Experiment set13S65 for Phocaeicola vulgatus CL09T03C04

Compare to:

beta-Cyclodextrin 2.5 mg/ml carbon source

Group: carbon source
Media: Varel_Bryant_medium + beta-Cyclodextrin (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 12 genes in this experiment

For carbon source beta-Cyclodextrin in Phocaeicola vulgatus CL09T03C04

For carbon source beta-Cyclodextrin across organisms

SEED Subsystems

Subsystem #Specific
Carboxysome 1
Cyanate hydrolysis 1
L-fucose utilization 1
L-fucose utilization temp 1
LOS core oligosaccharide biosynthesis 1
Phosphate metabolism 1
ZZ gjo need homes 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
CO2 fixation into oxaloacetate (anaplerotic) 2 1 1
cyanate degradation 3 2 1
incomplete reductive TCA cycle 7 5 1
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 1
glyphosate degradation III 7 2 1
(aminomethyl)phosphonate degradation 8 2 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 8 2
reductive TCA cycle I 11 8 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 5 1
gluconeogenesis III 12 10 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 10 1
3-hydroxypropanoate cycle 13 6 1
glyoxylate assimilation 13 3 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 7 1
superpathway of the 3-hydroxypropanoate cycle 18 6 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 6 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 18 2