Experiment set2IT010 for Bifidobacterium breve UCC2003

CDM1 without Histidine

Group: nutrient dropout
Media: CDM1 + no Histidine, 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 A10

Specific Phenotypes

For 8 genes in this experiment

For nutrient dropout no Histidine in Bifidobacterium breve UCC2003

For nutrient dropout no Histidine across organisms

SEED Subsystems

Subsystem	#Specific
Histidine Biosynthesis	7
Tryptophan synthesis	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
• Histidine metabolism
• Biosynthesis of plant hormones
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of phenylpropanoids
• Purine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Novobiocin biosynthesis
• Pyruvate metabolism
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-histidine biosynthesis	10	10	9
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tyrosine degradation I	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	39	9
superpathway of aromatic amino acid biosynthesis	18	18	3
L-tryptophan biosynthesis	6	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	1	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of chorismate metabolism	59	32	3
anaerobic aromatic compound degradation (Thauera aromatica)	27	1	1