Experiment set12IT043 for Bifidobacterium breve UCC2003

Recovery broth with Streptomycin sulfate salt 0.3 mM

Group: stress
Media: Recovery broth + Streptomycin sulfate salt (0.3 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 2/16/2020

Specific Phenotypes

For 21 genes in this experiment

For stress Streptomycin sulfate salt in Bifidobacterium breve UCC2003

For stress Streptomycin sulfate salt across organisms

SEED Subsystems

Subsystem	#Specific
Queuosine-Archaeosine Biosynthesis	2
Ammonia assimilation	1
Biotin biosynthesis	1
Lactose and Galactose Uptake and Utilization	1
Lactose utilization	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Ribosome biogenesis bacterial	1
Thiamin biosynthesis	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:

• Fatty acid metabolism
• Purine metabolism
• Pyrimidine metabolism
• Nicotinate and nicotinamide metabolism
• 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
long-chain fatty acid activation	1	1	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
pseudouridine degradation	2	1	1
NAD salvage pathway III (to nicotinamide riboside)	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
phytol degradation	4	3	1
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
queuosine biosynthesis I (de novo)	4	1	1
sporopollenin precursors biosynthesis	18	4	4
NAD salvage pathway II (PNC IV cycle)	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
queuosine biosynthesis III (queuosine salvage)	5	1	1
stearate biosynthesis II (bacteria and plants)	6	4	1
stearate biosynthesis IV	6	3	1
6-gingerol analog biosynthesis (engineered)	6	1	1
stearate biosynthesis I (animals)	6	1	1
fatty acid salvage	6	1	1
NAD salvage pathway I (PNC VI cycle)	7	6	1
ceramide degradation by α-oxidation	7	2	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-deoxy-D-ribose degradation II	8	2	1
suberin monomers biosynthesis	20	2	2
superpathway of fatty acid biosynthesis II (plant)	43	29	4
NAD salvage (plants)	11	6	1
palmitate biosynthesis II (type II fatty acid synthase)	31	22	2
cutin biosynthesis	16	1	1
superpathway of fatty acids biosynthesis (E. coli)	53	35	2
palmitate biosynthesis III	29	14	1
oleate β-oxidation	35	1	1