Experiment set1S416 for Parabacteroides merdae CL09T00C40

D-Glucose 10 mg/mL carbon source

Group: carbon source
Media: Varel_Bryant_medium + D-Glucose (10 mg/mL)
Culturing: Pmerdae_CL09T00C40_ML3, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 1/10/25
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-Glucose in Parabacteroides merdae CL09T00C40

For carbon source D-Glucose across organisms

SEED Subsystems

Subsystem	#Specific
N-linked Glycosylation in Bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid biosynthesis
• Fatty acid metabolism
• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Nucleotide sugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate 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
phosphatidylcholine acyl editing	4	2	1
phytol degradation	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	4	1
stearate biosynthesis IV	6	3	1
fatty acid salvage	6	2	1
stearate biosynthesis I (animals)	6	1	1
6-gingerol analog biosynthesis (engineered)	6	1	1
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
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of fatty acids biosynthesis (E. coli)	53	48	2
palmitate biosynthesis III	29	21	1
oleate β-oxidation	35	4	1