Experiment set2IT009 for Bifidobacterium breve UCC2003

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CDM1 without Glycine

Group: nutrient dropout
Media: CDM1 + no Glycine, 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 A9

Specific Phenotypes

For 4 genes in this experiment

For nutrient dropout no Glycine in Bifidobacterium breve UCC2003

For nutrient dropout no Glycine across organisms

SEED Subsystems

Subsystem #Specific
Acetoin, butanediol metabolism 1
Branched-Chain Amino Acid Biosynthesis 1
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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-aspartate biosynthesis 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
L-aspartate degradation I 1 1 1
pyruvate fermentation to (R)-acetoin II 2 2 1
L-glutamate degradation II 2 2 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
L-phenylalanine biosynthesis I 3 3 1
L-tyrosine biosynthesis I 3 3 1
pyruvate fermentation to (R)-acetoin I 3 2 1
pyruvate fermentation to (S)-acetoin 3 2 1
L-asparagine degradation III (mammalian) 3 1 1
L-phenylalanine degradation II (anaerobic) 3 1 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 1
(R)-cysteate degradation 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
sulfolactate degradation III 3 1 1
L-valine biosynthesis 4 4 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 2 1
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
L-tryptophan degradation VIII (to tryptophol) 4 1 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
superpathway of (R,R)-butanediol biosynthesis 5 3 1
trans-4-hydroxy-L-proline degradation I 5 2 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-tyrosine degradation I 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
superpathway of plastoquinol biosynthesis 5 1 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 6 2
superpathway of L-threonine biosynthesis 6 6 1
L-isoleucine biosynthesis IV 6 4 1
superpathway of 2,3-butanediol biosynthesis 6 2 1
TCA cycle VIII (Chlamydia) 6 2 1
superpathway of sulfolactate degradation 6 2 1
coenzyme M biosynthesis II 6 1 1
superpathway of L-isoleucine biosynthesis I 13 13 2
L-isoleucine biosynthesis I (from threonine) 7 7 1
anaerobic energy metabolism (invertebrates, cytosol) 7 4 1
L-isoleucine biosynthesis III 7 4 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 6 2
L-isoleucine biosynthesis II 8 6 1
superpathway of branched chain amino acid biosynthesis 17 17 2
superpathway of aromatic amino acid biosynthesis 18 18 2
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 1 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-tyrosine 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 rosmarinic acid biosynthesis 14 1 1
superpathway of anaerobic energy metabolism (invertebrates) 17 6 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
superpathway of L-threonine metabolism 18 13 1
aspartate superpathway 25 23 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 1 1
superpathway of chorismate metabolism 59 32 2
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 16 1