Experiment set5IT020 for Methanococcus maripaludis S2
Formate with Neomycin 12.5 mM
Group: stressMedia: McCas_formate_SO4Free_BicarbFree + Neomycin trisulfate salt hydrate (0.625 mM), pH=7
Culturing: Methanococcus_S2_ML1, 96 deep-well microplate; 1 mL volume, Anaerobic, at 37 (C)
By: Hans Carlson and Leslie Day on 26-Oct-22
Media components: 10.5 g/L Sodium Chloride, 1 g/L Ammonium chloride, 0.14 g/L Potassium phosphate dibasic, 0.0095 g/L Iron (II) chloride tetrahydrate, 0.001 g/L resazurin sodium salt, 0.84 g/L Sodium acetate, 13.6 g/L Sodium Formate, 2 g/L casamino acids, 0.5 g/L Dithiothreitol, 0.001 g/L Sodium sulfide nonahydrate, MOPS_2M_pH7 (0.002 M 3-(N-morpholino)propanesulfonic acid, 0.0005 M Sodium Hydroxide), Mc_general_salts_SO4free (0.335 g/L Potassium Chloride, 5.6 g/L Magnesium chloride hexahydrate, 0.105 g/L Calcium chloride), Mc_trace_minerals_SO4free (0.021 g/L Trisodium citrate dihydrate, 0.005 g/L Manganese (II) chloride tetrahydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc chloride, 0.0001 g/L copper (II) chloride dihydrate, 0.0001 g/L Aluminum chloride hydrate, 0.0001 g/L Boric Acid, 0.001 g/L Sodium Molybdate Dihydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.002 g/L Sodium selenate, 0.0001 g/L vanadium chloride, 3.3e-05 g/L Sodium tungstate dihydrate), Mc_vitamins (2e-05 g/L biotin, 2e-05 g/L Folic Acid, 0.0001 g/L Pyridoxine HCl, 5e-05 g/L Thiamine HCl, 5e-05 g/L Riboflavin, 5e-05 g/L Nicotinic Acid, 5e-05 g/L calcium pantothenate, 1e-06 g/L Cyanocobalamin, 5e-05 g/L 4-Aminobenzoic acid, 5e-05 g/L Lipoic acid)
Specific Phenotypes
For 1 genes in this experiment
For stress Neomycin trisulfate salt hydrate in Methanococcus maripaludis S2
For stress Neomycin trisulfate salt hydrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ketoisovalerate oxidoreductase | 1 |
| Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycolysis / Gluconeogenesis
- Pyruvate metabolism
- Propanoate metabolism
- Reductive carboxylate cycle (CO2 fixation)
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| acetate conversion to acetyl-CoA | 1 | 1 | 1 |
| acetate and ATP formation from acetyl-CoA III | 1 | 1 | 1 |
| L-isoleucine biosynthesis V | 3 | 3 | 1 |
| ethanol degradation II | 3 | 2 | 1 |
| ethanol degradation IV | 3 | 1 | 1 |
| superpathway of acetate utilization and formation | 3 | 1 | 1 |
| ethanol degradation III | 3 | 1 | 1 |
| chitin deacetylation | 4 | 1 | 1 |
| superpathway of bitter acids biosynthesis | 18 | 3 | 3 |
| adlupulone and adhumulone biosynthesis | 6 | 1 | 1 |
| lupulone and humulone biosynthesis | 6 | 1 | 1 |
| colupulone and cohumulone biosynthesis | 6 | 1 | 1 |
| reductive glycine pathway of autotrophic CO2 fixation | 9 | 2 | 1 |
| cis-geranyl-CoA degradation | 9 | 1 | 1 |
| 3-hydroxypropanoate cycle | 13 | 3 | 1 |
| glyoxylate assimilation | 13 | 3 | 1 |
| 3-hydroxypropanoate/4-hydroxybutanate cycle | 18 | 4 | 1 |
| superpathway of the 3-hydroxypropanoate cycle | 18 | 3 | 1 |