Experiment set18S1036 for Phocaeicola vulgatus CL09T03C04

D-Glucose-6-Phosphate sodium salt 10 mM carbon source mhCom Varel_Bryant_medium_lowCys Passage4

Group: mixed community
Media: Varel_Bryant_medium_lowCys + D-Glucose-6-Phosphate sodium salt (10 mM) + mhCom
Culturing: Bvulgatus_CL09T03C04_ML5, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 10/8/25
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 3 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 17 genes in this experiment

For mixed community D-Glucose-6-Phosphate sodium salt in Phocaeicola vulgatus CL09T03C04

For mixed community D-Glucose-6-Phosphate sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Capsular heptose biosynthesis	1
Colanic acid biosynthesis	1
Copper homeostasis: copper tolerance	1
Cysteine Biosynthesis	1
De Novo Purine Biosynthesis	1
Fermentations: Mixed acid	1
Maltose and Maltodextrin Utilization	1
Phosphate metabolism	1
Queuosine-Archaeosine Biosynthesis	1
Threonine anaerobic catabolism gene cluster	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Biosynthesis of steroids
• Purine metabolism
• Glutamate metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Biphenyl degradation
• Toluene and xylene degradation
• 1,4-Dichlorobenzene degradation
• Fluorene degradation
• Carbazole degradation
• Ethylbenzene degradation
• Styrene degradation
• Carotenoid biosynthesis - General

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
GDP-L-fucose biosynthesis I (from GDP-D-mannose)	3	3	2
reductive monocarboxylic acid cycle	2	2	1
pyruvate fermentation to acetate IV	3	3	1
pyruvate fermentation to ethanol I	3	2	1
2-hydroxypenta-2,4-dienoate degradation	3	1	1
5-aminoimidazole ribonucleotide biosynthesis II	5	5	1
5-aminoimidazole ribonucleotide biosynthesis I	5	5	1
catechol degradation I (meta-cleavage pathway)	5	1	1
colanic acid building blocks biosynthesis	11	9	2
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	8	2
toluene degradation I (aerobic) (via o-cresol)	7	1	1
toluene degradation V (aerobic) (via toluene-cis-diol)	7	1	1
catechol degradation II (meta-cleavage pathway)	7	1	1
p-cumate degradation	8	1	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	1	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	1
meta cleavage pathway of aromatic compounds	10	1	1
p-cymene degradation	11	1	1
L-tryptophan degradation XII (Geobacillus)	12	1	1
naphthalene degradation to acetyl-CoA	12	1	1
L-tryptophan degradation IX	12	1	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
toluene degradation IV (aerobic) (via catechol)	13	1	1
mixed acid fermentation	16	12	1
mandelate degradation to acetyl-CoA	18	1	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of N-acetylneuraminate degradation	22	17	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	1
superpathway of aerobic toluene degradation	30	2	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	3	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	3	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	1