Experiment set2IT059 for Bifidobacterium breve UCC2003

CDM1 without Lysine

Group: nutrient dropout
Media: CDM1 + no Lysine, 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 E11

Specific Phenotypes

For 4 genes in this experiment

For nutrient dropout no Lysine in Bifidobacterium breve UCC2003

For nutrient dropout no Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Acetoin, butanediol metabolism	1
Branched-Chain Amino Acid Biosynthesis	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyrimidine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine biosynthesis
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyruvate fermentation to (R)-acetoin II	2	2	1
pseudouridine degradation	2	1	1
pyruvate fermentation to (R)-acetoin I	3	2	1
pyruvate fermentation to (S)-acetoin	3	2	1
L-valine biosynthesis	4	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
superpathway of (R,R)-butanediol biosynthesis	5	3	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-lysine biosynthesis VI	7	6	1
L-lysine biosynthesis III	7	6	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	6	1
superpathway of branched chain amino acid biosynthesis	17	17	2
L-lysine biosynthesis I	9	9	1
L-lysine biosynthesis II	9	6	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of L-threonine metabolism	18	13	1
aspartate superpathway	25	23	1