Experiment set19S31 for Bifidobacterium breve UCC2003

cage3; mouse1; day4; diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs

Group: mouse preculture
Media: + diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs
Culturing: Bifido_ML2
By: Anthony Shiver on 4/3/2024

Specific Phenotypes

For 5 genes in this experiment

For mouse preculture diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs in Bifidobacterium breve UCC2003

For mouse preculture diet=PolysaccharideDeficient; sample=FecalPellet; coculture=Btheta_VPI5482; stagger=24hrs across organisms

SEED Subsystems

Subsystem	#Specific
Biotin biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Thiamin biosynthesis	1
Threonine and Homoserine Biosynthesis	1
n-Phenylalkanoic acid degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Thiamine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fatty acid metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
hydroxymethylpyrimidine salvage	2	2	2
L-alanine biosynthesis II	1	1	1
L-alanine degradation III	1	1	1
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
long-chain fatty acid activation	1	1	1
L-aspartate biosynthesis	1	1	1
thiamine diphosphate salvage II	5	4	3
superpathway of L-alanine biosynthesis	4	4	2
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
L-glutamate degradation II	2	2	1
L-alanine biosynthesis I	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
atromentin biosynthesis	2	1	1
L-alanine degradation V (oxidative Stickland reaction)	2	1	1
L-tyrosine degradation II	2	1	1
thiamine diphosphate salvage IV (yeast)	7	6	3
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	5	3
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	4
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
thiamine diphosphate salvage V	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
sulfolactate degradation III	3	1	1
pyruvate fermentation to acetate and alanine	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-alanine degradation II (to D-lactate)	3	1	1
oleate biosynthesis I (plants)	3	1	1
L-asparagine degradation III (mammalian)	3	1	1
alkane biosynthesis II	3	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	6	4
phytol degradation	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	2	1
long chain fatty acid ester synthesis (engineered)	4	1	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
sporopollenin precursors biosynthesis	18	4	4
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
trans-4-hydroxy-L-proline degradation I	5	2	1
superpathway of plastoquinol biosynthesis	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation I	5	1	1
superpathway of L-threonine biosynthesis	6	6	1
stearate biosynthesis II (bacteria and plants)	6	4	1
stearate biosynthesis IV	6	3	1
TCA cycle VIII (Chlamydia)	6	2	1
superpathway of sulfolactate degradation	6	2	1
fatty acid salvage	6	1	1
stearate biosynthesis I (animals)	6	1	1
coenzyme M biosynthesis II	6	1	1
L-alanine degradation VI (reductive Stickland reaction)	6	1	1
6-gingerol analog biosynthesis (engineered)	6	1	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	4	1
ceramide degradation by α-oxidation	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-deoxy-D-ribose degradation II	8	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	6	2
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
superpathway of L-alanine fermentation (Stickland reaction)	9	3	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	1	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of thiamine diphosphate biosynthesis I	10	6	1
suberin monomers biosynthesis	20	2	2
rosmarinic acid biosynthesis I	10	1	1
superpathway of fatty acid biosynthesis II (plant)	43	29	4
superpathway of thiamine diphosphate biosynthesis II	11	7	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	6	1
indole-3-acetate biosynthesis II	12	2	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	1	1
palmitate biosynthesis II (type II fatty acid synthase)	31	22	2
cutin biosynthesis	16	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	23	1
superpathway of fatty acids biosynthesis (E. coli)	53	35	2
anaerobic aromatic compound degradation (Thauera aromatica)	27	1	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	16	2
palmitate biosynthesis III	29	14	1
superpathway of chorismate metabolism	59	32	2
oleate β-oxidation	35	1	1