Experiment set10S126 for Methanococcus maripaludis S2

H2 N-free with 10mM N-Acetyl-D-Glucosamine

Group: nitrogen source
Media: Mc_H2_N_Free + N-Acetyl-D-Glucosamine (10 mM), pH=7
Culturing: Methanococcus_S2_ML1, 96 deep-well microplate; 1.0 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 4 genes in this experiment

For nitrogen source N-Acetyl-D-Glucosamine in Methanococcus maripaludis S2

For nitrogen source N-Acetyl-D-Glucosamine across organisms

SEED Subsystems

Subsystem	#Specific
Entner-Doudoroff Pathway	2
Glycolysis and Gluconeogenesis, including Archaeal enzymes	2

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
Entner-Doudoroff pathway III (semi-phosphorylative)	9	4	1
glycolysis V (Pyrococcus)	10	10	1
glycolysis IV	10	8	1
Rubisco shunt	10	8	1
photorespiration II	10	3	1
glycolysis II (from fructose 6-phosphate)	11	9	1
glycolysis III (from glucose)	11	8	1
glycolysis VI (from fructose)	11	7	1
homolactic fermentation	12	8	1
glycolysis I (from glucose 6-phosphate)	13	10	1
gluconeogenesis I	13	10	1
Bifidobacterium shunt	15	10	1
glycerol degradation to butanol	16	8	1
superpathway of glucose and xylose degradation	17	10	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	10	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	16	1
superpathway of hexitol degradation (bacteria)	18	10	1
superpathway of anaerobic sucrose degradation	19	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	10	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	12	1
superpathway of N-acetylneuraminate degradation	22	10	1
ethene biosynthesis V (engineered)	25	12	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	14	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	13	1
1-butanol autotrophic biosynthesis (engineered)	27	14	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	35	1