Experiment set18S326 for Rhodanobacter denitrificans FW104-10B01

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NLDM_defined_no_iron

Group: nldm_defined_no_iron
Media: NLDM_defined_no_iron
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 mineral mix minus iron (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 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), 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 17 genes in this experiment

SEED Subsystems

Subsystem #Specific
Glycine Biosynthesis 2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 2
Biogenesis of cytochrome c oxidases 1
Campylobacter Iron Metabolism 1
DNA repair, UvrABC system 1
Glycine and Serine Utilization 1
Lysine Biosynthesis DAP Pathway 1
Methionine Biosynthesis 1
Purine conversions 1
Threonine and Homoserine Biosynthesis 1
Threonine degradation 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-threonine degradation II 2 2 2
L-homoserine biosynthesis 3 3 2
L-threonine degradation III (to methylglyoxal) 3 2 2
xanthine and xanthosine salvage 2 2 1
guanine and guanosine salvage I 2 2 1
guanine and guanosine salvage II 2 2 1
aminopropanol phosphate biosynthesis II 4 2 2
acetoacetate degradation (to acetyl CoA) 2 1 1
5,6-dehydrokavain biosynthesis (engineered) 10 6 4
superpathway of L-threonine biosynthesis 6 6 2
benzoyl-CoA biosynthesis 3 3 1
ketolysis 3 3 1
polyhydroxybutanoate biosynthesis 3 2 1
adenine salvage 3 2 1
superpathway of guanine and guanosine salvage 3 2 1
superpathway of L-homoserine and L-methionine biosynthesis 8 6 2
adenine and adenosine salvage III 4 3 1
dipicolinate biosynthesis 4 3 1
(2S)-ethylmalonyl-CoA biosynthesis 4 3 1
spermidine biosynthesis II 4 2 1
L-methionine biosynthesis IV 4 2 1
oleate β-oxidation 35 32 8
superpathway of S-adenosyl-L-methionine biosynthesis 9 7 2
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 2
valproate β-oxidation 9 5 2
2-methyl-branched fatty acid β-oxidation 14 9 3
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 3 1
glutaryl-CoA degradation 5 3 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
ketogenesis 5 3 1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 2
ectoine biosynthesis 5 2 1
4-hydroxybenzoate biosynthesis III (plants) 5 2 1
ethylbenzene degradation (anaerobic) 5 1 1
isopropanol biosynthesis (engineered) 5 1 1
pyruvate fermentation to acetone 5 1 1
fatty acid β-oxidation VII (yeast peroxisome) 5 1 1
pyruvate fermentation to hexanol (engineered) 11 7 2
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 11 2
fatty acid salvage 6 5 1
superpathway of L-threonine metabolism 18 13 3
pyruvate fermentation to butanol II (engineered) 6 4 1
L-isoleucine degradation I 6 4 1
propanoate fermentation to 2-methylbutanoate 6 3 1
norspermidine biosynthesis 6 2 1
4-ethylphenol degradation (anaerobic) 6 1 1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast) 6 1 1
jasmonic acid biosynthesis 19 4 3
superpathway of L-isoleucine biosynthesis I 13 13 2
mevalonate pathway I (eukaryotes and bacteria) 7 6 1
L-lysine biosynthesis III 7 6 1
L-lysine biosynthesis VI 7 6 1
fatty acid β-oxidation I (generic) 7 6 1
acetyl-CoA fermentation to butanoate 7 5 1
mevalonate pathway II (haloarchaea) 7 4 1
3-dehydroquinate biosynthesis II (archaea) 7 3 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 1
pyruvate fermentation to butanoate 7 3 1
cremeomycin biosynthesis 7 2 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 2
isoprene biosynthesis II (engineered) 8 6 1
mevalonate pathway IV (archaea) 8 4 1
mevalonate pathway III (Thermoplasma) 8 3 1
pyruvate fermentation to butanol I 8 3 1
2-deoxy-D-ribose degradation II 8 2 1
superpathway of polyamine biosynthesis III 8 2 1
2-methylpropene degradation 8 2 1
grixazone biosynthesis 8 2 1
androstenedione degradation I (aerobic) 25 8 3
L-lysine biosynthesis I 9 9 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 2
L-lysine biosynthesis II 9 7 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 1
4-oxopentanoate degradation 9 2 1
superpathway of testosterone and androsterone degradation 28 8 3
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) 10 9 1
L-glutamate degradation V (via hydroxyglutarate) 10 6 1
3-phenylpropanoate degradation 10 5 1
methyl tert-butyl ether degradation 10 3 1
L-lysine fermentation to acetate and butanoate 10 3 1
superpathway of cholesterol degradation I (cholesterol oxidase) 42 10 4
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 5 1
ethylmalonyl-CoA pathway 11 3 1
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 10 4
chorismate biosynthesis II (archaea) 12 8 1
L-glutamate degradation VII (to butanoate) 12 4 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
aspartate superpathway 25 23 2
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 4 1
platensimycin biosynthesis 26 6 2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
androstenedione degradation II (anaerobic) 27 6 2
superpathway of purine nucleotide salvage 14 14 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
L-tryptophan degradation III (eukaryotic) 15 11 1
glycerol degradation to butanol 16 9 1
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 3 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 6 1
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 3 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 10 1
toluene degradation VI (anaerobic) 18 3 1
sitosterol degradation to androstenedione 18 1 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 2 1
superpathway of cholesterol degradation III (oxidase) 49 6 2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 17 1
superpathway of ergosterol biosynthesis I 26 8 1
1-butanol autotrophic biosynthesis (engineered) 27 18 1
superpathway of cholesterol biosynthesis 38 8 1
superpathway of L-lysine degradation 43 7 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 25 1