Experiment set3S306 for Phocaeicola dorei CL03T12C01

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Xylan from Beechwood; autoclaved 2.5 mg/ml carbon source

Group: carbon source
Media: Varel_Bryant_medium + Xylan from Beechwood; autoclaved (2.5 mg/ml)
Culturing: Bdorei_CL03T12C01_ML9, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya Tripathi on 3/20/24
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 11 genes in this experiment

For carbon source Xylan from Beechwood; autoclaved in Phocaeicola dorei CL03T12C01

For carbon source Xylan from Beechwood; autoclaved across organisms

SEED Subsystems

Subsystem #Specific
D-Galacturonate and D-Glucuronate Utilization 3
Xylose utilization 2
Iron acquisition in Vibrio 1
L-Arabinose utilization 1
Ton and Tol transport systems 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
long-chain fatty acid activation 1 1 1
D-fructuronate degradation 4 4 2
(1,4)-β-D-xylan degradation 2 2 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
cellulose and hemicellulose degradation (cellulolosome) 3 1 1
alkane biosynthesis II 3 1 1
superpathway of β-D-glucuronosides degradation 7 6 2
phytol degradation 4 2 1
wax esters biosynthesis II 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
phosphatidylcholine acyl editing 4 1 1
sporopollenin precursors biosynthesis 18 4 4
superpathway of hexuronide and hexuronate degradation 10 9 2
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
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
capsaicin biosynthesis 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
ceramide degradation by α-oxidation 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
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 13 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