Experiment set16IT011 for Bifidobacterium breve UCC2003

chicken 9; day 2; diet=StandardDiet; sample=FecalPellet

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

Specific Phenotypes

For 17 genes in this experiment

For chicken diet=StandardDiet; sample=FecalPellet in Bifidobacterium breve UCC2003

For chicken diet=StandardDiet; sample=FecalPellet across organisms

SEED Subsystems

Subsystem	#Specific
Ribonucleotide reduction	4
Ammonia assimilation	2
DNA repair, UvrABC system	2
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Heat shock dnaK gene cluster extended	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:

• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Purine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Lysine biosynthesis
• Glutathione metabolism
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
L-cysteine degradation II	3	3	2
ammonia assimilation cycle III	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
D-serine degradation	3	2	2
adenosine deoxyribonucleotides de novo biosynthesis II	4	2	2
guanosine deoxyribonucleotides de novo biosynthesis II	4	2	2
guanosine deoxyribonucleotides de novo biosynthesis I	2	1	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	1	1
glycine betaine degradation III	7	3	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	3	3
L-methionine biosynthesis II	6	5	2
glycine degradation	3	1	1
superpathway of adenosine nucleotides de novo biosynthesis II	7	5	2
L-glutamate and L-glutamine biosynthesis	7	5	2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	9	4
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	5	2
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	2	2
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	6	2
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	5	2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	3
tRNA processing	10	8	2
superpathway of adenosine nucleotides de novo biosynthesis I	5	4	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	4	1
superpathway of purine nucleotides de novo biosynthesis II	26	21	4
L-lysine biosynthesis VI	7	6	1
L-lysine biosynthesis III	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
purine nucleobases degradation II (anaerobic)	24	8	3
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 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 I	18	16	1
aspartate superpathway	25	23	1