Experiment set1IT047 for Methanococcus maripaludis JJ

Formate McCas, 2.5g/L bicarb, 200 mM MOPs, 20 psi N2CO2, SO4 & Vitamin FREE

Group: nutrient t2
Media: Mc_defined_formate + Sodium acetate (10 mM) + casamino acids (2 mg/mL), pH=7
Culturing: Methanococcus_JJ_ML1, 5 mL Balch Tube, Anaerobic, at 37 (C)
Growth: about 9.8 generations
By: Leslie Day on 10-Oct
Media components: 10.5 g/L Sodium Chloride, 2.5 g/L Sodium bicarbonate, 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, 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)

Specific Phenotypes

For 5 genes in this experiment

For nutrient t2 Sodium acetate in Methanococcus maripaludis JJ

For nutrient t2 Sodium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Archease	1
Serine-glyoxylate cycle	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Penicillin and cephalosporin biosynthesis
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• 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
malate/L-aspartate shuttle pathway	2	2	1
TCA cycle VIII (Chlamydia)	6	4	1
glyoxylate cycle	6	1	1
incomplete reductive TCA cycle	7	6	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
pyruvate fermentation to propanoate I	7	2	1
TCA cycle V (2-oxoglutarate synthase)	9	4	1
TCA cycle II (plants and fungi)	9	3	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	2	1
TCA cycle III (animals)	10	4	1
TCA cycle I (prokaryotic)	10	3	1
reductive TCA cycle I	11	6	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	4	1
L-glutamate degradation VIII (to propanoate)	11	2	1
gluconeogenesis III	12	9	1
reductive TCA cycle II	12	5	1
superpathway of glyoxylate bypass and TCA	12	3	1
gluconeogenesis I	13	10	1
formaldehyde assimilation I (serine pathway)	13	5	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	3	1
superpathway of glyoxylate cycle and fatty acid degradation	14	2	1
mixed acid fermentation	16	3	1
superpathway of anaerobic energy metabolism (invertebrates)	17	6	1
methylaspartate cycle	19	3	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	12	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	13	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	34	1