Experiment set1IT048 for Phocaeicola vulgatus CL09T03C04

Polygalacturonic acid 5 mg/ml carbon source

Group: carbon source
Media: Varel_Bryant_medium + polygalacturonic acid (5 mg/ml)
Culturing: Bvulgatus_CL09T03C04_ML5, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 34 (C), shaken=0 rpm
By: Surya Tripathi on 12/22/21
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 19 genes in this experiment

For carbon source polygalacturonic acid in Phocaeicola vulgatus CL09T03C04

For carbon source polygalacturonic acid across organisms

SEED Subsystems

Subsystem	#Specific
Cobalt-zinc-cadmium resistance	1
Teichoic and lipoteichoic acids biosynthesis	1
p-Aminobenzoyl-Glutamate Utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lipopolysaccharide biosynthesis
• Glycosphingolipid biosynthesis - ganglio series
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Fructose and mannose metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
3-methyl-branched fatty acid α-oxidation	6	2	2
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
phytol degradation	4	2	1
phosphatidylcholine acyl editing	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
wax esters biosynthesis II	4	1	1
sporopollenin precursors biosynthesis	18	4	4
sphingosine and sphingosine-1-phosphate metabolism	10	2	2
octane oxidation	5	1	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
fatty acid salvage	6	2	1
6-gingerol analog biosynthesis (engineered)	6	1	1
stearate biosynthesis I (animals)	6	1	1
Arg/N-end rule pathway (eukaryotic)	14	6	2
capsaicin biosynthesis	7	1	1
ceramide degradation by α-oxidation	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
ceramide and sphingolipid recycling and degradation (yeast)	16	2	2
suberin monomers biosynthesis	20	2	2
superpathway of fatty acid biosynthesis II (plant)	43	37	4
poly(glycerol phosphate) wall teichoic acid biosynthesis	11	2	1
colanic acid (Escherichia coli K12) biosynthesis	11	1	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of fatty acids biosynthesis (E. coli)	53	47	2
palmitate biosynthesis III	29	21	1
oleate β-oxidation	35	4	1