Experiment set2IT025 for Bifidobacterium breve UCC2003

CDM1 without Isoleucine

Group: nutrient dropout
Media: CDM1 + no Isoleucine, 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 C1

Specific Phenotypes

For 3 genes in this experiment

For nutrient dropout no Isoleucine in Bifidobacterium breve UCC2003

For nutrient dropout no Isoleucine across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	3
Acetoin, butanediol metabolism	1
Glycine and Serine Utilization	1
Threonine anaerobic catabolism gene cluster	1
Threonine degradation	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
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine
• Glycine, serine and threonine metabolism
• Butanoate metabolism
• C5-Branched dibasic acid metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-isoleucine biosynthesis I (from threonine)	7	7	5
L-methionine degradation II	3	2	2
L-threonine degradation I	6	6	3
L-valine biosynthesis	4	4	2
pyruvate fermentation to (R)-acetoin II	2	2	1
L-threonine degradation V	2	1	1
superpathway of branched chain amino acid biosynthesis	17	17	7
pyruvate fermentation to isobutanol (engineered)	5	4	2
superpathway of L-isoleucine biosynthesis I	13	13	5
L-isoleucine biosynthesis IV	6	4	2
pyruvate fermentation to (R)-acetoin I	3	2	1
pyruvate fermentation to (S)-acetoin	3	2	1
L-isoleucine biosynthesis III	7	4	2
superpathway of L-threonine metabolism	18	13	5
L-isoleucine biosynthesis II	8	6	2
hypoglycin biosynthesis	14	3	3
superpathway of (R,R)-butanediol biosynthesis	5	3	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
cyclosporin A biosynthesis	15	2	1