Experiment set3S353 for Phocaeicola vulgatus CL09T03C04

diet=PolysaccharideDeficient; sample=FecalPellet; inoculation=Mono; mouse17; day9

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

Specific Phenotypes

For 22 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
Cysteine Biosynthesis	3
Carotenoids	1
Chitin and N-acetylglucosamine utilization	1
Cobalamin synthesis	1
Coenzyme B12 biosynthesis	1
Fatty Acid Biosynthesis FASII	1
O-Methyl Phosphoramidate Capsule Modification in Campylobacter	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:

• Sulfur metabolism
• Fatty acid biosynthesis
• Purine metabolism
• Selenoamino acid metabolism
• Porphyrin and chlorophyll metabolism
• Biosynthesis of unsaturated fatty acids
• Tyrosine metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Limonene and pinene degradation
• Biosynthesis of type II polyketide backbone

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
sulfate activation for sulfonation	2	2	2
assimilatory sulfate reduction IV	4	2	2
assimilatory sulfate reduction I	4	2	2
assimilatory sulfate reduction III	3	1	1
sulfite oxidation III	3	1	1
assimilatory sulfate reduction II	3	1	1
gondoate biosynthesis (anaerobic)	4	4	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	9	3
penicillin G and penicillin V biosynthesis	4	3	1
siroheme biosynthesis	4	3	1
phenylacetate degradation II (anaerobic)	4	1	1
palmitate biosynthesis III	29	21	7
tetradecanoate biosynthesis (mitochondria)	25	17	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
superpathway of sulfate assimilation and cysteine biosynthesis	9	7	2
oleate biosynthesis IV (anaerobic)	14	13	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
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	4	2
selenate reduction	5	2	1
dissimilatory sulfate reduction I (to hydrogen sufide))	5	1	1
superpathway of fatty acid biosynthesis II (plant)	43	37	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
even iso-branched-chain fatty acid biosynthesis	34	25	6
odd iso-branched-chain fatty acid biosynthesis	34	25	6
anteiso-branched-chain fatty acid biosynthesis	34	25	6
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis I	6	5	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	8	2
stearate biosynthesis IV	6	4	1
(5Z)-dodecenoate biosynthesis II	6	4	1
petroselinate biosynthesis	6	2	1
superpathway of sulfur metabolism (Desulfocapsa sulfoexigens)	6	1	1
cyanophycin metabolism	6	1	1
superpathway of thiosulfate metabolism (Desulfovibrio sulfodismutans)	6	1	1
streptorubin B biosynthesis	34	20	5
factor 430 biosynthesis	7	3	1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion)	15	14	2
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	14	2
2-allylmalonyl-CoA biosynthesis	8	2	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	2	1
phenylacetate degradation I (aerobic)	9	1	1
superpathway of phenylethylamine degradation	11	1	1
superpathway of sulfide oxidation (phototrophic sulfur bacteria)	12	2	1
adenosylcobalamin biosynthesis I (anaerobic)	36	26	2
superpathway of seleno-compound metabolism	19	5	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
mycolate biosynthesis	205	23	5
superpathway of mycolate biosynthesis	239	24	5