Experiment set3S356 for Phocaeicola vulgatus CL09T03C04

diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=Mono; mouse20; day9

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

Specific Phenotypes

For 25 genes in this experiment

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

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

SEED Subsystems

Subsystem	#Specific
Terminal cytochrome d ubiquinol oxidases	2
Terminal cytochrome oxidases	2
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Branched-Chain Amino Acid Biosynthesis	1
Chitin and N-acetylglucosamine utilization	1
Coenzyme B12 biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Fatty Acid Biosynthesis FASII	1
Galactosylceramide and Sulfatide metabolism	1
Lactose and Galactose Uptake and Utilization	1
Lactose utilization	1
Mannose Metabolism	1
NAD regulation	1
Predicted carbohydrate hydrolases	1
Serine-glyoxylate cycle	1
TCA Cycle	1
Threonine degradation	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycosphingolipid biosynthesis - ganglio series
• Biosynthesis of alkaloids derived from shikimate pathway
• Citrate cycle (TCA cycle)
• Galactose metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Other glycan degradation
• Glycosaminoglycan degradation
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
lactose degradation III	1	1	1
L-methionine degradation II	3	2	2
L-threonine degradation I	6	6	3
malate/L-aspartate shuttle pathway	2	2	1
L-threonine degradation V	2	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
xyloglucan degradation II (exoglucanase)	8	5	3
gondoate biosynthesis (anaerobic)	4	4	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	9	3
palmitate biosynthesis III	29	21	7
tetradecanoate biosynthesis (mitochondria)	25	17	6
superpathway of L-isoleucine biosynthesis I	13	12	3
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
hypoglycin biosynthesis	14	3	3
superpathway of fatty acids biosynthesis (E. coli)	53	47	11
fatty acid elongation -- saturated	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	17	4
8-amino-7-oxononanoate biosynthesis IV	5	4	1
cis-vaccenate biosynthesis	5	4	1
mammalian high-mannose N-glycan degradation	5	2	1
superpathway of fatty acid biosynthesis II (plant)	43	37	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
superpathway of branched chain amino acid biosynthesis	17	17	3
odd iso-branched-chain fatty acid biosynthesis	34	25	6
anteiso-branched-chain fatty acid biosynthesis	34	25	6
even iso-branched-chain fatty acid biosynthesis	34	25	6
superpathway of L-threonine metabolism	18	15	3
(5Z)-dodecenoate biosynthesis I	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
TCA cycle VIII (Chlamydia)	6	4	1
glyoxylate cycle	6	4	1
stearate biosynthesis IV	6	4	1
(5Z)-dodecenoate biosynthesis II	6	4	1
petroselinate biosynthesis	6	2	1
streptorubin B biosynthesis	34	20	5
pyruvate fermentation to propanoate I	7	5	1
incomplete reductive TCA cycle	7	5	1
β-(1,4)-mannan degradation	7	4	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	14	2
2-allylmalonyl-CoA biosynthesis	8	2	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle II (plants and fungi)	9	6	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	1
TCA cycle I (prokaryotic)	10	7	1
TCA cycle III (animals)	10	7	1
reductive TCA cycle I	11	8	1
L-glutamate degradation VIII (to propanoate)	11	5	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	5	1
gluconeogenesis III	12	10	1
superpathway of glyoxylate bypass and TCA	12	7	1
reductive TCA cycle II	12	6	1
gluconeogenesis I	13	11	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
formaldehyde assimilation I (serine pathway)	13	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	6	1
cyclosporin A biosynthesis	15	2	1
mixed acid fermentation	16	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
methylaspartate cycle	19	10	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	16	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	19	1
mycolate biosynthesis	205	23	5
superpathway of mycolate biosynthesis	239	24	5
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	18	1