Experiment set1IT058 for Escherichia coli BW25113

D-Serine carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + D-Serine (20 mM)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
Growth: about 5.8 generations
By: Kelly on 6/19/2014
Media components: 2 mM Magnesium sulfate, 0.1 mM Calcium chloride, 12.8 g/L Sodium phosphate dibasic heptahydrate, 3 g/L Potassium phosphate monobasic, 0.5 g/L Sodium Chloride, 1 g/L Ammonium chloride

Specific Phenotypes

For 26 genes in this experiment

For carbon source D-Serine in Escherichia coli BW25113

For carbon source D-Serine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	5
Glycine and Serine Utilization	2
Glycolysis and Gluconeogenesis	2
Glycolysis and Gluconeogenesis, including Archaeal enzymes	2
Pyruvate metabolism I: anaplerotic reactions, PEP	2
CBSS-562.2.peg.5158 SK3 including	1
Chorismate Synthesis	1
Coenzyme B12 biosynthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Entner-Doudoroff Pathway	1
Leucine Biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Universal stress protein family	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glycine, serine and threonine metabolism
• Pyruvate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Puromycin biosynthesis
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• alpha-Linolenic acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Trinitrotoluene degradation
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-serine degradation	3	3	3
L-tryptophan degradation II (via pyruvate)	3	3	2
L-serine degradation	3	3	2
L-cysteine degradation II	3	2	2
polyphosphate metabolism	2	2	1
2-O-α-mannosyl-D-glycerate degradation	2	2	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
L-methionine biosynthesis II	6	5	2
L-methionine degradation II	3	2	1
microcin B17 biosynthesis	3	1	1
glycine betaine degradation III	7	4	2
queuosine biosynthesis I (de novo)	4	4	1
D-galactarate degradation I	4	4	1
D-glucarate degradation I	4	4	1
glycolate and glyoxylate degradation I	4	4	1
glycine betaine degradation I	8	4	2
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	2
superpathway of D-glucarate and D-galactarate degradation	5	5	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
glycolysis V (Pyrococcus)	10	7	2
queuosine biosynthesis III (queuosine salvage)	5	3	1
glycolysis II (from fructose 6-phosphate)	11	11	2
ppGpp metabolism	6	6	1
L-threonine degradation I	6	6	1
glycolysis I (from glucose 6-phosphate)	13	13	2
chorismate biosynthesis I	7	7	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
superpathway of glycol metabolism and degradation	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
2-deoxy-D-ribose degradation II	8	3	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	2
superpathway of hexitol degradation (bacteria)	18	18	2
Entner-Doudoroff pathway I	9	9	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
photorespiration I	9	5	1
photorespiration III	9	5	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	2
superpathway of anaerobic sucrose degradation	19	17	2
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
Rubisco shunt	10	9	1
glycolysis IV	10	8	1
peptidoglycan recycling II	10	7	1
photorespiration II	10	6	1
superpathway of N-acetylneuraminate degradation	22	22	2
glycolysis III (from glucose)	11	11	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	12	1
purine nucleobases degradation II (anaerobic)	24	17	2
chorismate biosynthesis II (archaea)	12	8	1
gluconeogenesis I	13	13	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	2
formaldehyde assimilation I (serine pathway)	13	8	1
peptidoglycan recycling I	14	14	1
hypoglycin biosynthesis	14	4	1
Bifidobacterium shunt	15	13	1
mixed acid fermentation	16	16	1
glycerol degradation to butanol	16	11	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of L-threonine metabolism	18	16	1
heterolactic fermentation	18	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1
superpathway of chorismate metabolism	59	54	1