Experiment set19S38 for Bifidobacterium breve UCC2003

cage1; mouse2; day5; diet=StandardDiet; sample=FecalPellet; coculture=Btheta_VPI5482

Group: mouse coculture
Media: + diet=StandardDiet; sample=FecalPellet; coculture=Btheta_VPI5482
Culturing: Bifido_ML2
By: Anthony Shiver on 4/2/2024

Specific Phenotypes

For 11 genes in this experiment

For mouse coculture diet=StandardDiet; sample=FecalPellet; coculture=Btheta_VPI5482 in Bifidobacterium breve UCC2003

For mouse coculture diet=StandardDiet; sample=FecalPellet; coculture=Btheta_VPI5482 across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	4
Ammonia assimilation	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Acetoin, butanediol metabolism	1
Coenzyme A Biosynthesis	1
Leucine Biosynthesis	1
Sialic Acid Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of alkaloids derived from histidine and purine
• Valine, leucine and isoleucine biosynthesis
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glutamate metabolism
• Nucleotide sugars metabolism
• Nitrogen metabolism
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Cysteine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Aminosugars metabolism
• Pyruvate metabolism
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
L-glutamate biosynthesis IV	1	1	1
L-valine biosynthesis	4	4	3
ammonia assimilation cycle III	3	3	2
pyruvate fermentation to isobutanol (engineered)	5	4	3
pyruvate fermentation to (R)-acetoin II	2	2	1
ammonia assimilation cycle I	2	2	1
L-isoleucine biosynthesis IV	6	4	3
trehalose degradation II (cytosolic)	2	1	1
trehalose degradation I (low osmolarity)	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
L-glutamate and L-glutamine biosynthesis	7	5	3
L-isoleucine biosynthesis III	7	4	3
superpathway of branched chain amino acid biosynthesis	17	17	7
L-isoleucine biosynthesis II	8	6	3
trehalose degradation IV	3	3	1
GDP-α-D-glucose biosynthesis	3	2	1
pyruvate fermentation to (R)-acetoin I	3	2	1
trehalose degradation V	3	2	1
pyruvate fermentation to (S)-acetoin	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
sucrose degradation III (sucrose invertase)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
phosphopantothenate biosynthesis I	4	2	1
N-acetylneuraminate and N-acetylmannosamine degradation I	4	2	1
phosphopantothenate biosynthesis III (archaea)	4	1	1
superpathway of L-isoleucine biosynthesis I	13	13	3
superpathway of (R,R)-butanediol biosynthesis	5	3	1
glucose and glucose-1-phosphate degradation	5	3	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	2	1
L-leucine biosynthesis	6	6	1
superpathway of L-threonine metabolism	18	13	3
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	4	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
glycogen degradation II	6	4	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
3-methylbutanol biosynthesis (engineered)	7	6	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
glycogen degradation I	8	7	1
sucrose biosynthesis II	8	6	1
L-citrulline biosynthesis	8	5	1
chitin biosynthesis	9	5	1
1,3-propanediol biosynthesis (engineered)	9	4	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	4	1
superpathway of coenzyme A biosynthesis II (plants)	10	2	1
glycolysis III (from glucose)	11	10	1
homolactic fermentation	12	11	1
superpathway of L-citrulline metabolism	12	7	1
Bifidobacterium shunt	15	15	1
superpathway of CMP-sialic acids biosynthesis	15	2	1
heterolactic fermentation	18	16	1
superpathway of N-acetylneuraminate degradation	22	17	1