Experiment set2IT074 for Bifidobacterium breve UCC2003

CDM1 without Phenylalanine

Group: nutrient dropout
Media: CDM1 + no Phenylalanine, 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 G2

Specific Phenotypes

For 19 genes in this experiment

For nutrient dropout no Phenylalanine in Bifidobacterium breve UCC2003

For nutrient dropout no Phenylalanine across organisms

SEED Subsystems

Subsystem	#Specific
Chorismate Synthesis	2
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
DNA-replication	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Heat shock dnaK gene cluster extended	1
Lactose and Galactose Uptake and Utilization	1
Lactose utilization	1
Leucine Biosynthesis	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Proline Synthesis	1
Transcription factors bacterial	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
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Purine metabolism
• Glutamate metabolism
• Arginine and proline metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• C5-Branched dibasic acid metabolism
• Folate biosynthesis
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• 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
L-glutamate biosynthesis III	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
3-dehydroquinate biosynthesis I	2	2	1
L-leucine biosynthesis	6	6	2
L-phenylalanine biosynthesis I	3	3	1
3-methylbutanol biosynthesis (engineered)	7	6	2
superpathway of L-phenylalanine biosynthesis	10	10	2
chorismate biosynthesis I	7	7	1
L-glutamate and L-glutamine biosynthesis	7	5	1
L-isoleucine biosynthesis II	8	6	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-tryptophan biosynthesis	13	13	1
2,5-xylenol and 3,5-xylenol degradation	13	1	1
superpathway of chorismate metabolism	59	32	2