Experiment set6S192 for Phocaeicola vulgatus CL09T03C04

diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse12; day7

Group: mouse
Media: + diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm
Culturing: Bvulgatus_CL09T03C04_ML5
By: Surya Tripathi on 12/1/24

Specific Phenotypes

For 23 genes in this experiment

For mouse diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm in Phocaeicola vulgatus CL09T03C04

For mouse diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm across organisms

SEED Subsystems

Subsystem	#Specific
Predicted carbohydrate hydrolases	2
Cysteine Biosynthesis	1
De Novo Purine Biosynthesis	1
Deoxyribose and Deoxynucleoside Catabolism	1
Galactosylceramide and Sulfatide metabolism	1
Heat shock dnaK gene cluster extended	1
Heme and Siroheme Biosynthesis	1
Iron acquisition in Vibrio	1
Oxidative stress	1
Queuosine-Archaeosine Biosynthesis	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:

• Purine metabolism
• Pentose phosphate pathway
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Biosynthesis of steroids
• Glutamate metabolism
• Selenoamino acid metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Sulfur metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
sulfate activation for sulfonation	2	2	1
GDP-L-fucose biosynthesis II (from L-fucose)	2	1	1
2-deoxy-D-ribose degradation I	3	2	1
sulfite oxidation III	3	1	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	1	1
assimilatory sulfate reduction III	3	1	1
assimilatory sulfate reduction II	3	1	1
assimilatory sulfate reduction I	4	2	1
assimilatory sulfate reduction IV	4	2	1
5-aminoimidazole ribonucleotide biosynthesis II	5	5	1
5-aminoimidazole ribonucleotide biosynthesis I	5	5	1
selenate reduction	5	2	1
dissimilatory sulfate reduction I (to hydrogen sufide))	5	1	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	3	1
superpathway of thiosulfate metabolism (Desulfovibrio sulfodismutans)	6	1	1
superpathway of sulfur metabolism (Desulfocapsa sulfoexigens)	6	1	1
β-(1,4)-mannan degradation	7	4	1
superpathway of purine deoxyribonucleosides degradation	7	4	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	7	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	4	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	8	1
superpathway of sulfide oxidation (phototrophic sulfur bacteria)	12	2	1
superpathway of seleno-compound metabolism	19	5	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	1