Experiment set2S334 for Parabacteroides merdae CL09T00C40

diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=MixComm; mouse10; day4

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

Specific Phenotypes

For 43 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
DNA repair, UvrABC system	2
Galactosylceramide and Sulfatide metabolism	2
Lactose and Galactose Uptake and Utilization	2
Lactose utilization	2
Maltose and Maltodextrin Utilization	2
Transport of Zinc	2
Acid resistance mechanisms	1
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
De Novo Purine Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutamine synthetases	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Glycogen metabolism	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Histidine Degradation	1
Iron acquisition in Vibrio	1
Lipoic acid metabolism	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
Peptidoglycan Biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Queuosine-Archaeosine Biosynthesis	1
Sialic Acid Metabolism	1
Thiamin biosynthesis	1
Ton and Tol transport systems	1
Trehalose Biosynthesis	1
tRNA processing	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
• Histidine metabolism
• Starch and sucrose metabolism
• Carotenoid biosynthesis - General
• Pentose and glucuronate interconversions
• Galactose metabolism
• Biosynthesis of steroids
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Other glycan degradation
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• Carbon fixation in photosynthetic organisms
• Thiamine metabolism
• Lipoic acid metabolism
• Porphyrin and chlorophyll metabolism
• 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
thiamine diphosphate biosynthesis II (Bacillus)	2	2	1
thiamine diphosphate biosynthesis I (E. coli)	2	2	1
ammonia assimilation cycle I	2	2	1
lipoate biosynthesis and incorporation I	2	2	1
pseudouridine degradation	2	1	1
ammonia assimilation cycle II	2	1	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	1	1
putrescine biosynthesis I	2	1	1
xyloglucan degradation II (exoglucanase)	8	5	3
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
ammonia assimilation cycle III	3	3	1
putrescine biosynthesis II	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
lipoate biosynthesis and incorporation III (Bacillus)	3	2	1
lipoate biosynthesis and incorporation V (mammals)	3	2	1
thiamine diphosphate biosynthesis IV (eukaryotes)	3	2	1
thiamine diphosphate salvage V	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
thiamine diphosphate biosynthesis III (Staphylococcus)	3	2	1
L-aspartate degradation II (aerobic)	3	1	1
L-aspartate degradation III (anaerobic)	3	1	1
L-histidine degradation I	4	3	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
thiamine diphosphate salvage II	5	4	1
L-histidine degradation II	5	3	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
L-histidine degradation III	6	6	1
L-glutamate and L-glutamine biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
thiamine diphosphate salvage IV (yeast)	7	4	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	4	1
lipoate biosynthesis and incorporation IV (yeast)	7	4	1
glycogen degradation I	8	7	1
L-histidine degradation VI	8	7	1
sucrose biosynthesis II	8	5	1
nitrogen remobilization from senescing leaves	8	5	1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	4	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 thiamine diphosphate biosynthesis I	10	6	1
superpathway of thiamine diphosphate biosynthesis II	11	7	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	5	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	1	1
superpathway of L-arginine and L-ornithine degradation	13	2	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	7	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