Experiment set16IT021 for Bifidobacterium breve UCC2003

chicken 10; day 5; diet=StandardDiet; sample=FecalPellet

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

Specific Phenotypes

For 29 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
DNA repair, UvrABC system	2
Fructooligosaccharides(FOS) and Raffinose Utilization	2
Mannose Metabolism	2
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA-replication	1
De Novo Pyrimidine Synthesis	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Heat shock dnaK gene cluster extended	1
Polysaccharide deacetylases	1
Predicted carbohydrate hydrolases	1
Protein chaperones	1
Transport of Zinc	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Pyrimidine metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Glutathione metabolism
• Other glycan degradation
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Folate biosynthesis
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
L-cysteine degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
D-serine degradation	3	2	2
guanosine deoxyribonucleotides de novo biosynthesis II	4	2	2
adenosine 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
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	9	4
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 adenosine nucleotides de novo biosynthesis I	5	4	1
UMP biosynthesis II	6	6	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	4	1
superpathway of purine nucleotides de novo biosynthesis II	26	21	4
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	4	1
purine nucleobases degradation II (anaerobic)	24	8	3
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	13	2
superpathway of purine nucleotides de novo biosynthesis I	21	18	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	39	4
superpathway of purine nucleotide salvage	14	9	1