Experiment set4IT002 for Bifidobacterium breve UCC2003

Recovery broth with Choline chloride 200 mM

Group: stress
Media: Recovery broth + Choline chloride (200 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 9 genes in this experiment

For stress Choline chloride in Bifidobacterium breve UCC2003

For stress Choline chloride across organisms

SEED Subsystems

Subsystem	#Specific
Thiamin biosynthesis	2
Purine conversions	1
Queuosine-Archaeosine Biosynthesis	1
Serine-glyoxylate cycle	1
Staphylococcal pathogenicity islands SaPI	1
TCA Cycle	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:

• Biosynthesis of alkaloids derived from histidine and purine
• Purine metabolism
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Glutamate metabolism
• Glyoxylate and dicarboxylate metabolism
• Drug metabolism - other enzymes
• 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 terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine degradation I	1	1	1
L-glutamate biosynthesis I	2	2	1
ammonia assimilation cycle III	3	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
guanosine ribonucleotides de novo biosynthesis	4	3	1
queuosine biosynthesis I (de novo)	4	1	1
queuosine biosynthesis III (queuosine salvage)	5	1	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	4	1
glyoxylate cycle	6	3	1
L-glutamate and L-glutamine biosynthesis	7	5	1
partial TCA cycle (obligate autotrophs)	8	5	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	5	1
L-citrulline biosynthesis	8	5	1
nitrogen remobilization from senescing leaves	8	5	1
TCA cycle V (2-oxoglutarate synthase)	9	5	1
TCA cycle VII (acetate-producers)	9	4	1
TCA cycle II (plants and fungi)	9	4	1
TCA cycle VI (Helicobacter)	9	4	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	4	1
TCA cycle III (animals)	10	5	1
TCA cycle I (prokaryotic)	10	5	1
superpathway of L-citrulline metabolism	12	7	1
superpathway of glyoxylate bypass and TCA	12	5	1
superpathway of purine nucleotide salvage	14	9	1
superpathway of glyoxylate cycle and fatty acid degradation	14	3	1
mixed acid fermentation	16	11	1
methylaspartate cycle	19	6	1
superpathway of purine nucleotides de novo biosynthesis I	21	18	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	12	1
ethene biosynthesis V (engineered)	25	16	1
superpathway of purine nucleotides de novo biosynthesis II	26	21	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	15	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	39	1