Experiment set3S453 for Parabacteroides merdae CL09T00C40

diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=Mono; mouse19; day7

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

Specific Phenotypes

For 16 genes in this experiment

For mouse diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=Mono in Parabacteroides merdae CL09T00C40

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

SEED Subsystems

Subsystem	#Specific
Aromatic amino acid interconversions with aryl acids	1
Chitin and N-acetylglucosamine utilization	1
Cysteine Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
N-Acetyl-Galactosamine and Galactosamine Utilization	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Sialic Acid Metabolism	1
Threonine and Homoserine 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:

• Nucleotide sugars metabolism
• Aminosugars metabolism
• Biosynthesis of plant hormones
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Other glycan degradation
• Glycosaminoglycan degradation
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Benzoate degradation via CoA ligation
• Carbon fixation in photosynthetic organisms
• Limonene and pinene degradation
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
malate/L-aspartate shuttle pathway	2	2	1
L-tyrosine degradation II	2	1	1
L-glutamate degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
N-acetylneuraminate and N-acetylmannosamine degradation II	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
chitin degradation II (Vibrio)	6	2	2
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
sulfolactate degradation III	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
dipicolinate biosynthesis	4	3	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-tyrosine degradation III	4	1	1
N-acetylneuraminate and N-acetylmannosamine degradation I	4	1	1
L-phenylalanine degradation III	4	1	1
trans-4-hydroxy-L-proline degradation I	5	4	1
superpathway of plastoquinol biosynthesis	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tyrosine degradation I	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	5	2
superpathway of L-threonine biosynthesis	6	5	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	3	1
TCA cycle VIII (Chlamydia)	6	3	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
L-lysine biosynthesis VI	7	7	1
L-lysine biosynthesis III	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	7	2
chitin degradation III (Serratia)	7	2	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-lysine biosynthesis II	9	7	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	12	2
L-lysine biosynthesis I	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	2	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
peptidoglycan recycling II	10	2	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	9	1
indole-3-acetate biosynthesis II	12	3	1
aspartate superpathway	25	19	2
superpathway of L-isoleucine biosynthesis I	13	11	1
peptidoglycan recycling I	14	7	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	1
superpathway of N-acetylneuraminate degradation	22	16	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	2	1
superpathway of chorismate metabolism	59	37	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	19	1