Experiment set5IT062 for Rhodanobacter denitrificans FW104-10B01

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casamino acids 2 mg/mL

Group: carbon source
Media: Hans_Basal_Media_plus_0.2x_20AA_mix + casamino acids (2 mg/mL)
Culturing: rhodanobacter_10B01_ML12, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 28 (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: 1 D10

Specific Phenotypes

For 3 genes in this experiment

For carbon source casamino acids in Rhodanobacter denitrificans FW104-10B01

For carbon source casamino acids across organisms

SEED Subsystems

Subsystem #Specific
Calvin-Benson cycle 1
DNA-binding regulatory proteins, strays 1
Glycolysis and Gluconeogenesis 1
Glycolysis and Gluconeogenesis, including Archaeal enzymes 1
Oxidative stress 1
Thioredoxin-disulfide reductase 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
sucrose biosynthesis I (from photosynthesis) 9 7 1
glycolysis II (from fructose 6-phosphate) 11 11 1
formaldehyde assimilation III (dihydroxyacetone cycle) 12 10 1
gluconeogenesis III 12 10 1
glycolysis I (from glucose 6-phosphate) 13 12 1
gluconeogenesis I 13 11 1
Calvin-Benson-Bassham cycle 13 9 1
superpathway of glycolysis and the Entner-Doudoroff pathway 17 16 1
oxygenic photosynthesis 17 10 1
superpathway of hexitol degradation (bacteria) 18 14 1
superpathway of anaerobic sucrose degradation 19 16 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 14 1
superpathway of N-acetylneuraminate degradation 22 16 1
ethene biosynthesis V (engineered) 25 17 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 23 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 17 1
1-butanol autotrophic biosynthesis (engineered) 27 18 1