Experiment set2S322 for Parabacteroides merdae CL09T00C40

diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day3

Group: mouse mixed community
Media: + diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm
Culturing: Pmerdae_CL09T00C40_ML3
By: Saria on 5/21/25

Specific Phenotypes

For 27 genes in this experiment

For mouse mixed community diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm in Parabacteroides merdae CL09T00C40

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

SEED Subsystems

Subsystem	#Specific
Galactosylceramide and Sulfatide metabolism	2
Lactose and Galactose Uptake and Utilization	2
Lactose utilization	2
Maltose and Maltodextrin Utilization	2
Acid resistance mechanisms	1
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
DNA repair, UvrABC system	1
De Novo Purine Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutamine synthetases	1
Glycogen metabolism	1
Iron acquisition in Vibrio	1
Lipoic acid metabolism	1
Peptidoglycan Biosynthesis	1
Polyamine Metabolism	1
Sialic Acid Metabolism	1
Ton and Tol transport systems	1
Transport of Zinc	1
Trehalose Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Arginine and proline metabolism
• Starch and sucrose metabolism
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Other glycan degradation
• Glycosaminoglycan degradation
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Naphthalene and anthracene degradation
• Lipoic acid metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
lactose degradation III	1	1	1
L-glutamine biosynthesis I	1	1	1
arginine dependent acid resistance	1	1	1
lipoate biosynthesis and incorporation I	2	2	1
ammonia assimilation cycle I	2	2	1
putrescine biosynthesis I	2	1	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	1	1
ammonia assimilation cycle II	2	1	1
xyloglucan degradation II (exoglucanase)	8	5	3
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
ammonia assimilation cycle III	3	3	1
putrescine biosynthesis II	3	3	1
lipoate biosynthesis and incorporation V (mammals)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
lipoate biosynthesis and incorporation III (Bacillus)	3	2	1
L-aspartate degradation II (aerobic)	3	1	1
L-aspartate degradation III (anaerobic)	3	1	1
starch degradation V	4	3	1
superpathway of putrescine biosynthesis	4	2	1
spermidine biosynthesis III	4	1	1
5-aminoimidazole ribonucleotide biosynthesis II	5	5	1
5-aminoimidazole ribonucleotide biosynthesis I	5	5	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
L-glutamate and L-glutamine biosynthesis	7	5	1
lipoate biosynthesis and incorporation IV (yeast)	7	4	1
glycogen degradation I	8	7	1
sucrose biosynthesis II	8	5	1
superpathway of polyamine biosynthesis II	8	4	1
superpathway of polyamine biosynthesis I	8	2	1
starch degradation II	9	1	1
L-arginine biosynthesis II (acetyl cycle)	10	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	1	1
superpathway of L-arginine and L-ornithine degradation	13	2	1
superpathway of arginine and polyamine biosynthesis	17	10	1
superpathway of purine nucleotides de novo biosynthesis I	21	18	1
superpathway of purine nucleotides de novo biosynthesis II	26	20	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	38	1