Experiment set4IT005 for Methanococcus maripaludis JJ

H2 N-free with 2mM Adenosine

Group: nitrogen source
Media: Mc_H2_N_Free + Adenosine (2 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 9 genes in this experiment

For nitrogen source Adenosine in Methanococcus maripaludis JJ

For nitrogen source Adenosine across organisms

SEED Subsystems

Subsystem	#Specific
De Novo Pyrimidine Synthesis	1
Formaldehyde assimilation: Ribulose monophosphate pathway	1
Heat shock dnaK gene cluster extended	1
Purine conversions	1
Queuosine-Archaeosine Biosynthesis	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:

• Pentose and glucuronate interconversions
• Methane metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Naphthalene and anthracene degradation
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pentose phosphate pathway (oxidative branch) II	2	2	2
guanine and guanosine salvage I	2	2	1
adenine and adenosine salvage I	2	1	1
adenine and adenosine salvage II	2	1	1
guanine and guanosine salvage II	2	1	1
superpathway of guanine and guanosine salvage	3	3	1
formaldehyde oxidation I	6	3	2
adenine salvage	3	1	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	8	2
UMP biosynthesis II	6	6	1
UMP biosynthesis III	6	5	1
UMP biosynthesis I	6	5	1
superpathway of purine nucleotide salvage	14	10	2
glyphosate degradation III	7	2	1
(aminomethyl)phosphonate degradation	8	2	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