Experiment set19S37 for Bifidobacterium breve UCC2003

cage1; mouse1; 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 7 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
Ammonia assimilation	2
Branched-Chain Amino Acid Biosynthesis	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Coenzyme A Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Valine, leucine and isoleucine biosynthesis
• Pantothenate and CoA biosynthesis
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Cysteine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
L-glutamate biosynthesis IV	1	1	1
L-glutamine degradation II	1	1	1
ammonia assimilation cycle III	3	3	2
L-valine biosynthesis	4	4	2
ammonia assimilation cycle I	2	2	1
L-glutamate and L-glutamine biosynthesis	7	5	3
pyruvate fermentation to isobutanol (engineered)	5	4	2
L-isoleucine biosynthesis IV	6	4	2
superpathway of ammonia assimilation (plants)	3	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	2
L-isoleucine biosynthesis III	7	4	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-isoleucine biosynthesis II	8	6	2
phosphopantothenate biosynthesis I	4	2	1
phosphopantothenate biosynthesis III (archaea)	4	1	1
superpathway of branched chain amino acid biosynthesis	17	17	4
superpathway of L-isoleucine biosynthesis I	13	13	2
L-citrulline biosynthesis	8	5	1
superpathway of L-threonine metabolism	18	13	2
superpathway of coenzyme A biosynthesis I (bacteria)	9	4	1
superpathway of coenzyme A biosynthesis II (plants)	10	2	1
superpathway of L-citrulline metabolism	12	7	1