Experiment set11S569 for Pantoea sp. MT58

Ying_Others16 rep A; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_Others16
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_Others16 1x includes: 160 uM Gamma-Aminobutyric Acid Hydrochloride, 160 uM Ectoine, 160 uM Betaine, 160 uM N-Acetyl-L-Glutamic Acid, 160 uM Nicotinamide, 160 uM L-Ornithine, 160 uM Shikimic Acid, 160 uM spermidine, 160 uM Taurine, 160 uM Trigonelline HCl, 160 uM L-Carnitine hydrochloride, 160 uM Choline, 160 uM N-alpha-Acetyl-L-glutamate, 160 uM n-Acetyl-lysine, 160 uM n-Acetyl-muramic acid, 160 uM sn-glycero-3-phosphocholine

Specific Phenotypes

For 28 genes in this experiment

For carbon source Ying_Others16 in Pantoea sp. MT58

For carbon source Ying_Others16 across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	4
Glycolysis and Gluconeogenesis	2
Glycolysis and Gluconeogenesis, including Archaeal enzymes	2
Pyruvate metabolism I: anaplerotic reactions, PEP	2
Sialic Acid Metabolism	2
2-phosphoglycolate salvage	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
DNA-binding regulatory proteins, strays	1
De Novo Pyrimidine Synthesis	1
Entner-Doudoroff Pathway	1
F0F1-type ATP synthase	1
Folate Biosynthesis	1
Glutathione: Redox cycle	1
Glycine cleavage system	1
Glycolate, glyoxylate interconversions	1
Ketoisovalerate oxidoreductase	1
Lactate utilization	1
Lysine Biosynthesis DAP Pathway	1
Methionine Biosynthesis	1
Orphan regulatory proteins	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Respiratory dehydrogenases 1	1
Thioredoxin-disulfide reductase	1
Threonine and Homoserine Biosynthesis	1
Ton and Tol transport systems	1
Trehalose Uptake and Utilization	1
p-Aminobenzoyl-Glutamate Utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Pyruvate metabolism
• Glycolysis / Gluconeogenesis
• Lysine biosynthesis
• Butanoate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Geraniol degradation
• Lysine degradation
• Histidine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Folate biosynthesis
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate and ATP formation from acetyl-CoA III	1	1	1
pyruvate fermentation to (R)-lactate	1	1	1
L-malate degradation II	1	1	1
acetate conversion to acetyl-CoA	1	1	1
L-arginine degradation II (AST pathway)	5	5	4
L-homoserine biosynthesis	3	3	2
4-aminobenzoate biosynthesis II	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
trehalose degradation VI (periplasmic)	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
trehalose degradation II (cytosolic)	2	2	1
4-aminobutanoate degradation I	2	2	1
4-aminobutanoate degradation III	2	2	1
chitin deacetylation	4	3	2
D-lactate to cytochrome bo oxidase electron transfer	2	1	1
spermine and spermidine degradation I	5	2	2
superpathway of L-threonine biosynthesis	6	6	2
L-alanine degradation II (to D-lactate)	3	3	1
ethanol degradation II	3	3	1
2-chloroacrylate degradation I	3	3	1
ethanol degradation IV	3	3	1
superpathway of acetate utilization and formation	3	3	1
L-isoleucine biosynthesis V	3	2	1
superpathway of 4-aminobutanoate degradation	3	2	1
vancomycin resistance I	3	2	1
glutathione-peroxide redox reactions	3	2	1
ethanol degradation III	3	2	1
4-aminobutanoate degradation IV	3	1	1
N-methylpyrrolidone degradation	3	1	1
L-carnitine degradation II	3	1	1
gluconeogenesis I	13	12	4
superpathway of L-homoserine and L-methionine biosynthesis	8	8	2
dipicolinate biosynthesis	4	3	1
GABA shunt I	4	3	1
putrescine degradation III	4	2	1
L-methionine biosynthesis IV	4	2	1
spermidine biosynthesis II	4	2	1
GABA shunt II	4	2	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	2
L-ornithine biosynthesis I	5	5	1
glycolysis V (Pyrococcus)	10	7	2
photorespiration II	10	6	2
ectoine biosynthesis	5	3	1
2-methylcitrate cycle I	5	2	1
L-lysine degradation IV	5	2	1
glycolysis II (from fructose 6-phosphate)	11	11	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	2
UMP biosynthesis II	6	6	1
UMP biosynthesis I	6	6	1
glyoxylate cycle	6	6	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	2
UMP biosynthesis III	6	5	1
TCA cycle VIII (Chlamydia)	6	5	1
norspermidine biosynthesis	6	4	1
L-isoleucine biosynthesis IV	6	4	1
L-lysine degradation X	6	3	1
methylgallate degradation	6	2	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
2-methylcitrate cycle II	6	2	1
L-lysine degradation III	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
β-alanine biosynthesis II	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
superpathway of L-isoleucine biosynthesis I	13	13	2
glycolysis I (from glucose 6-phosphate)	13	13	2
L-lysine biosynthesis III	7	6	1
L-lysine biosynthesis VI	7	6	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
incomplete reductive TCA cycle	7	3	1
L-lysine degradation I	7	3	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
cremeomycin biosynthesis	7	2	1
pyruvate fermentation to propanoate I	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
mixed acid fermentation	16	14	2
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	4	1
superpathway of polyamine biosynthesis III	8	4	1
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
grixazone biosynthesis	8	2	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	2
superpathway of glucose and xylose degradation	17	16	2
superpathway of anaerobic energy metabolism (invertebrates)	17	10	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	3
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	2
L-lysine biosynthesis I	9	9	1
superpathway of pyrimidine ribonucleotides de novo biosynthesis	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
superpathway of hexitol degradation (bacteria)	18	16	2
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
TCA cycle II (plants and fungi)	9	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
L-lysine biosynthesis II	9	7	1
chitin biosynthesis	9	6	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	1
photorespiration I	9	5	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
photorespiration III	9	5	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	2
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
cis-geranyl-CoA degradation	9	1	1
superpathway of anaerobic sucrose degradation	19	17	2
hexitol fermentation to lactate, formate, ethanol and acetate	19	17	2
Rubisco shunt	10	9	1
TCA cycle I (prokaryotic)	10	9	1
L-arginine biosynthesis II (acetyl cycle)	10	9	1
superpathway of tetrahydrofolate biosynthesis	10	9	1
TCA cycle III (animals)	10	8	1
glycolysis IV	10	8	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
superpathway of vanillin and vanillate degradation	10	3	1
glycolysis III (from glucose)	11	11	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
superpathway of N-acetylneuraminate degradation	22	18	2
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	8	1
glycolysis VI (from fructose)	11	8	1
reductive TCA cycle I	11	6	1
superpathway of candicidin biosynthesis	11	3	1
L-glutamate degradation VIII (to propanoate)	11	2	1
superpathway of glyoxylate bypass and TCA	12	11	1
homolactic fermentation	12	11	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	11	1
gluconeogenesis III	12	9	1
chorismate biosynthesis II (archaea)	12	8	1
reductive TCA cycle II	12	5	1
syringate degradation	12	3	1
aspartate superpathway	25	24	2
superpathway of L-arginine and L-ornithine degradation	13	10	1
formaldehyde assimilation I (serine pathway)	13	8	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
peptidoglycan recycling I	14	14	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
Bifidobacterium shunt	15	14	1
glycerol degradation to butanol	16	11	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	18	1
heterolactic fermentation	18	16	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	3
methylaspartate cycle	19	9	1
ethene biosynthesis V (engineered)	25	18	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of L-lysine degradation	43	12	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	46	1
superpathway of chorismate metabolism	59	44	1