Experiment set57IT045 for Escherichia coli BW25113

Ying_OrganicAcid7 rep C; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_OrganicAcid7
Culturing: Keio_ML9a, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying on 19-Oct-22
Media components: 1.5 g/L Ammonium chloride, 0.6 g/L Potassium phosphate monobasic, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Ying_OrganicAcid7 1x includes: 366 uM Sodium L-Lactate, 366 uM D,L-Malic Acid, 366 uM Citric Acid, 366 uM Succinic Acid, 366 uM Sodium pyruvate, 366 uM a-Ketoglutaric acid disodium salt hydrate, 366 uM L-Citrulline

Specific Phenotypes

For 15 genes in this experiment

For carbon source Ying_OrganicAcid7 in Escherichia coli BW25113

For carbon source Ying_OrganicAcid7 across organisms

SEED Subsystems

Subsystem	#Specific
Pyruvate metabolism I: anaplerotic reactions, PEP	3
Alanine biosynthesis	2
Pyruvate Alanine Serine Interconversions	2
Branched-Chain Amino Acid Biosynthesis	1
Coenzyme B12 biosynthesis	1
DNA-binding regulatory proteins, strays	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Pentose phosphate pathway	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Proteolysis in bacteria, ATP-dependent	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Biosynthesis of phenylpropanoids
• Pentose phosphate pathway
• Alanine and aspartate metabolism
• Methionine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine biosynthesis
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• D-Alanine metabolism
• Glutathione metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-malate degradation II	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
alanine racemization	1	1	1
L-alanine biosynthesis I	2	2	1
L-alanine degradation I	2	2	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
pentose phosphate pathway (oxidative branch) I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-leucine degradation III	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-carnitine degradation II	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	2
superpathway of L-alanine biosynthesis	4	4	1
L-tyrosine biosynthesis III	4	3	1
chitin deacetylation	4	3	1
L-tyrosine degradation III	4	2	1
L-tyrosine biosynthesis II	4	2	1
L-phenylalanine biosynthesis II	4	2	1
L-phenylalanine degradation III	4	2	1
gluconeogenesis I	13	13	3
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	2	1
L-tyrosine degradation I	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	2
superpathway of anaerobic energy metabolism (invertebrates)	17	12	3
L-leucine biosynthesis	6	6	1
glyoxylate cycle	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
methylgallate degradation	6	2	1
L-leucine degradation I	6	2	1
pyruvate fermentation to propanoate I	7	5	1
incomplete reductive TCA cycle	7	5	1
pentose phosphate pathway	8	8	1
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
superpathway of aromatic amino acid biosynthesis	18	18	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle II (plants and fungi)	9	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
ansatrienin biosynthesis	9	1	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
TCA cycle I (prokaryotic)	10	9	1
TCA cycle III (animals)	10	8	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
glycolysis V (Pyrococcus)	10	7	1
superpathway of vanillin and vanillate degradation	10	3	1
rosmarinic acid biosynthesis I	10	1	1
glycolysis II (from fructose 6-phosphate)	11	11	1
reductive TCA cycle I	11	8	1
L-glutamate degradation VIII (to propanoate)	11	5	1
(S)-reticuline biosynthesis I	11	1	1
tropane alkaloids biosynthesis	11	1	1
superpathway of glyoxylate bypass and TCA	12	11	1
gluconeogenesis III	12	9	1
reductive TCA cycle II	12	8	1
syringate degradation	12	3	1
glycolysis I (from glucose 6-phosphate)	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	2
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
formaldehyde assimilation I (serine pathway)	13	8	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
superpathway of rosmarinic acid biosynthesis	14	2	1
cyclosporin A biosynthesis	15	2	1
mixed acid fermentation	16	16	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of hexitol degradation (bacteria)	18	18	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	17	1
methylaspartate cycle	19	9	1
superpathway of N-acetylneuraminate degradation	22	22	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	2
superpathway of chorismate metabolism	59	54	2
odd iso-branched-chain fatty acid biosynthesis	34	24	1