Experiment set5S684 for Mucilaginibacter yixingensis YX-36 DSM 26809

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polygalacturonic acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + polygalacturonic acid (5 mg/ml)
Culturing: Mucilaginibacter_YX36_ML5a, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Marta on 6/27/25
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, 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)

Specific Phenotypes

For 43 genes in this experiment

For carbon source polygalacturonic acid in Mucilaginibacter yixingensis YX-36 DSM 26809

For carbon source polygalacturonic acid across organisms

SEED Subsystems

Subsystem #Specific
D-Galacturonate and D-Glucuronate Utilization 2
Iron acquisition in Vibrio 2
Methionine Biosynthesis 2
Methionine Degradation 2
Ton and Tol transport systems 2
Alginate metabolism 1
Auxin degradation 1
Bacterial Chemotaxis 1
Cysteine Biosynthesis 1
Glycine and Serine Utilization 1
Multidrug Resistance Efflux Pumps 1
NAD and NADP cofactor biosynthesis global 1
NAD regulation 1
Nitrate and nitrite ammonification 1
Oxidative stress 1
Phosphate metabolism 1
Photorespiration (oxidative C2 cycle) 1
Predicted carbohydrate hydrolases 1
cAMP signaling in bacteria 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-cysteine degradation II 3 3 3
long-chain fatty acid activation 1 1 1
betanidin degradation 1 1 1
L-serine degradation 3 3 2
L-methionine degradation II 3 2 2
L-tryptophan degradation II (via pyruvate) 3 2 2
D-serine degradation 3 2 2
L-cysteine biosynthesis III (from L-homocysteine) 2 2 1
isoniazid activation 2 2 1
superoxide radicals degradation 2 2 1
NAD biosynthesis from nicotinamide 2 2 1
L-methionine biosynthesis II 6 5 3
homocysteine and cysteine interconversion 4 3 2
methanol oxidation to formaldehyde IV 2 1 1
γ-linolenate biosynthesis II (animals) 2 1 1
baicalein degradation (hydrogen peroxide detoxification) 2 1 1
linoleate biosynthesis II (animals) 2 1 1
D-galacturonate degradation I 5 5 2
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis 5 2 2
ethanol degradation IV 3 3 1
superpathway of L-cysteine biosynthesis (fungi) 6 5 2
oleate biosynthesis I (plants) 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
L-threonine degradation I 6 3 2
alkane biosynthesis II 3 1 1
L-isoleucine biosynthesis I (from threonine) 7 7 2
glycine betaine degradation III 7 4 2
reactive oxygen species degradation 4 4 1
phytol degradation 4 3 1
luteolin triglucuronide degradation 4 3 1
glycine betaine degradation I 8 4 2
L-mimosine degradation 8 4 2
glutathione-mediated detoxification I 8 3 2
long chain fatty acid ester synthesis (engineered) 4 1 1
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 4 1 1
xanthommatin biosynthesis 4 1 1
sporopollenin precursors biosynthesis 18 4 4
superpathway of hexuronide and hexuronate degradation 10 10 2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 9 2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 3
superpathway of L-cysteine biosynthesis (mammalian) 5 4 1
L-methionine biosynthesis I 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
octane oxidation 5 2 1
stearate biosynthesis II (bacteria and plants) 6 5 1
stearate biosynthesis IV 6 4 1
hydrogen sulfide biosynthesis II (mammalian) 6 4 1
fatty acid salvage 6 4 1
6-gingerol analog biosynthesis (engineered) 6 2 1
stearate biosynthesis I (animals) 6 1 1
superpathway of L-isoleucine biosynthesis I 13 13 2
L-cysteine biosynthesis VI (reverse transsulfuration) 7 3 1
ceramide degradation by α-oxidation 7 2 1
hypoglycin biosynthesis 14 3 2
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
capsaicin biosynthesis 7 1 1
superpathway of L-homoserine and L-methionine biosynthesis 8 6 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
sesamin biosynthesis 8 1 1
superpathway of branched chain amino acid biosynthesis 17 17 2
superpathway of S-adenosyl-L-methionine biosynthesis 9 7 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
superpathway of L-threonine metabolism 18 11 2
suberin monomers biosynthesis 20 2 2
matairesinol biosynthesis 10 1 1
justicidin B biosynthesis 10 1 1
superpathway of fatty acid biosynthesis II (plant) 43 39 4
purine nucleobases degradation II (anaerobic) 24 10 2
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 13 2
superpathway of L-methionine salvage and degradation 16 9 1
cutin biosynthesis 16 1 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 14 1
aspartate superpathway 25 21 1
superpathway of fatty acids biosynthesis (E. coli) 53 48 2
palmitate biosynthesis III 29 28 1
oleate β-oxidation 35 23 1