Experiment set11S565 for Pantoea sp. MT58

Ying_OrganicAcid7 rep C; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_OrganicAcid7
Culturing: MT058_ML2, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on 1-Sep-23
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 14 genes in this experiment

For carbon source Ying_OrganicAcid7 in Pantoea sp. MT58

For carbon source Ying_OrganicAcid7 across organisms

SEED Subsystems

Subsystem	#Specific
Pyruvate metabolism I: anaplerotic reactions, PEP	3
Acetoin, butanediol metabolism	2
Branched-Chain Amino Acid Biosynthesis	2
Cobalamin synthesis	1
Coenzyme B12 biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Serine-glyoxylate cycle	1
Threonine and Homoserine Biosynthesis	1
Ton and Tol transport systems	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Pantothenate and CoA biosynthesis
• Porphyrin and chlorophyll metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

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
adenosylcobalamin salvage from cobalamin	5	5	4
adenosylcobinamide-GDP salvage from cobinamide I	5	4	3
L-cysteine degradation III	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
L-glutamate degradation II	2	2	1
pyruvate fermentation to (R)-acetoin II	2	2	1
cobalamin salvage (eukaryotic)	8	4	4
adenosylcobinamide-GDP salvage from cobinamide II	6	3	3
adenosylcobinamide-GDP biosynthesis from cobyrinate a,c-diamide	6	3	3
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
superpathway of adenosylcobalamin salvage from cobinamide I	8	4	3
L-tyrosine biosynthesis I	3	3	1
pyruvate fermentation to (R)-acetoin I	3	3	1
pyruvate fermentation to (S)-acetoin	3	3	1
L-phenylalanine biosynthesis I	3	3	1
indole-3-acetate biosynthesis VI (bacteria)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
superpathway of adenosylcobalamin salvage from cobinamide II	9	3	3
(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	4	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	2	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	7	3
superpathway of (R,R)-butanediol biosynthesis	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-tyrosine degradation I	5	2	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	2
superpathway of L-threonine biosynthesis	6	6	1
superpathway of 2,3-butanediol biosynthesis	6	5	1
TCA cycle VIII (Chlamydia)	6	5	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
superpathway of L-isoleucine biosynthesis I	13	13	2
gluconeogenesis I	13	12	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	4	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	9	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
glycolysis V (Pyrococcus)	10	7	1
rosmarinic acid biosynthesis I	10	1	1
glycolysis II (from fructose 6-phosphate)	11	11	1
adenosylcobalamin biosynthesis II (aerobic)	33	13	3
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	1
adenosylcobalamin biosynthesis I (anaerobic)	36	12	3
indole-3-acetate biosynthesis II	12	4	1
glycolysis I (from glucose 6-phosphate)	13	13	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
superpathway of hexitol degradation (bacteria)	18	16	1
superpathway of L-threonine metabolism	18	15	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	17	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of N-acetylneuraminate degradation	22	18	1
aspartate superpathway	25	24	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	2
superpathway of chorismate metabolism	59	44	2