Experiment set2IT093 for Methanococcus maripaludis JJ

H2 McCas, 5g/L bicarb, 40 psi H2CO2

Group: rich t2
Media: McCas, pH=7
Culturing: Methanococcus_JJ_ML1, 5 mL Balch Tube, Anaerobic, at 37 (C), shaken=180 rpm
Growth: about 9.4 generations
By: Leslie Day on 10-Oct
Media components: 22 g/L Sodium Chloride, 5 g/L Sodium bicarbonate, 1 g/L Ammonium chloride, 0.14 g/L Potassium phosphate dibasic, 0.0095 g/L Iron (II) sulfate heptahydrate, 0.001 g/L resazurin sodium salt, 0.84 g/L Sodium acetate, 2 g/L casamino acids, 0.5 g/L Dithiothreitol, 0.001 g/L Sodium sulfide nonahydrate, Mc_general_salts (0.335 g/L Potassium Chloride, 2.75 g/L Magnesium chloride hexahydrate, 3.45 g/L Magnesium Sulfate Heptahydrate, 0.105 g/L Calcium chloride), Mc_trace_minerals (0.021 g/L Trisodium citrate dihydrate, 0.005 g/L manganese(II) sulfate dihydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.0001 g/L copper (II) chloride dihydrate, 0.0001 g/L Aluminum potassium sulfate dodecahydrate, 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 28 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Coenzyme F420 hydrogenase	4
Hydrogenases	2
Cobalt-zinc-cadmium resistance	1
Ketoisovalerate oxidoreductase	1
Methionine Salvage	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Universal GTPases	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Ubiquinone and menaquinone biosynthesis
• Methionine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Peptidoglycan biosynthesis
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
di-trans,poly-cis-undecaprenyl phosphate biosynthesis	2	2	1
L-isoleucine biosynthesis V	3	3	1
5'-deoxyadenosine degradation I	3	2	1
ethanol degradation IV	3	1	1
ethanol degradation III	3	1	1
ethanol degradation II	3	1	1
superpathway of acetate utilization and formation	3	1	1
coenzyme B/coenzyme M regeneration I (methanophenazine-dependent)	4	2	1
chitin deacetylation	4	1	1
5'-deoxyadenosine degradation II	4	1	1
polyisoprenoid biosynthesis (E. coli)	5	4	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	2	1
superpathway of bitter acids biosynthesis	18	3	3
lupulone and humulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
coenzyme M biosynthesis I	7	4	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	1	1
reductive glycine pathway of autotrophic CO2 fixation	9	2	1
cis-geranyl-CoA degradation	9	1	1
L-methionine salvage cycle III	11	5	1
L-methionine salvage cycle II (plants)	11	2	1
L-methionine salvage cycle I (bacteria and plants)	12	4	1
glyoxylate assimilation	13	3	1
3-hydroxypropanoate cycle	13	3	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	4	1
superpathway of the 3-hydroxypropanoate cycle	18	3	1