Experiment set2IT068 for Bifidobacterium breve UCC2003

CDM1 without Glutamate

Group: nutrient dropout
Media: CDM1 + no Glutamate, pH=7
Culturing: Bifido_ML2, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Anthony Shiver on 12/10/2019
Growth plate: CDM1_nutrientdrop F8

Specific Phenotypes

For 6 genes in this experiment

For nutrient dropout no Glutamate in Bifidobacterium breve UCC2003

For nutrient dropout no Glutamate across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	2
Leucine Biosynthesis	2
Arginine and Ornithine Degradation	1
Coenzyme A Biosynthesis	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Proline Synthesis	1
Serine-glyoxylate cycle	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Citrate cycle (TCA cycle)
• Glutamate metabolism
• Arginine and proline metabolism
• Glyoxylate and dicarboxylate metabolism
• C5-Branched dibasic acid metabolism
• Pantothenate and CoA biosynthesis
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
L-glutamate biosynthesis III	1	1	1
L-leucine biosynthesis	6	6	4
3-methylbutanol biosynthesis (engineered)	7	6	4
aliphatic glucosinolate biosynthesis, side chain elongation cycle	30	10	10
phosphopantothenate biosynthesis II	3	1	1
L-isoleucine biosynthesis II	8	6	2
phosphopantothenate biosynthesis I	4	2	1
superpathway of branched chain amino acid biosynthesis	17	17	4
superpathway of coenzyme A biosynthesis III (mammals)	5	3	1
glyoxylate cycle	6	3	1
L-glutamate and L-glutamine biosynthesis	7	5	1
partial TCA cycle (obligate autotrophs)	8	5	1
nitrogen remobilization from senescing leaves	8	5	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
TCA cycle V (2-oxoglutarate synthase)	9	5	1
TCA cycle II (plants and fungi)	9	4	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	4	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	4	1
TCA cycle VII (acetate-producers)	9	4	1
TCA cycle VI (Helicobacter)	9	4	1
TCA cycle I (prokaryotic)	10	5	1
TCA cycle III (animals)	10	5	1
superpathway of coenzyme A biosynthesis II (plants)	10	2	1
superpathway of glyoxylate bypass and TCA	12	5	1
2,5-xylenol and 3,5-xylenol degradation	13	1	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 cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	12	1
ethene biosynthesis V (engineered)	25	16	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	15	1