Experiment set15S232 for Phocaeicola vulgatus CL09T03C04

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Uridine 5.-monophosphate disodium salt 1 mM phosphorus source

Group: phosphorus source
Media: Varel_Bryant_medium_Glucose_minusP + Uridine 5-monophosphate disodium salt (1 mM)
Culturing: Bvulgatus_CL09T03C04_ML5, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 7/3/25
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, 20 mM D-Glucose, Mineral 3B solution minus phosphorus (6.6 mM Potassium Chloride, 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 4 genes in this experiment

For phosphorus source Uridine 5-monophosphate disodium salt in Phocaeicola vulgatus CL09T03C04

For phosphorus source Uridine 5-monophosphate disodium salt across organisms

SEED Subsystems

Subsystem #Specific
Carboxysome 1
Cyanate hydrolysis 1
De Novo Pyrimidine Synthesis 1
LMPTP YwlE cluster 1
LOS core oligosaccharide 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
pyrimidine nucleobases salvage I 1 1 1
pyrimidine nucleobases salvage II 2 1 1
CO2 fixation into oxaloacetate (anaplerotic) 2 1 1
cyanate degradation 3 2 1
superpathway of pyrimidine nucleobases salvage 4 4 1
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 1
superpathway of pyrimidine ribonucleosides salvage 10 9 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
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 8 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 6 1
superpathway of the 3-hydroxypropanoate cycle 18 6 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 18 1