Experiment set18S331 for Rhodanobacter denitrificans FW104-10B01

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NLDM_defined

Group: nldm_defined
Media: NLDM_defined
Culturing: rhodanobacter_10B01_ML12, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Allison on 7-Jan-26
Media components: 1 mM Ammonium chloride, 3.3 mM Potassium Chloride, 0.812 mM Magnesium Sulfate Heptahydrate, 0.68 mM Calcium chloride dihydrate, 4.05 mM Disodium phosphate, 0.95 mM Sodium phosphate monobasic, ATCC Wolfe's mineral mix (5 mg/L EDTA, 3 mg/L Magnesium Sulfate Heptahydrate, 5 mg/L Manganese (II) sulfate monohydrate, 10 mg/L Sodium Chloride, 1 mg/L Iron (II) sulfate heptahydrate, 1 mg/L Cobalt(II) nitrate hexahydrate, 1 mg/L Calcium chloride dihydrate, 1 mg/L Zinc sulfate heptahydrate, 0.1 mg/L Copper (II) sulfate pentahydrate, 0.1 mg/L Aluminum potassium sulfate dodecahydrate, 0.1 mg/L Boric Acid, 0.1 mg/L Sodium Molybdate Dihydrate, 0.01 mg/L Sodium selenite pentahydrate, 0.1 mg/L Sodium tungstate dihydrate, 0.2 mg/L Nickel (II) chloride hexahydrate), ATCC Wolfe's vitamin mix (20 ug/L Folic Acid, 100 ug/L Pyridoxine HCl, 50 ug/L Riboflavin, 20 ug/L biotin, 50 ug/L Thiamine HCl, 50 ug/L Nicotinic Acid, 50 ug/L calcium pantothenate, 1 ug/L Cyanocobalamin, 50 ug/L 4-Aminobenzoic acid, 50 ug/L Lipoic acid), NLDM_metabolites (875 uM Sucrose, 875 uM D-Glucose, 875 uM D-Trehalose dihydrate, 875 uM m-Inositol, 875 uM D-Xylose, 875 uM D-Mannitol, 875 uM N-Acetyl-D-Glucosamine, 525 uM Sodium L-Lactate, 525 uM D,L-Malic Acid, 525 uM Citric Acid, 525 uM Sodium succinate dibasic hexahydrate, 525 uM Sodium pyruvate, 525 uM a-Ketoglutaric acid disodium salt hydrate, 525 uM L-Citrulline, 175 uM L-Alanine, 175 uM L-Arginine, 175 uM L-Asparagine, 175 uM L-Aspartic Acid, 175 uM L-Cysteine, 175 uM L-Glutamic acid, 175 uM L-Glutamine, 175 uM Glycine, 175 uM L-Histidine, 175 uM L-Isoleucine, 175 uM L-Leucine, 175 uM L-Lysine, 175 uM L-Methionine, 175 uM L-Phenylalanine, 175 uM L-Proline, 175 uM L-Serine, 175 uM L-Threonine, 175 uM L-Tryptophan, 175 uM L-tyrosine, 175 uM L-Valine, 17.5 uM 5-methyluridine, 17.5 uM Adenine hydrochloride hydrate, 17.5 uM Adenosine, 17.5 uM Cytidine, 17.5 uM Cytosine, 17.5 uM Guanine, 17.5 uM Guanosine, 17.5 uM Hypoxanthine, 17.5 uM Inosine, 17.5 uM Thymine, 17.5 uM Uracil, 17.5 uM Uridine, 17.5 uM Xanthine, 17.5 uM Xanthosine, 17.5 uM Gamma-Aminobutyric Acid Hydrochloride, 17.5 uM Ectoine, 17.5 uM Betaine, 17.5 uM N-Acetyl-glutamic acid, 17.5 uM Nicotinamide, 17.5 uM L-Ornithine, 17.5 uM Shikimic Acid, 17.5 uM spermidine, 17.5 uM Taurine, 17.5 uM Trigonelline HCl, 17.5 uM Carnitine Hydrochloride, 17.5 uM Choline chloride, 17.5 uM n-Acetyl-glutamine, 17.5 uM n-Acetyl-lysine, 17.5 uM n-Acetyl-muramic acid, 17.5 uM sn-glycero-3-phosphocholine)

Specific Phenotypes

For 14 genes in this experiment

SEED Subsystems

Subsystem #Specific
Methionine Biosynthesis 3
Chitin and N-acetylglucosamine utilization 2
Glycine Biosynthesis 1
Maltose and Maltodextrin Utilization 1
Methionine Degradation 1
NAD and NADP cofactor biosynthesis global 1
Quinolinic acid and its derivatives 1
Threonine degradation 1
Trehalose Biosynthesis 1
Trehalose Uptake and Utilization 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
trehalose degradation IV 3 3 3
maltose degradation 2 2 2
L-threonine degradation III (to methylglyoxal) 3 2 2
trehalose degradation II (cytosolic) 2 2 1
L-threonine degradation II 2 2 1
aminopropanol phosphate biosynthesis II 4 2 2
trehalose degradation I (low osmolarity) 2 1 1
trehalose degradation III 2 1 1
kojibiose degradation 2 1 1
S-adenosyl-L-methionine salvage II 3 3 1
N-acetylglucosamine degradation II 3 3 1
L-methionine degradation I (to L-homocysteine) 3 2 1
GDP-α-D-glucose biosynthesis 3 2 1
trehalose degradation V 3 2 1
L-methionine salvage from L-homocysteine 3 1 1
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde 4 4 1
L-methionine biosynthesis III 4 3 1
sucrose degradation III (sucrose invertase) 4 3 1
NAD de novo biosynthesis II (from tryptophan) 9 9 2
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde 5 5 1
superpathway of L-cysteine biosynthesis (mammalian) 5 4 1
glucose and glucose-1-phosphate degradation 5 3 1
L-methionine biosynthesis I 5 3 1
UDP-N-acetyl-D-glucosamine biosynthesis II 6 4 1
glycogen degradation II 6 2 1
superpathway of NAD biosynthesis in eukaryotes 14 11 2
UDP-N-acetyl-D-galactosamine biosynthesis II 7 5 1
2-nitrobenzoate degradation I 7 4 1
superpathway of L-homoserine and L-methionine biosynthesis 8 6 1
superpathway of L-methionine salvage and degradation 16 8 2
sucrose biosynthesis II 8 4 1
glycogen degradation I 8 3 1
chitin derivatives degradation 8 3 1
folate transformations III (E. coli) 9 9 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 7 1
superpathway of L-threonine metabolism 18 13 2
chitin biosynthesis 9 6 1
1,3-propanediol biosynthesis (engineered) 9 5 1
glycolysis III (from glucose) 11 11 1
folate transformations II (plants) 11 10 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 11 1
homolactic fermentation 12 11 1
L-tryptophan degradation IX 12 8 1
L-tryptophan degradation XII (Geobacillus) 12 7 1
folate transformations I 13 8 1
Bifidobacterium shunt 15 14 1
L-tryptophan degradation III (eukaryotic) 15 11 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
heterolactic fermentation 18 15 1
L-tryptophan degradation XI (mammalian, via kynurenine) 23 12 1
aspartate superpathway 25 23 1