Experiment set5IT078 for Rhodanobacter denitrificans FW104-10B01

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N-Acetyl-D-Glucosamine 20 mM

Group: carbon source
Media: Hans_Basal_Media_plus_0.2x_20AA_mix + N-Acetyl-D-Glucosamine (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 24-Aug-21
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 F10

Specific Phenotypes

For 4 genes in this experiment

For carbon source N-Acetyl-D-Glucosamine in Rhodanobacter denitrificans FW104-10B01

For carbon source N-Acetyl-D-Glucosamine across organisms

SEED Subsystems

Subsystem #Specific
Methionine Biosynthesis 2
Fermentations: Mixed acid 1
Pyruvate metabolism I: anaplerotic reactions, PEP 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
CO2 fixation into oxaloacetate (anaplerotic) 2 2 1
L-serine degradation 3 3 1
D-serine degradation 3 3 1
L-cysteine degradation II 3 3 1
L-methionine degradation II 3 2 1
L-tryptophan degradation II (via pyruvate) 3 2 1
L-methionine salvage from L-homocysteine 3 1 1
L-methionine biosynthesis III 4 3 1
L-methionine biosynthesis I 5 3 1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis 5 2 1
L-methionine biosynthesis II 6 5 1
L-threonine degradation I 6 5 1
L-isoleucine biosynthesis I (from threonine) 7 7 1
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 1
glycine betaine degradation III 7 4 1
nitrogen remobilization from senescing leaves 8 7 1
partial TCA cycle (obligate autotrophs) 8 7 1
superpathway of L-homoserine and L-methionine biosynthesis 8 6 1
glycine betaine degradation I 8 4 1
L-mimosine degradation 8 4 1
glutathione-mediated detoxification I 8 3 1
folate transformations III (E. coli) 9 9 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 7 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
folate transformations II (plants) 11 10 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 7 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 11 1
superpathway of L-isoleucine biosynthesis I 13 13 1
folate transformations I 13 8 1
formaldehyde assimilation I (serine pathway) 13 6 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 8 1
hypoglycin biosynthesis 14 4 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 1
mixed acid fermentation 16 12 1
superpathway of L-methionine salvage and degradation 16 8 1
superpathway of branched chain amino acid biosynthesis 17 17 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
superpathway of L-threonine metabolism 18 13 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 8 1
purine nucleobases degradation II (anaerobic) 24 9 1
aspartate superpathway 25 23 1
ethene biosynthesis V (engineered) 25 17 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 25 1