Experiment set16IT024 for Bifidobacterium breve UCC2003

chicken 5; day 7; diet=StandardDiet; sample=FecalPellet

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

Specific Phenotypes

For 44 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-replication	2
DNA repair, UvrABC system	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
ZZ gjo need homes	2
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA repair, bacterial	1
De Novo Pyrimidine Synthesis	1
Fructooligosaccharides(FOS) and Raffinose Utilization	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Mannose Metabolism	1
Polysaccharide deacetylases	1
Predicted carbohydrate hydrolases	1
Purine conversions	1
Sucrose utilization	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
• alpha-Linolenic acid metabolism
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Lysine biosynthesis
• Glutathione metabolism
• Other glycan degradation
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• Nicotinate and nicotinamide metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

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
ammonia assimilation cycle III	3	3	2
L-cysteine degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
D-serine degradation	3	2	2
L-glutamate degradation II	2	2	1
guanosine deoxyribonucleotides de novo biosynthesis II	4	2	2
adenosine deoxyribonucleotides de novo biosynthesis II	4	2	2
methylglyoxal degradation III	2	1	1
phosphatidylcholine resynthesis via glycerophosphocholine	2	1	1
glycerophosphodiester degradation	2	1	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	1	1
guanosine 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
L-aspartate degradation II (aerobic)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
glycine degradation	3	1	1
superpathway of adenosine nucleotides de novo biosynthesis II	7	5	2
UTP and CTP dephosphorylation I	7	5	2
L-glutamate and L-glutamine biosynthesis	7	5	2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	9	4
purine nucleotides degradation II (aerobic)	11	4	3
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
adenosine nucleotides degradation I	8	5	2
superpathway of guanosine nucleotides de novo biosynthesis II	8	5	2
purine nucleotides degradation I (plants)	12	7	3
L-mimosine degradation	8	4	2
guanosine nucleotides degradation I	4	2	1
inosine 5'-phosphate degradation	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	2	1
guanosine nucleotides degradation II	4	2	1
glutathione-mediated detoxification I	8	2	2
guanosine nucleotides degradation III	4	1	1
glycerol and glycerophosphodiester degradation	4	1	1
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
superpathway of adenosine nucleotides de novo biosynthesis I	5	4	1
adenosine nucleotides degradation II	5	1	1
UMP biosynthesis II	6	6	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	4	1
superpathway of guanosine nucleotides degradation (plants)	6	3	1
superpathway of purines degradation in plants	18	7	3
L-canavanine degradation II	6	1	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
ureide biosynthesis	7	2	1
L-citrulline biosynthesis	8	5	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	4	1
purine nucleobases degradation II (anaerobic)	24	8	3
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
tunicamycin biosynthesis	9	2	1
detoxification of reactive carbonyls in chloroplasts	10	1	1
superpathway of purine nucleotides de novo biosynthesis I	21	18	2
NAD salvage (plants)	11	6	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	39	4
superpathway of L-citrulline metabolism	12	7	1
anandamide biosynthesis I	12	2	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