MetaCyc Pathway: Methanobacterium thermoautotrophicum biosynthetic metabolism in Rhodosporidium toruloides IFO0880

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sn-glycerol-1-phosphate dehydrogenase (in reverse):
glycerone phosphate + NAD(P)H + H+sn-glycerol 1-phosphate + NAD(P)+
(EC 1.1.1.261)
No genes
Carbon-monoxide dehydrogenase (ferredoxin) (in reverse):
CO2 + 2 H+ + 2 a reduced ferredoxin [iron-sulfur] cluster→carbon monoxide + 2 an oxidized ferredoxin [iron-sulfur] cluster + H2O
(EC 1.2.7.4; 2.3.3.M4; 2.3.3.M5)
No genes
CO2 + NADPH→formate + NADP+ (EC 1.17.1.10)
No genes
CO2 + a methanofuran + H+ + 2 a reduced ferredoxin [iron-sulfur] cluster→a formylmethanofuran + 2 an oxidized ferredoxin [iron-sulfur] cluster + H2O (EC 1.2.7.12)
No genes
Dimethylallyltranstransferase:
prenyl diphosphate + 3-methylbut-3-en-1-yl diphosphate→geranyl diphosphate + diphosphate
(EC 2.5.1.1)
mRNA_4576 (12944)
mRNA_8135 (16503)
Carbonate dehydratase (in reverse):
CO2 + H2O→hydrogencarbonate + H+
(EC 4.2.1.1)
mRNA_4213 (12581)
mRNA_7775 (16143)
Formylmethanofuran--tetrahydromethanopterin N-formyltransferase:
a formylmethanofuran + tetrahydromethanopterin + H+→5-formyl-tetrahydromethanopterin + a methanofuran
(EC 2.3.1.101)
No genes
Formate--tetrahydrofolate ligase:
formate + ATP + a tetrahydrofolate→an N10-formyltetrahydrofolate + ADP + phosphate
(EC 6.3.4.3)
mRNA_6998 (15366)
Geranyltranstransferase:
geranyl diphosphate + 3-methylbut-3-en-1-yl diphosphate→(2E,6E)-farnesyl diphosphate + diphosphate
(EC 2.5.1.10)
mRNA_4576 (12944)
mRNA_8135 (16503)
Methenyltetrahydromethanopterin cyclohydrolase (in reverse):
5-formyl-tetrahydromethanopterin + H+→5,10-methenyltetrahydromethanopterin + H2O
(EC 3.5.4.27)
No genes
Farnesyltranstransferase:
(2E,6E)-farnesyl diphosphate + 3-methylbut-3-en-1-yl diphosphate→geranylgeranyl diphosphate + diphosphate
(EC 2.5.1.29)
mRNA_8135 (16503)
Methenyltetrahydrofolate cyclohydrolase (in reverse):
an N10-formyltetrahydrofolate + H+→a 5,10-methenyltetrahydrofolate + H2O
(EC 3.5.4.9)
mRNA_4257 (12625)
mRNA_6998 (15366)
Phosphoglycerol geranylgeranyltransferase:
geranylgeranyl diphosphate + sn-glycerol 1-phosphate→3-(O-geranylgeranyl)-sn-glycerol 1-phosphate + diphosphate
(EC 2.5.1.41)
No genes
5,10-methenyltetrahydromethanopterin hydrogenase:
5,10-methenyltetrahydromethanopterin + H2→5,10-methylene-tetrahydromethanopterin + H+
(EC 1.12.98.2)
No genes
Methylenetetrahydrofolate dehydrogenase (NADP(+)) (in reverse):
a 5,10-methenyltetrahydrofolate + NADPH→a 5,10-methylenetetrahydrofolate + NADP+
(EC 1.5.1.5)
mRNA_4257 (12625)
mRNA_6998 (15366)
Geranylgeranylglycerol-phosphate geranylgeranyltransferase:
geranylgeranyl diphosphate + 3-(O-geranylgeranyl)-sn-glycerol 1-phosphate→2,3-bis-O-(geranylgeranyl)-sn-glycerol 1-phosphate + diphosphate
(EC 2.5.1.42)
No genes
5,10-methylene-tetrahydromethanopterin + a reduced factor 420→N5-methyltetrahydromethanopterin + an oxidized factor 420 (EC 1.5.98.2)
No genes
a 5,10-methylenetetrahydrofolate + 2 NADH + 2 an oxidized ferredoxin [iron-sulfur] cluster→a 5-methyltetrahydrofolate + 2 NAD+ + 2 a reduced ferredoxin [iron-sulfur] cluster (EC 1.5.1.M4)
No genes
a 5,10-methylenetetrahydrofolate + NADH + H+→a 5-methyltetrahydrofolate + NAD+ (EC 1.5.1.54)
No genes
Methylenetetrahydrofolate reductase (ferredoxin) (in reverse):
a 5,10-methylenetetrahydrofolate + 2 H+ + 2 a reduced ferredoxin [iron-sulfur] cluster→a 5-methyltetrahydrofolate + 2 an oxidized ferredoxin [iron-sulfur] cluster
(EC 1.5.7.1)
No genes
a 5-methyltetrahydrofolate + a [Co(I) corrinoid Fe-S protein] + H+→a [methyl-Co(III) corrinoid Fe-S protein] + a tetrahydrofolate (EC 2.1.1.258)
No genes
2,3-bis-O-(geranylgeranyl)-sn-glycerol 1-phosphate + 8 NAD(P)H + 8 H+→2,3-bis-O-phytanyl-sn-glycerol 1-phosphate + 8 NAD(P)+ (EC 1.3.1.101)
No genes
2,3-bis-O-(geranylgeranyl)-sn-glycerol 1-phosphate + 16 H+ + 16 a reduced ferredoxin [iron-sulfur] cluster→2,3-bis-O-phytanyl-sn-glycerol 1-phosphate + 16 an oxidized ferredoxin [iron-sulfur] cluster (EC 1.3.7.11)
No genes
N5-methyltetrahydromethanopterin + a [Co(I) corrinoid Fe-S protein] + H+→a [methyl-Co(III) corrinoid Fe-S protein] + tetrahydromethanopterin (EC 2.1.1.245; 2.3.3.M4)
No genes
CDP-archaeol synthase:
2,3-bis-O-(geranylgeranyl)-sn-glycerol 1-phosphate + CTP + H+→unsaturated CDP-archaeol + diphosphate
(EC 2.7.7.67)
No genes
CO-methylating acetyl-CoA synthase (in reverse):
carbon monoxide + a [methyl-Co(III) corrinoid Fe-S protein] + coenzyme A→acetyl-CoA + a [Co(I) corrinoid Fe-S protein] + H+
(EC 2.3.1.169; 2.3.3.M4; 2.3.3.M5)
No genes
CDP-archaeol synthase:
2,3-bis-O-phytanyl-sn-glycerol 1-phosphate + CTP + H+→saturated CDP-archaeol + diphosphate
(EC 2.7.7.67)
No genes
unsaturated CDP-archaeol + L-serine→unsaturated archaetidylserine + CMP + H+ (EC 2.7.8.38)
No genes
Acetyl-CoA C-acyltransferase:
2 acetyl-CoA→acetoacetyl-CoA + coenzyme A
(EC 2.3.1.16; 2.3.1.9)
mRNA_5445 (13813)
mRNA_5687 (14055)
mRNA_6860 (15228)
mRNA_310 (8678)
mRNA_517 (8885)
mRNA_697 (9065)
Pyruvate synthase (in reverse):
acetyl-CoA + CO2 + H+ + 2 a reduced ferredoxin [iron-sulfur] cluster→pyruvate + coenzyme A + 2 an oxidized ferredoxin [iron-sulfur] cluster
(EC 1.2.7.1)
No genes
unsaturated archaetidylserine + H+→unsaturated archaetidylethanolamine + CO2
No genes
saturated CDP-archaeol + L-serine→saturated archaetidylserine + CMP + H+ (EC 2.7.8.38)
No genes
Alanine transaminase (in reverse):
pyruvate + L-glutamate→L-alanine + 2-oxoglutarate
(EC 2.6.1.2)
mRNA_1267 (9635)
Hydroxymethylglutaryl-CoA synthase:
acetoacetyl-CoA + acetyl-CoA + H2O→(S)-3-hydroxy-3-methylglutaryl-CoA + coenzyme A + H+
(EC 2.3.3.10)
mRNA_3754 (12122)
Pyruvate, water dikinase:
pyruvate + ATP + H2O→phosphoenolpyruvate + AMP + 2 H+ + phosphate
(EC 2.7.9.2)
No genes
Pyruvate carboxylase:
hydrogencarbonate + pyruvate + ATP→oxaloacetate + ADP + H+ + phosphate
(EC 6.4.1.1)
mRNA_8262 (16630)
saturated archaetidylserine + H+→saturated archaetidylethanolamine + CO2
No genes
Hydroxymethylglutaryl-CoA reductase (NADPH) (in reverse):
(S)-3-hydroxy-3-methylglutaryl-CoA + 2 NADPH + 2 H+→(R)-mevalonate + coenzyme A + 2 NADP+
(EC 1.1.1.34)
mRNA_1206 (9574)
Phosphopyruvate hydratase (in reverse):
phosphoenolpyruvate + H2O→2-phospho-D-glycerate
(EC 4.2.1.11)
mRNA_4451 (12819)
mRNA_8034 (16402)
mRNA_669 (9037)
Aspartate transaminase (in reverse):
oxaloacetate + L-glutamate→L-aspartate + 2-oxoglutarate
(EC 2.6.1.1)
mRNA_5562 (13930)
mRNA_5913 (14281)
mRNA_7697 (16065)
mRNA_172 (8540)
mRNA_568 (8936)
mRNA_1267 (9635)
Malate dehydrogenase (in reverse):
oxaloacetate + NADH + H+→(S)-malate + NAD+
(EC 1.1.1.37; 1.1.1.38)
mRNA_2246 (10614)
mRNA_2810 (11178)
mRNA_4393 (12761)
mRNA_5549 (13917)
Pyruvate kinase (in reverse):
phosphoenolpyruvate + ADP + H+→pyruvate + ATP
(EC 2.7.1.40)
mRNA_2701 (11069)
mRNA_4634 (13002)
2-phospho-D-glycerate→3-phospho-D-glycerate (EC 5.4.2.12)
mRNA_4025 (12393)
mRNA_1542 (9910)
Fumarate hydratase:
(S)-malate→fumarate + H2O
(EC 4.2.1.2)
mRNA_5633 (14001)
Mevalonate kinase:
(R)-mevalonate + ATP→(R)-5-phosphomevalonate + ADP + H+
(EC 2.7.1.36)
mRNA_390 (8758)
Phosphoenolpyruvate carboxylase (in reverse):
hydrogencarbonate + phosphoenolpyruvate→oxaloacetate + phosphate
(EC 4.1.1.31)
No genes
Glyceraldehyde-3-phosphate dehydrogenase (ferredoxin) (in reverse):
3-phospho-D-glycerate + 3 H+ + 2 a reduced ferredoxin [iron-sulfur] cluster→D-glyceraldehyde 3-phosphate + 2 an oxidized ferredoxin [iron-sulfur] cluster + H2O
(EC 1.2.7.6)
No genes
Phosphomevalonate kinase:
(R)-5-phosphomevalonate + ATP→(R)-mevalonate diphosphate + ADP
(EC 2.7.4.2)
mRNA_334 (8702)
fumarate[in] + a menaquinol→succinate[in] + a menaquinone (EC 1.3.5.4)
No genes
Diphosphomevalonate decarboxylase:
(R)-mevalonate diphosphate + ATP→3-methylbut-3-en-1-yl diphosphate + CO2 + ADP + phosphate
(EC 4.1.1.33)
mRNA_3542 (11910)
Succinate--CoA ligase (ADP-forming):
succinate + ATP + coenzyme A→succinyl-CoA + ADP + phosphate
(EC 6.2.1.5)
mRNA_7599 (15967)
mRNA_7776 (16144)
Triose-phosphate isomerase:
D-glyceraldehyde 3-phosphate→glycerone phosphate
(EC 5.3.1.1)
mRNA_6808 (15176)
mRNA_7700 (16068)
mRNA_8276 (16644)
mRNA_932 (9300)
2-oxoglutarate synthase (in reverse):
succinyl-CoA + CO2 + H+ + 2 a reduced ferredoxin [iron-sulfur] cluster→2-oxoglutarate + coenzyme A + 2 an oxidized ferredoxin [iron-sulfur] cluster
(EC 1.2.7.3)
No genes
Fructose-bisphosphate aldolase (in reverse):
glycerone phosphate + D-glyceraldehyde 3-phosphate→β-D-fructofuranose 1,6-bisphosphate
(EC 4.1.2.13)
mRNA_7052 (15420)
Isopentenyl-diphosphate Delta-isomerase:
3-methylbut-3-en-1-yl diphosphate→prenyl diphosphate
(EC 5.3.3.2)
mRNA_7835 (16203)
ADP-specific phosphofructokinase (in reverse):
β-D-fructofuranose 1,6-bisphosphate + AMP + H+→β-D-fructofuranose 6-phosphate + ADP
(EC 2.7.1.146)
No genes
Glucose-6-phosphate isomerase (in reverse):
β-D-fructofuranose 6-phosphate→D-glucopyranose 6-phosphate
(EC 5.3.1.9)
mRNA_1221 (9589)

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Candidate genes for each reaction are identified from best hits to MetaCyc; by matching EC numbers (which are assigned by TIGRFam, SEED, or best hits to KEGG); or by matching SEED roles to KEGG reactions to MetaCyc reactions. See the "Protein" tab of each gene for more information