Experiment set2IT007 for Bifidobacterium breve UCC2003

CDM1 without Alanine

Group: nutrient dropout
Media: CDM1 + no Alanine, 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 A7

Specific Phenotypes

For 1 genes in this experiment

For nutrient dropout no Alanine in Bifidobacterium breve UCC2003

For nutrient dropout no Alanine across organisms

SEED Subsystems

Subsystem	#Specific
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Alanine and aspartate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Cysteine metabolism
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-alanine biosynthesis II	1	1	1
L-aspartate biosynthesis	1	1	1
L-alanine degradation III	1	1	1
superpathway of L-alanine biosynthesis	4	4	2
L-alanine biosynthesis I	2	2	1
L-glutamate degradation II	2	2	1
L-alanine degradation V (oxidative Stickland reaction)	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	4
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
sulfolactate degradation III	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
pyruvate fermentation to acetate and alanine	3	1	1
L-alanine degradation II (to D-lactate)	3	1	1
L-asparagine degradation III (mammalian)	3	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	6	4
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
trans-4-hydroxy-L-proline degradation I	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation I	5	1	1
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	2	1
superpathway of sulfolactate degradation	6	2	1
L-alanine degradation VI (reductive Stickland reaction)	6	1	1
coenzyme M biosynthesis II	6	1	1
superpathway of anaerobic energy metabolism (invertebrates)	17	6	2
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
superpathway of L-alanine fermentation (Stickland reaction)	9	3	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	1	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	6	1
indole-3-acetate biosynthesis II	12	2	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	23	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	1	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	16	2
superpathway of chorismate metabolism	59	32	2