Experiment set13S64 for Phocaeicola vulgatus CL09T03C04

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Dextrin from potato starch 2.5 mg/ml carbon source

Group: carbon source
Media: Varel_Bryant_medium + Dextrin from potato starch (2.5 mg/ml)
Culturing: Bvulgatus_CL09T03C04_ML5, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 6/18/25
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 7 genes in this experiment

For carbon source Dextrin from potato starch in Phocaeicola vulgatus CL09T03C04

For carbon source Dextrin from potato starch across organisms

SEED Subsystems

Subsystem #Specific
Carboxysome 1
Chitin and N-acetylglucosamine utilization 1
Cyanate hydrolysis 1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 1
Sialic Acid Metabolism 1
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis 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
N-acetylglucosamine degradation I 2 2 1
CO2 fixation into oxaloacetate (anaplerotic) 2 1 1
N-acetylglucosamine degradation II 3 3 1
cyanate degradation 3 2 1
D-galactosamine and N-acetyl-D-galactosamine degradation 4 2 1
N-acetyl-D-galactosamine degradation 5 2 1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation 6 3 1
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 1
chitin derivatives degradation 8 3 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 5 1
3-hydroxypropanoate cycle 13 6 1
glyoxylate assimilation 13 3 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 7 1
peptidoglycan recycling I 14 6 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 8 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 6 1
superpathway of the 3-hydroxypropanoate cycle 18 6 1
superpathway of N-acetylneuraminate degradation 22 17 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 18 1