Experiment set2IT021 for Bifidobacterium breve UCC2003

CDM1 without Cysteine

Group: nutrient dropout
Media: CDM1 + no Cysteine, 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 B9

Specific Phenotypes

For 9 genes in this experiment

For nutrient dropout no Cysteine in Bifidobacterium breve UCC2003

For nutrient dropout no Cysteine across organisms

SEED Subsystems

Subsystem	#Specific
Methionine Biosynthesis	3
Arginine and Ornithine Degradation	1
Cysteine Biosynthesis	1
Glycine and Serine Utilization	1
Methionine Degradation	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
• Selenoamino acid metabolism
• Glycine, serine and threonine metabolism
• Sulfur metabolism
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-cysteine biosynthesis III (from L-homocysteine)	2	2	2
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
homocysteine and cysteine interconversion	4	3	3
superpathway of L-cysteine biosynthesis (fungi)	6	4	4
hydrogen sulfide biosynthesis II (mammalian)	6	4	3
L-homocysteine biosynthesis	2	1	1
sterculate biosynthesis	2	1	1
superpathway of L-cysteine biosynthesis (mammalian)	5	3	2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	4	4
taurine biosynthesis III	3	1	1
L-methionine biosynthesis III	4	2	1
L-methionine biosynthesis I	5	3	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
L-methionine biosynthesis II	6	5	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	5	1
superpathway of L-homoserine and L-methionine biosynthesis	8	6	1
superpathway of L-methionine salvage and degradation	16	5	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	7	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	6	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
aspartate superpathway	25	23	1
mycolate biosynthesis	205	17	3
superpathway of mycolate biosynthesis	239	18	3