Experiment set4IT039 for Bifidobacterium breve UCC2003

Recovery broth with Bicyclomycin 0.05 mM

Group: stress
Media: Recovery broth + Bicyclomycin (0.05 mM), pH=6.8
Culturing: Bifido_ML2, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Anthony Shiver on 2/15/2020

Specific Phenotypes

For 14 genes in this experiment

For stress Bicyclomycin in Bifidobacterium breve UCC2003

For stress Bicyclomycin across organisms

SEED Subsystems

Subsystem	#Specific
Lactose and Galactose Uptake and Utilization	2
Lactose utilization	2
Galactosylceramide and Sulfatide metabolism	1
Glycogen metabolism	1
Maltose and Maltodextrin Utilization	1
Sialic Acid Metabolism	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:

• Galactose metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Glycolysis / Gluconeogenesis
• Other glycan degradation
• Streptomycin biosynthesis
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
lactose degradation III	1	1	1
trehalose degradation I (low osmolarity)	2	1	1
trehalose degradation II (cytosolic)	2	1	1
xyloglucan degradation II (exoglucanase)	8	3	3
trehalose degradation IV	3	3	1
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
sucrose degradation III (sucrose invertase)	4	4	1
glycogen degradation I	8	7	2
sucrose biosynthesis II	8	6	2
starch degradation V	4	3	1
N-acetylneuraminate and N-acetylmannosamine degradation I	4	2	1
glucose and glucose-1-phosphate degradation	5	3	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	2	1
glycogen degradation II	6	4	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	4	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
chitin biosynthesis	9	5	1
1,3-propanediol biosynthesis (engineered)	9	4	1
starch degradation II	9	1	1
glycolysis III (from glucose)	11	10	1
homolactic fermentation	12	11	1
Bifidobacterium shunt	15	15	1
superpathway of CMP-sialic acids biosynthesis	15	2	1
heterolactic fermentation	18	16	1
superpathway of N-acetylneuraminate degradation	22	17	1