Experiment set16IT018 for Bifidobacterium breve UCC2003

Compare to:

chicken 2; 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 49 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 3
tRNA processing 3
DNA repair, UvrABC system 2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Heat shock dnaK gene cluster extended 2
Biotin biosynthesis 1
DNA-replication 1
Glutaredoxins 1
Glutathione: Redox cycle 1
Protein chaperones 1
Protein degradation 1
Purine conversions 1
Ribosomal protein S12p Asp methylthiotransferase 1
Sialic Acid Metabolism 1
Sucrose utilization 1
Thiamin biosynthesis 1
Transport of Zinc 1
ZZ gjo need homes 1
n-Phenylalkanoic acid degradation 1
p-Aminobenzoyl-Glutamate Utilization 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

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
long-chain fatty acid activation 1 1 1
cis-cyclopropane fatty acid (CFA) biosynthesis 1 1 1
L-glutamate biosynthesis IV 1 1 1
L-glutamine degradation I 1 1 1
L-glutamine degradation II 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
pyrimidine nucleobases salvage II 2 2 1
pyrimidine ribonucleosides salvage III 2 2 1
ammonia assimilation cycle I 2 2 1
guanosine deoxyribonucleotides de novo biosynthesis II 4 2 2
adenosine deoxyribonucleotides de novo biosynthesis II 4 2 2
linoleate biosynthesis II (animals) 2 1 1
adenosine deoxyribonucleotides de novo biosynthesis I 2 1 1
γ-linolenate biosynthesis II (animals) 2 1 1
methylglyoxal degradation III 2 1 1
pseudouridine degradation 2 1 1
sterculate biosynthesis 2 1 1
guanosine deoxyribonucleotides de novo biosynthesis I 2 1 1
L-glutamate and L-glutamine biosynthesis 7 5 3
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
superpathway of ammonia assimilation (plants) 3 2 1
thiamine diphosphate salvage V 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
N-acetylneuraminate and N-acetylmannosamine degradation II 3 1 1
glycine degradation 3 1 1
alkane biosynthesis II 3 1 1
oleate biosynthesis I (plants) 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
glutaminyl-tRNAgln biosynthesis via transamidation 4 4 1
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
phytol degradation 4 3 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
long chain fatty acid ester synthesis (engineered) 4 1 1
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 4 1 1
pyrimidine deoxyribonucleotides de novo biosynthesis I 9 6 2
pyrimidine deoxyribonucleotides de novo biosynthesis III 9 5 2
sporopollenin precursors biosynthesis 18 4 4
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
thiamine diphosphate salvage II 5 4 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
octane oxidation 5 2 1
stearate biosynthesis II (bacteria and plants) 6 4 1
superpathway of guanosine nucleotides de novo biosynthesis I 6 4 1
stearate biosynthesis IV 6 3 1
stearate biosynthesis I (animals) 6 1 1
6-gingerol analog biosynthesis (engineered) 6 1 1
fatty acid salvage 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
thiamine diphosphate salvage IV (yeast) 7 6 1
pyrimidine deoxyribonucleotides de novo biosynthesis IV 7 4 1
ceramide degradation by α-oxidation 7 2 1
capsaicin biosynthesis 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
L-citrulline biosynthesis 8 5 1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast) 8 5 1
pyrimidine deoxyribonucleotides biosynthesis from CTP 8 4 1
purine nucleobases degradation II (anaerobic) 24 8 3
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
2-deoxy-D-ribose degradation II 8 2 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
suberin monomers biosynthesis 20 2 2
detoxification of reactive carbonyls in chloroplasts 10 1 1
superpathway of purine nucleotides de novo biosynthesis I 21 18 2
superpathway of fatty acid biosynthesis II (plant) 43 29 4
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
palmitate biosynthesis II (type II fatty acid synthase) 31 22 2
cutin biosynthesis 16 1 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
aspartate superpathway 25 23 1
superpathway of fatty acids biosynthesis (E. coli) 53 35 2
palmitate biosynthesis III 29 14 1
oleate β-oxidation 35 1 1
mycolate biosynthesis 205 17 3
superpathway of mycolate biosynthesis 239 18 3