Experiment set5IT080 for Rhodanobacter denitrificans FW104-10B01

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D-Glucose-6-Phosphate sodium salt 20 mM

Group: carbon source
Media: Hans_Basal_Media_plus_0.2x_20AA_mix + D-Glucose-6-Phosphate sodium salt (20 mM)
Culturing: rhodanobacter_10B01_ML12, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Hans Carlson and Trenton Owens on 08/24/2021
Media components: 0.03 M PIPES sesquisodium salt, 0.1 g/L Potassium Chloride, 0.01 g/L Sodium Chloride, 0.01 g/L Calcium chloride dihydrate, 0.1 g/L Magnesium chloride hexahydrate, 0.1 g/L Sodium sulfate, 0.25 g/L Ammonium chloride, 0.1 g/L Disodium phosphate, 20AA_mix (0.1 mM L-Arginine, 0.1 mM L-Histidine, 0.1 mM L-Lysine, 0.1 mM L-Aspartic Acid, 0.1 mM L-Glutamic acid monopotassium salt monohydrate, 0.1 mM L-Serine, 0.1 mM L-Threonine, 0.1 mM L-Asparagine, 0.1 mM L-Glutamine, 0.1 mM L-Cysteine hydrochloride monohydrate, 0.1 mM Glycine, 0.1 mM L-Proline, 0.1 mM L-Alanine, 0.1 mM L-Valine, 0.1 mM L-Isoleucine, 0.1 mM L-Leucine, 0.1 mM L-Methionine, 0.1 mM L-Phenylalanine, 0.1 mM L-tyrosine disodium salt, 0.1 mM L-Tryptophan), DL vitamins (0.0002 mg/L biotin, 0.0002 mg/L Folic Acid, 0.001 mg/L Pyridoxine HCl, 0.0005 mg/L Riboflavin, 0.0005 mg/L Thiamine HCl, 0.0005 mg/L Nicotinic Acid, 0.0005 mg/L calcium pantothenate, 1e-05 mg/L Cyanocobalamin, 0.0005 mg/L 4-Aminobenzoic acid, 0.0005 mg/L Lipoic acid), Sulfur-free DL minerals (0.0003 g/L Magnesium chloride hexahydrate, 0.00015 g/L Nitrilotriacetic acid disodium salt, 0.0001 g/L Sodium Chloride, 5e-05 g/L Manganese (II) chloride tetrahydrate, 1e-05 g/L Cobalt chloride hexahydrate, 1.3e-05 g/L Zinc chloride, 1e-05 g/L Calcium chloride dihydrate, 1e-05 g/L Iron (II) chloride tetrahydrate, 2.5e-06 g/L Nickel (II) chloride hexahydrate, 2e-06 g/L Aluminum chloride hydrate, 1e-06 g/L copper (II) chloride dihydrate, 1e-06 g/L Boric Acid, 1e-06 g/L Sodium Molybdate Dihydrate, 3e-05 g/L Sodium selenite pentahydrate, 2.5e-05 g/L Sodium tungstate dihydrate)
Growth plate: 2 D3

Specific Phenotypes

For 11 genes in this experiment

For carbon source D-Glucose-6-Phosphate sodium salt in Rhodanobacter denitrificans FW104-10B01

For carbon source D-Glucose-6-Phosphate sodium salt across organisms

SEED Subsystems

Subsystem #Specific
Protein chaperones 2
Campylobacter Iron Metabolism 1
DNA-binding regulatory proteins, strays 1
Entner-Doudoroff Pathway 1
Fatty Acid Biosynthesis FASII 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Mannose Metabolism 1
Methylglyoxal Metabolism 1
Nudix proteins (nucleoside triphosphate hydrolases) 1
Oxidative stress 1
Proteolysis in bacteria, ATP-dependent 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Thioredoxin-disulfide reductase 1
mycolic acid synthesis 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
ethylene glycol degradation 2 1 1
putrescine degradation I 2 1 1
putrescine degradation V 2 1 1
ethanol degradation IV 3 3 1
ethanol degradation II 3 3 1
ethanol degradation III 3 2 1
hypotaurine degradation 3 2 1
putrescine degradation IV 3 2 1
histamine degradation 3 1 1
gondoate biosynthesis (anaerobic) 4 4 1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast) 12 9 3
phytol degradation 4 3 1
fatty acid α-oxidation I (plants) 4 2 1
putrescine degradation III 4 1 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 1 1
4-methylphenol degradation to protocatechuate 4 1 1
D-arabinose degradation II 4 1 1
palmitate biosynthesis III 29 21 7
tetradecanoate biosynthesis (mitochondria) 25 17 6
palmitate biosynthesis II (type II fatty acid synthase) 31 29 7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate) 9 8 2
oleate biosynthesis IV (anaerobic) 14 13 3
superpathway of fatty acids biosynthesis (E. coli) 53 49 11
superpathway of unsaturated fatty acids biosynthesis (E. coli) 20 18 4
fatty acid elongation -- saturated 5 4 1
8-amino-7-oxononanoate biosynthesis IV 5 4 1
cis-vaccenate biosynthesis 5 4 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
mitochondrial NADPH production (yeast) 5 2 1
octane oxidation 5 2 1
dopamine degradation 5 1 1
superpathway of fatty acid biosynthesis II (plant) 43 38 8
8-amino-7-oxononanoate biosynthesis I 11 10 2
even iso-branched-chain fatty acid biosynthesis 34 24 6
anteiso-branched-chain fatty acid biosynthesis 34 24 6
odd iso-branched-chain fatty acid biosynthesis 34 24 6
(5Z)-dodecenoate biosynthesis I 6 6 1
(5Z)-dodecenoate biosynthesis II 6 5 1
stearate biosynthesis II (bacteria and plants) 6 5 1
stearate biosynthesis IV 6 4 1
3-methyl-branched fatty acid α-oxidation 6 3 1
petroselinate biosynthesis 6 2 1
alkane oxidation 6 1 1
4-hydroxymandelate degradation 6 1 1
noradrenaline and adrenaline degradation 13 4 2
streptorubin B biosynthesis 34 20 5
superpathway of glycol metabolism and degradation 7 4 1
serotonin degradation 7 3 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
2,4-xylenol degradation to protocatechuate 7 1 1
biotin biosynthesis I 15 14 2
superpathway of fatty acid biosynthesis I (E. coli) 16 14 2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
2-allylmalonyl-CoA biosynthesis 8 2 1
superpathway of ornithine degradation 8 2 1
aromatic biogenic amine degradation (bacteria) 8 1 1
Entner-Doudoroff pathway II (non-phosphorylative) 9 4 1
toluene degradation III (aerobic) (via p-cresol) 11 5 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 3 1
superpathway of L-arginine and L-ornithine degradation 13 4 1
superpathway of aerobic toluene degradation 30 7 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 11 1
mycolate biosynthesis 205 20 5
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 8 1
superpathway of pentose and pentitol degradation 42 4 1
superpathway of mycolate biosynthesis 239 21 5