Experiment set2IT019 for Bifidobacterium breve UCC2003

CDM1 without Methionine

Group: nutrient dropout
Media: CDM1 + no Methionine, 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 B7

Specific Phenotypes

For 8 genes in this experiment

For nutrient dropout no Methionine in Bifidobacterium breve UCC2003

For nutrient dropout no Methionine across organisms

SEED Subsystems

Subsystem	#Specific
Methionine Biosynthesis	3
Coenzyme A Biosynthesis	1
Heat shock dnaK gene cluster extended	1
One-carbon metabolism by tetrahydropterines	1
Protein chaperones	1
Serine-glyoxylate cycle	1
Transport of Zinc	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Methionine metabolism
• Cysteine metabolism
• Biosynthesis of plant hormones
• Lysine biosynthesis
• Selenoamino acid metabolism
• One carbon pool by folate
• Methane metabolism
• Pantothenate and CoA biosynthesis
• Sulfur metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-methionine biosynthesis III	4	2	2
L-homocysteine biosynthesis	2	1	1
L-methionine biosynthesis I	5	3	2
L-methionine biosynthesis II	6	5	2
superpathway of L-cysteine biosynthesis (fungi)	6	4	2
S-adenosyl-L-methionine salvage II	3	2	1
phosphopantothenate biosynthesis II	3	1	1
S-adenosyl-L-methionine salvage I	4	4	1
superpathway of L-homoserine and L-methionine biosynthesis	8	6	2
homocysteine and cysteine interconversion	4	3	1
phosphopantothenate biosynthesis I	4	2	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	7	2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	3
superpathway of coenzyme A biosynthesis III (mammals)	5	3	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	4	2
seleno-amino acid biosynthesis (plants)	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	3
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	6	2
L-lysine biosynthesis VI	7	6	1
L-lysine biosynthesis III	7	6	1
aspartate superpathway	25	23	3
L-lysine biosynthesis I	9	9	1
L-lysine biosynthesis II	9	6	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	4	1
superpathway of coenzyme A biosynthesis II (plants)	10	2	1
folate transformations I	13	4	1
superpathway of seleno-compound metabolism	19	4	1