Experiment set2IT015 for Bifidobacterium breve UCC2003

CDM1 without Valine

Group: nutrient dropout
Media: CDM1 + no Valine, 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 B3

Specific Phenotypes

For 11 genes in this experiment

For nutrient dropout no Valine in Bifidobacterium breve UCC2003

For nutrient dropout no Valine across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	7
Acetoin, butanediol metabolism	2
Coenzyme A Biosynthesis	2
ECF class transporters	2
Leucine Biosynthesis	2
DNA Repair Base Excision	1
Methionine Biosynthesis	1
Thiamin biosynthesis	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
• Biosynthesis of alkaloids derived from histidine and purine
• Pantothenate and CoA biosynthesis
• C5-Branched dibasic acid metabolism
• Methionine metabolism
• Butanoate metabolism
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-valine biosynthesis	4	4	3
L-leucine biosynthesis	6	6	4
L-isoleucine biosynthesis II	8	6	5
pyruvate fermentation to isobutanol (engineered)	5	4	3
superpathway of branched chain amino acid biosynthesis	17	17	10
3-methylbutanol biosynthesis (engineered)	7	6	4
pyruvate fermentation to (R)-acetoin II	2	2	1
L-isoleucine biosynthesis IV	6	4	3
L-isoleucine biosynthesis I (from threonine)	7	7	3
L-isoleucine biosynthesis III	7	4	3
pyruvate fermentation to (R)-acetoin I	3	2	1
S-adenosyl-L-methionine salvage II	3	2	1
pyruvate fermentation to (S)-acetoin	3	2	1
aliphatic glucosinolate biosynthesis, side chain elongation cycle	30	10	10
S-adenosyl-L-methionine salvage I	4	4	1
phosphopantothenate biosynthesis I	4	2	1
L-methionine biosynthesis III	4	2	1
phosphopantothenate biosynthesis III (archaea)	4	1	1
superpathway of L-isoleucine biosynthesis I	13	13	3
superpathway of (R,R)-butanediol biosynthesis	5	3	1
L-methionine biosynthesis I	5	3	1
seleno-amino acid biosynthesis (plants)	5	2	1
L-methionine biosynthesis II	6	5	1
superpathway of L-threonine metabolism	18	13	3
superpathway of 2,3-butanediol biosynthesis	6	2	1
superpathway of L-homoserine and L-methionine biosynthesis	8	6	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	7	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	4	1
superpathway of coenzyme A biosynthesis II (plants)	10	2	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	6	1
2,5-xylenol and 3,5-xylenol degradation	13	1	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 seleno-compound metabolism	19	4	1
aspartate superpathway	25	23	1