Experiment set16IT035 for Bifidobacterium breve UCC2003

chicken 21; day 7; diet=StandardDiet; sample=Cecum

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

Specific Phenotypes

For 43 genes in this experiment

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

For chicken diet=StandardDiet; sample=Cecum across organisms

SEED Subsystems

Subsystem	#Specific
Fructooligosaccharides(FOS) and Raffinose Utilization	3
Mannose Metabolism	3
Ribonucleotide reduction	3
Ammonia assimilation	2
DNA-replication	2
DNA repair, UvrABC system	2
Choline Transport	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Chorismate Synthesis	1
DNA repair, bacterial	1
De Novo Pyrimidine Synthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
L-rhamnose utilization	1
Methionine Biosynthesis	1
Methionine Degradation	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Polysaccharide deacetylases	1
Predicted carbohydrate hydrolases	1
Purine conversions	1
Sialic Acid Metabolism	1
ZZ gjo need homes	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
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Alanine and aspartate metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Glutathione metabolism
• Other glycan degradation
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
pyrimidine nucleobases salvage II	2	2	1
L-glutamate degradation II	2	2	1
pyrimidine ribonucleosides salvage III	2	2	1
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
L-phenylalanine biosynthesis I	3	3	1
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
N-acetylneuraminate and N-acetylmannosamine degradation II	3	1	1
choline-O-sulfate 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
superpathway of L-aspartate and L-asparagine biosynthesis	4	2	1
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
L-canavanine degradation II	6	1	1
superpathway of purine nucleotides de novo biosynthesis II	26	21	4
L-lysine biosynthesis III	7	6	1
L-lysine biosynthesis VI	7	6	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	4	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	4	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
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
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