Experiment set15IT091 for Bifidobacterium breve UCC2003

chicken 2; day 7; diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron

Group: chicken coculture
Media: + diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron
Culturing: Bifido_ML2
By: Anthony Shiver on 4/3/2021

Specific Phenotypes

For 49 genes in this experiment

For chicken coculture diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron in Bifidobacterium breve UCC2003

For chicken coculture diet=StandardDiet; sample=FecalPellet; coculture_with=Bacteroides thetaiotaomicron across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	4
Branched-Chain Amino Acid Biosynthesis	4
Ribonucleotide reduction	4
Coenzyme A Biosynthesis	2
DNA repair, UvrABC system	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Heat shock dnaK gene cluster extended	2
ZZ gjo need homes	2
Acetoin, butanediol metabolism	1
Chorismate Synthesis	1
DNA-replication	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Leucine Biosynthesis	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Protein chaperones	1
Protein degradation	1
Sialic Acid Metabolism	1
Transport of Zinc	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine biosynthesis
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Purine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Nitrogen metabolism
• Cysteine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Glutathione metabolism
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Folate biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway

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
pyrimidine nucleobases salvage II	2	2	1
ammonia assimilation cycle I	2	2	1
pyrimidine ribonucleosides salvage III	2	2	1
pyruvate fermentation to (R)-acetoin II	2	2	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
L-isoleucine biosynthesis IV	6	4	3
guanosine deoxyribonucleotides de novo biosynthesis II	4	2	2
adenosine deoxyribonucleotides de novo biosynthesis II	4	2	2
phosphopantothenate biosynthesis I	4	2	2
methylglyoxal degradation III	2	1	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	1	1
guanosine deoxyribonucleotides de novo biosynthesis I	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
L-phenylalanine biosynthesis I	3	3	1
pyruvate fermentation to (R)-acetoin I	3	2	1
pyruvate fermentation to (S)-acetoin	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
phosphopantothenate biosynthesis II	3	1	1
superpathway of adenosine nucleotides de novo biosynthesis II	7	5	2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	9	4
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	5	2
phosphopantothenate biosynthesis III (archaea)	4	1	1
superpathway of L-isoleucine biosynthesis I	13	13	3
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	6	2
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	5	2
superpathway of coenzyme A biosynthesis I (bacteria)	9	4	2
tRNA processing	10	8	2
superpathway of adenosine nucleotides de novo biosynthesis I	5	4	1
superpathway of coenzyme A biosynthesis III (mammals)	5	3	1
superpathway of (R,R)-butanediol biosynthesis	5	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	2	2
L-leucine biosynthesis	6	6	1
superpathway of L-threonine metabolism	18	13	3
superpathway of guanosine nucleotides de novo biosynthesis I	6	4	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
superpathway of purine nucleotides de novo biosynthesis II	26	21	4
3-methylbutanol biosynthesis (engineered)	7	6	1
L-lysine biosynthesis III	7	6	1
L-lysine biosynthesis VI	7	6	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	4	1
L-citrulline biosynthesis	8	5	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	4	1
superpathway of methylglyoxal degradation	8	2	1
L-lysine biosynthesis I	9	9	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	13	2
L-lysine biosynthesis II	9	6	1
superpathway of L-phenylalanine biosynthesis	10	10	1
detoxification of reactive carbonyls in chloroplasts	10	1	1
superpathway of purine nucleotides de novo biosynthesis I	21	18	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	39	4
superpathway of L-citrulline metabolism	12	7	1
superpathway of purine nucleotide salvage	14	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	23	1
superpathway of chorismate metabolism	59	32	1