Experiment set2IT017 for Bifidobacterium breve UCC2003

CDM1 without Tryptophan

Group: nutrient dropout
Media: CDM1 + no Tryptophan, pH=7
Culturing: Bifido_ML2, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Anthony Shiver on 12/9/2019
Growth plate: CDM1_nutrientdrop B5

Specific Phenotypes

For 6 genes in this experiment

For nutrient dropout no Tryptophan in Bifidobacterium breve UCC2003

For nutrient dropout no Tryptophan across organisms

SEED Subsystems

Subsystem	#Specific
Tryptophan synthesis	6
Auxin biosynthesis	3
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	2
Histidine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Glycine, serine and threonine metabolism
• Histidine metabolism
• Folate biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-tryptophan biosynthesis	6	6	6
L-glutamine degradation I	1	1	1
L-glutamate biosynthesis I	2	2	1
4-aminobenzoate biosynthesis I	2	1	1
superpathway of L-tryptophan biosynthesis	13	13	6
superpathway of aromatic amino acid biosynthesis	18	18	6
ammonia assimilation cycle III	3	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
acridone alkaloid biosynthesis	4	1	1
4-hydroxy-2(1H)-quinolone biosynthesis	5	2	1
DIBOA-glucoside biosynthesis	6	1	1
L-glutamate and L-glutamine biosynthesis	7	5	1
L-citrulline biosynthesis	8	5	1
superpathway of chorismate metabolism	59	32	7
chloramphenicol biosynthesis	9	1	1
L-histidine biosynthesis	10	10	1
superpathway of tetrahydrofolate biosynthesis	10	7	1
superpathway of quinolone and alkylquinolone biosynthesis	10	2	1
superpathway of candicidin biosynthesis	11	2	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	9	1
superpathway of L-citrulline metabolism	12	7	1
superpathway of benzoxazinoid glucosides biosynthesis	13	1	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	39	1