Experiment set4IT021 for Methanococcus maripaludis JJ
H2 N-free with 10mM D-glucosamine
Group: nitrogen sourceMedia: Mc_H2_N_Free + D-glucosamine (10 mM), pH=7
Culturing: Methanococcus_JJ_ML1, 96 deep-well microplate; 1 mL volume, Anaerobic, at 37 (C), shaken=180 rpm
By: Leslie Day on 2-Dec-22
Media components: 22 g/L Sodium Chloride, 2.5 g/L Sodium bicarbonate, 0.14 g/L Potassium phosphate dibasic, 0.0095 g/L Iron (II) chloride tetrahydrate, 0.001 g/L resazurin sodium salt, 0.5 g/L Dithiothreitol, 0.001 g/L Sodium sulfide nonahydrate, 0.84 g/L Sodium acetate, 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)
Specific Phenotypes
For 13 genes in this experiment
For nitrogen source D-glucosamine in Methanococcus maripaludis JJ
For nitrogen source D-glucosamine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Nitrogen fixation | 5 |
| Ammonia assimilation | 3 |
| De Novo Pyrimidine Synthesis | 1 |
| Molybdenum cofactor biosynthesis | 1 |
| Transport of Molybdenum | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pyrimidine metabolism
- Tetrachloroethene degradation
- Nitrogen metabolism
- Drug metabolism - other enzymes
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| nitrogen fixation I (ferredoxin) | 1 | 1 | 1 |
| UMP biosynthesis II | 6 | 6 | 1 |
| UMP biosynthesis III | 6 | 5 | 1 |
| UMP biosynthesis I | 6 | 5 | 1 |
| FeMo cofactor biosynthesis | 6 | 1 | 1 |
| superpathway of pyrimidine ribonucleotides de novo biosynthesis | 9 | 8 | 1 |
| superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis | 18 | 15 | 1 |
| superpathway of histidine, purine, and pyrimidine biosynthesis | 46 | 35 | 1 |