Experiment set1IT057 for Methanococcus maripaludis JJ
Formate pooled triplicate biofilm cells
Group: biofilmMedia: McCas_formate_SO4, pH=7
Culturing: Methanococcus_JJ_ML1, 20 mL Serum bottle, Anaerobic, at 37 (C)
By: Emily Hanson and Leslie Day on 8-Sept
Media components: 2.5 g/L Sodium bicarbonate, 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 (0.335 g/L Potassium Chloride, 2.75 g/L Magnesium chloride hexahydrate, 3.45 g/L Magnesium Sulfate Heptahydrate, 0.105 g/L Calcium chloride), Mc_trace_minerals (0.021 g/L Trisodium citrate dihydrate, 0.005 g/L manganese(II) sulfate dihydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.0001 g/L copper (II) chloride dihydrate, 0.0001 g/L Aluminum potassium sulfate dodecahydrate, 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 3 genes in this experiment
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ketoisovalerate oxidoreductase | 2 |
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 |
|---|---|---|---|
| 2-oxobutanoate degradation II | 2 | 1 | 1 |
| L-isoleucine biosynthesis V | 3 | 3 | 1 |
| L-leucine degradation V (oxidative Stickland reaction) | 3 | 2 | 1 |
| L-valine degradation III (oxidative Stickland reaction) | 3 | 2 | 1 |
| L-isoleucine degradation III (oxidative Stickland reaction) | 3 | 2 | 1 |
| L-isoleucine biosynthesis IV | 6 | 5 | 1 |