12	7	2
superpathway of glyoxylate bypass and TCA	12	7	2
superpathway of glyoxylate cycle and fatty acid degradation	14	6	2
glyphosate degradation III	7	2	1
mixed acid fermentation	16	11	2
(aminomethyl)phosphonate degradation	8	2	1
methylaspartate cycle	19	10	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	16	2
superpathway of fucose and rhamnose degradation	12	6	1
ethene biosynthesis V (engineered)	25	15	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	19	2
superpathway of pentose and pentitol degradation	42	5	1