Experiment set5IT067 for Rhodanobacter denitrificans FW104-10B01
D-Glucosamine Hydrochloride 20 mM
Group: carbon sourceMedia: Hans_Basal_Media_plus_0.2x_20AA_mix + D-Glucosamine Hydrochloride (20 mM)
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 G10
Specific Phenotypes
For 5 genes in this experiment
For carbon source D-Glucosamine Hydrochloride in Rhodanobacter denitrificans FW104-10B01
For carbon source D-Glucosamine Hydrochloride across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Chitin and N-acetylglucosamine utilization | 3 |
| Glycine Biosynthesis | 2 |
| Glycine and Serine Utilization | 1 |
| Threonine degradation | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycine, serine and threonine metabolism
- Nucleotide sugars metabolism
- Glycolysis / Gluconeogenesis
- Galactose metabolism
- Starch and sucrose metabolism
- Streptomycin biosynthesis
- Aminosugars metabolism
- Biosynthesis of phenylpropanoids
- Biosynthesis of terpenoids and steroids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of alkaloids derived from terpenoid and polyketide
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-threonine degradation II | 2 | 2 | 2 |
| L-threonine degradation III (to methylglyoxal) | 3 | 2 | 2 |
| trehalose degradation II (cytosolic) | 2 | 2 | 1 |
| aminopropanol phosphate biosynthesis II | 4 | 2 | 2 |
| trehalose degradation I (low osmolarity) | 2 | 1 | 1 |
| trehalose degradation IV | 3 | 3 | 1 |
| N-acetylglucosamine degradation II | 3 | 3 | 1 |
| GDP-α-D-glucose biosynthesis | 3 | 2 | 1 |
| trehalose degradation V | 3 | 2 | 1 |
| sucrose degradation III (sucrose invertase) | 4 | 3 | 1 |
| glucose and glucose-1-phosphate degradation | 5 | 3 | 1 |
| superpathway of L-threonine metabolism | 18 | 13 | 3 |
| UDP-N-acetyl-D-glucosamine biosynthesis II | 6 | 4 | 1 |
| glycogen degradation II | 6 | 2 | 1 |
| UDP-N-acetyl-D-galactosamine biosynthesis II | 7 | 5 | 1 |
| sucrose biosynthesis II | 8 | 4 | 1 |
| chitin derivatives degradation | 8 | 3 | 1 |
| glycogen degradation I | 8 | 3 | 1 |
| chitin biosynthesis | 9 | 6 | 1 |
| 1,3-propanediol biosynthesis (engineered) | 9 | 5 | 1 |
| glycolysis III (from glucose) | 11 | 11 | 1 |
| homolactic fermentation | 12 | 11 | 1 |
| Bifidobacterium shunt | 15 | 14 | 1 |
| heterolactic fermentation | 18 | 15 | 1 |