Experiment set16IT008 for Bifidobacterium breve UCC2003

chicken 1; 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 25 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
Heat shock dnaK gene cluster extended	3
DNA-replication	2
Ammonia assimilation	1
Biotin biosynthesis	1
Choline Transport	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
DNA repair, UvrABC system	1
DNA repair, bacterial	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Protein chaperones	1
Thiamin biosynthesis	1
Transport of Zinc	1
n-Phenylalkanoic acid degradation	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Thiamine metabolism
• Purine metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fatty acid metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Lysine biosynthesis
• Glutathione metabolism
• Lipopolysaccharide biosynthesis
• Folate biosynthesis
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
hydroxymethylpyrimidine salvage	2	2	2
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
L-glutamine degradation II	1	1	1
long-chain fatty acid activation	1	1	1
ammonia assimilation cycle III	3	3	2
thiamine diphosphate salvage II	5	4	3
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis II	4	2	2
guanosine deoxyribonucleotides de novo biosynthesis II	4	2	2
γ-linolenate biosynthesis II (animals)	2	1	1
sterculate biosynthesis	2	1	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	1	1
guanosine deoxyribonucleotides de novo biosynthesis I	2	1	1
methylglyoxal degradation III	2	1	1
linoleate biosynthesis II (animals)	2	1	1
thiamine diphosphate salvage IV (yeast)	7	6	3
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	5	3
thiamine diphosphate salvage V	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
choline-O-sulfate degradation	3	1	1
L-glutamate and L-glutamine biosynthesis	7	5	2
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
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	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
tRNA processing	10	8	2
superpathway of adenosine nucleotides de novo biosynthesis I	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
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	4	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	4	1
ceramide degradation by α-oxidation	7	2	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
L-citrulline biosynthesis	8	5	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	4	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of methylglyoxal degradation	8	2	1
2-deoxy-D-ribose degradation II	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
superpathway of thiamine diphosphate biosynthesis I	10	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 thiamine diphosphate biosynthesis II	11	7	1
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 II	15	13	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