Experiment set4IT011 for Methanococcus maripaludis JJ

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Formate N-free with 2mM Adenosine

Group: nitrogen source
Media: Mc_formate_N_Free + Adenosine (2 mM), pH=7
Culturing: Methanococcus_JJ_ML1, 96 deep-well microplate; 1 mL volume, Anaerobic, at 37 (C)
By: Leslie Day on 2-Dec-22
Media components: 2.5 g/L Sodium bicarbonate, 10.5 g/L Sodium 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, 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 17 genes in this experiment

For nitrogen source Adenosine in Methanococcus maripaludis JJ

For nitrogen source Adenosine across organisms

SEED Subsystems

Subsystem #Specific
Nitrogen fixation 2
Queuosine-Archaeosine Biosynthesis 2
Anaerobic respiratory reductases 1
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Conserved gene cluster associated with Met-tRNA formyltransferase 1
H2:CoM-S-S-HTP oxidoreductase 1
Methanogenesis 1
Purine conversions 1
Ribosome biogenesis bacterial 1
cAMP signaling in bacteria 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
acetate and ATP formation from acetyl-CoA III 1 1 1
coenzyme B/coenzyme M regeneration V (formate-dependent) 1 1 1
acetate conversion to acetyl-CoA 1 1 1
guanine and guanosine salvage I 2 2 1
guanine and guanosine salvage II 2 1 1
adenine and adenosine salvage II 2 1 1
adenine and adenosine salvage I 2 1 1
superpathway of guanine and guanosine salvage 3 3 1
L-isoleucine biosynthesis V 3 3 1
adenine salvage 3 1 1
ethanol degradation II 3 1 1
ethanol degradation III 3 1 1
superpathway of acetate utilization and formation 3 1 1
ethanol degradation IV 3 1 1
erythro-tetrahydrobiopterin biosynthesis I 4 2 1
coenzyme B/coenzyme M regeneration I (methanophenazine-dependent) 4 2 1
threo-tetrahydrobiopterin biosynthesis 4 2 1
chitin deacetylation 4 1 1
superpathway of bitter acids biosynthesis 18 3 3
FeMo cofactor biosynthesis 6 1 1
lupulone and humulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
superpathway of purine nucleotide salvage 14 10 2
drosopterin and aurodrosopterin biosynthesis 7 4 1
glyphosate degradation III 7 2 1
(aminomethyl)phosphonate degradation 8 2 1
reductive glycine pathway of autotrophic CO2 fixation 9 2 1
cis-geranyl-CoA degradation 9 1 1