Experiment set2IT057 for Bifidobacterium breve UCC2003

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 12/10/2019
Growth plate: CDM1_nutrientdrop E9

Specific Phenotypes

For 12 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
Ammonia assimilation	1
Branched-Chain Amino Acid Biosynthesis	1
Entner-Doudoroff Pathway	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycolysis and Gluconeogenesis	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:

• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Cysteine metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Methionine metabolism
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Selenoamino acid metabolism
• Streptomycin biosynthesis
• Aminosugars metabolism
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Carbon fixation in photosynthetic organisms
• Pantothenate and CoA biosynthesis
• Nitrogen metabolism
• Sulfur metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-glutamate degradation II	2	2	1
pyruvate fermentation to (R)-acetoin II	2	2	1
L-tyrosine degradation II	2	1	1
trehalose degradation II (cytosolic)	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
trehalose degradation I (low osmolarity)	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
atromentin biosynthesis	2	1	1
trehalose degradation IV	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
pyruvate fermentation to (S)-acetoin	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
pyruvate fermentation to (R)-acetoin I	3	2	1
sulfolactate degradation III	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	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
sucrose degradation III (sucrose invertase)	4	4	1
L-valine biosynthesis	4	4	1
L-phenylalanine degradation III	4	2	1
L-tyrosine 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
pyruvate fermentation to isobutanol (engineered)	5	4	1
glucose and glucose-1-phosphate degradation	5	3	1
superpathway of (R,R)-butanediol biosynthesis	5	3	1
trans-4-hydroxy-L-proline degradation I	5	2	1
L-tyrosine degradation I	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	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
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
glycogen degradation II	6	4	1
TCA cycle VIII (Chlamydia)	6	2	1
superpathway of sulfolactate degradation	6	2	1
superpathway of 2,3-butanediol biosynthesis	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
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
L-isoleucine biosynthesis III	7	4	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	6	2
glycogen degradation I	8	7	1
sucrose biosynthesis II	8	6	1
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
chitin biosynthesis	9	5	1
1,3-propanediol biosynthesis (engineered)	9	4	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
glycolysis III (from glucose)	11	10	1
(S)-reticuline biosynthesis I	11	1	1
homolactic fermentation	12	11	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
Bifidobacterium shunt	15	15	1
superpathway of anaerobic energy metabolism (invertebrates)	17	6	1
heterolactic fermentation	18	16	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