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Home , Coenzyme F420, List of enzymes, Selenate reductase, Sulfhydrogenase, Sulfite dehydrogenase, Sulfite oxidase

Supplemental Material: Annu. Rev. Microbiol. 2016. 70:45–62 doi: 10.1146/annurev-micro-102215-095521 The Role of Microbial Electron Transfer in the Coevolution of the Biosphere and Geosphere Jelen, Giovannelli, and Falkowski

Supplemental Table 1. Complete list of the 392 EC1 homologs identified through a manually refined search of all KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) pathways directly involved in reactions of biogeochemical interest.

Pathway Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

Cytochrome c type c type A Ammonification no EC K02569 protein NapC protein NapC

Ferredoxin-Type Ferredoxin-Type A Ammonification no EC K02573 ferredoxin protein NapG protein NapG

Ferredoxin-Type Ferredoxin-Type A Ammonification no EC K02574 ferredoxin protein NapH protein NapH

nitrate alpha , A Ammonification 1.7.99.4 K00370 subunit 4Fe-4S

nitrate reductase beta A Ammonification nitrate reductase 1.7.99.4 K00371 4Fe-4S, 3Fe-4S subunit

nitrate reductase A Ammonification nitrate reductase 1.7.99.4 K00374 heme gamma subunit

periplasmic nitrate molybdopterin, A Ammonification nitrate reductase 1.7.99.4 K02567 reductase NapA 4Fe-4S

cytochrome c-type A Ammonification nitrate reductase 1.7.99.4 K02568 heme protein NapB

nitrite reductase A Ammonification (cytochrome; 1.7.2.2 K03385 heme (cytochrome c-552) ammonia-forming)

nitrite reductase nitrite reductase 4Fe-4S, heme, A Ammonification 1.7.1.15 K00362 (NADH) (NADH) large subunit flavoprotein

nitrite reductase nitrite reductase A Ammonification 1.7.1.15 K00363 2Fe-2S, NAD (NADH) (NADH) small subunit

nitrite reductase cytochrome c nitrite A Ammonification 1.7.1.15 K15876 heme (NADH) reductase small subunit

Nitrogen ferredoxin-nitrate ferredoxin-nitrate molybdopterin, A 1.7.7.2 K00367 Assimilation reductase reductase 4Fe-4S

Nitrogen ferredoxin-nitrite ferredoxin-nitrite A 1.7.7.1 K00366 4Fe-4S, heme Assimilation reductase reductase nitrate reductase Nitrogen nitrate reductase molybdopterin, A 1.7.1.1 K10534 (NAD(P)H)(also Assimilation (NADH) heme, flavoprotein 1.7.1.2 and 1.7.1.3) Nitrogen nitrite reductase nitrite reductase 4Fe-4S, 2Fe-2S, A 1.7.1.4 K17877 Assimilation [NAD(P)H] (NAD(P)H) heme, flavoprotein photosystem P840 Anoxygenic Type I AP 1.97.1.12 K08940 reaction center large Photosynthesis Photosystem subunit Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology photosystem P840 Anoxygenic Type I AP 1.97.1.12 K08941 reaction center iron- Photosynthesis Photosystem protein photosystem P840 Anoxygenic Type I AP 1.97.1.12 K08942 reaction center heme Photosynthesis Photosystem cytochrome c551 photosystem P840 Anoxygenic Type I AP 1.97.1.12 K08943 reaction center protein Photosynthesis Photosystem PscD Anoxygenic Type II photosynthetic reaction AP no EC K08928 magnesium, iron Photosynthesis Photosystem center L subunit

Anoxygenic Type II photosynthetic reaction AP no EC K08929 magnesium, iron Photosynthesis Photosystem center M subunit magnesium, Anoxygenic Type II photosynthetic reaction AP no EC K13991 quinone, Photosynthesis Photosystem center H subunit ubiquinone Anoxygenic Type II photosynthetic reaction AP no EC K13994 Photosynthesis Photosystem center PufX protein

photosynthetic reaction Anoxygenic Type II AP no EC K13992 center cytochrome c heme Photosynthesis Photosystem subunit

Oxidative cytochrome-c cytochrome c AR 1.9.3.1 K00404 heme, copper Phosphorylation oxidase cbb3-type subunit I

Oxidative cytochrome-c AR 1.9.3.1 K00405 Phosphorylation oxidase cbb3-type subunit II

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K00406 heme Phosphorylation oxidase cbb3-type subunit III

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K00407 Phosphorylation oxidase cbb3-type subunit IV

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02256 heme, copper Phosphorylation oxidase subunit 1

Oxidative cytochrome-c cytochrome c oxidase copper, AR 1.9.3.1 K02261 Phosphorylation oxidase subunit 2 magnesium

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02262 Phosphorylation oxidase subunit 3

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02263 Phosphorylation oxidase subunit 4

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02264 heme Phosphorylation oxidase subunit 5a

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02265 zinc Phosphorylation oxidase subunit 5b

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02266 Phosphorylation oxidase subunit 6a

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02267 Phosphorylation oxidase subunit 6b Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02268 Phosphorylation oxidase subunit 6c

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02269 Phosphorylation oxidase subunit 7

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02270 Phosphorylation oxidase subunit 7a

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02271 Phosphorylation oxidase subunit 7b

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02272 Phosphorylation oxidase subunit 7c

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02273 Phosphorylation oxidase subunit 8

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02274 heme, copper Phosphorylation oxidase subunit I

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02275 heme, copper Phosphorylation oxidase subunit II

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02276 Phosphorylation oxidase subunit III

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K02277 heme, copper Phosphorylation oxidase subunit IV

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K15408 heme, copper Phosphorylation oxidase subunit I+III

Oxidative cytochrome-c cytochrome c oxidase AR 1.9.3.1 K15862 Phosphorylation oxidase cbb3-type subunit I/II 3- 3- 3-hydroxypropionate hydroxypropionate AU Hydroxypropion 1.1.1.298 K15039 dehydrogenase ate bi-cycle (NADP+) (NADP+) 3- malonyl-CoA reductase 3- hydroxypropionate / 3-hydroxypropionate AU Hydroxypropion 1.2.1.75 K14468 dehydrogenase dehydrogenase ate bi-cycle (NADP+) (NADP+)

acrylyl-CoA reductase (NADPH) / 3- 3- acryloyl-coenzyme hydroxypropionyl-CoA AU Hydroxypropion 1.3.1.84 K14469 A reductase dehydratase / 3- ate bi-cycle hydroxypropionyl-CoA synthetase

3- acryloyl-coenzyme acryloyl- AU Hydroxypropion 1.3.1.84 K15020 zinc, NAD(P) A reductase reductase ate bi-cycle 3- fumarate reductase Heme, AU Hydroxypropion fumarate reductase 1.3.5.4 K00244 flavoprotein subunit flavoprotein ate bi-cycle Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology 3- fumarate reductase 4Fe-4S, 2Fe-2S, AU Hydroxypropion fumarate reductase 1.3.5.4 K00245 iron-sulfur subunit 3Fe-4S ate bi-cycle 3- fumarate reductase AU Hydroxypropion fumarate reductase 1.3.5.4 K00246 heme subunit C ate bi-cycle 3- fumarate reductase AU Hydroxypropion fumarate reductase 1.3.5.4 K00247 subunit D ate bi-cycle malonyl- 3- malonyl-CoA/succinyl- CoA/succinyl-CoA 1.2.1.75; NADP, NAD, AU Hydroxypropion K15017 CoA reductase reductase 1.2.1.76 Mg(2+), Mn(2+) ate bi-cycle (NADPH) (NADPH) 3- succinate succinate AU Hydroxypropion 1.3.5.1 K00239 dehydrogenase FAD, Flavoprotein dehydrogenase ate bi-cycle flavoprotein subunit 3- succinate succinate 4Fe-4S, 2Fe-2S, AU Hydroxypropion 1.3.5.1 K00240 dehydrogenase iron- dehydrogenase 3Fe-4S ate bi-cycle sulfur subunit succinate 3- AU Hydroxypropion 1.3.5.1 K00241 heme dehydrogenase cytochrome b556 ate bi-cycle subunit succinate 3- succinate dehydrogenase AU Hydroxypropion 1.3.5.1 K00242 heme dehydrogenase membrane anchor ate bi-cycle subunit Carbon fixation fumarate reductase fumarate reductase AU pathways in 1.3.4.1 K18209 (CoM/CoB) (CoM/CoB) subunit A prokaryotes Carbon fixation fumarate reductase fumarate reductase AU pathways in 1.3.4.1 K18210 (CoM/CoB) (CoM/CoB) subunit B prokaryotes Carbon fixation NADH-dependent fumarate reductase AU pathways in 1.3.1.6 K18556 fumarate reductase (NADH) prokaryotes subunit A Carbon fixation NADH-dependent fumarate reductase AU pathways in 1.3.1.6 K18557 fumarate reductase (NADH) prokaryotes subunit B Dicarboxylate- 3-hydroxyacyl- enoyl-CoA hydratase / AU hydroxybutyrate CoA 1.1.1.35 K15016 3-hydroxyacyl-CoA cycle dehydrogenase dehydrogenase

3-hydroxyacyl-CoA Dicarboxylate- 3-hydroxyacyl- dehydrogenase / enoyl- AU hydroxybutyrate CoA 1.1.1.35 K01782 CoA hydratase / 3- FAD, NAD cycle dehydrogenase hydroxybutyryl-CoA epimerase

3-hydroxyacyl-CoA dehydrogenase / enoyl- Dicarboxylate- 3-hydroxyacyl- CoA hydratase / 3- AU hydroxybutyrate CoA 1.1.1.35 K01825 FAD, NAD hydroxybutyryl-CoA cycle dehydrogenase epimerase / enoyl-CoA Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology Dicarboxylate- 3-hydroxyacyl- 3-hydroxyacyl-CoA AU hydroxybutyrate CoA 1.1.1.35 K07516 dehydrogenase cycle dehydrogenase Dicarboxylate- FAD, fumarate reductase AU hydroxybutyrate fumarate reductase 1.3.5.4 K00244 Flavoprotein, flavoprotein subunit cycle heme, Fe(3+) Dicarboxylate- fumarate reductase 4Fe-4S, 2Fe-2S, AU hydroxybutyrate fumarate reductase 1.3.5.4 K00245 iron-sulfur subunit 3Fe-4S cycle Dicarboxylate- fumarate reductase AU hydroxybutyrate fumarate reductase 1.3.5.4 K00246 heme subunit C cycle Dicarboxylate- fumarate reductase AU hydroxybutyrate fumarate reductase 1.3.5.4 K00247 subunit D cycle Dicarboxylate- malate AU hydroxybutyrate 1.1.1.37 K00024 NAD, NADP dehydrogenase cycle malonyl- Dicarboxylate- malonyl-CoA/succinyl- CoA/succinyl-CoA 1.2.1.75 NADP, NAD, AU hydroxybutyrate K15017 CoA reductase reductase 1.2.1.76 Mg(2+), Mn(2+) cycle (NADPH) (NADPH) Dicarboxylate- pyruvate pyruvate ferredoxin AU hydroxybutyrate ferredoxin 1.2.7.1 K00169 , alpha cycle oxidoreductase subunit [EC:]

Dicarboxylate- pyruvate pyruvate ferredoxin AU hydroxybutyrate ferredoxin 1.2.7.1 K00170 oxidoreductase, beta 4Fe-4S cycle oxidoreductase subunit [EC:1.2.7.1]

Dicarboxylate- pyruvate pyruvate ferredoxin AU hydroxybutyrate ferredoxin 1.2.7.1 K00171 oxidoreductase, delta 4Fe-4S cycle oxidoreductase subunit [EC:1.2.7.1]

Dicarboxylate- pyruvate pyruvate ferredoxin AU hydroxybutyrate ferredoxin 1.2.7.1 K00172 oxidoreductase, gamma 4Fe-4S cycle oxidoreductase subunit [EC:1.2.7.1] Dicarboxylate- pyruvate- putative pyruvate- AU hydroxybutyrate flavodoxin 1.2.7.- K03737 flavodoxin 4Fe-4S cycle oxidoreductase oxidoreductase Dicarboxylate- succinate succinate AU hydroxybutyrate 1.3.5.1 K00239 dehydrogenase FAD, Flavoprotein dehydrogenase cycle flavoprotein subunit Dicarboxylate- succinate succinate 4Fe-4S, 2Fe-2S, AU hydroxybutyrate 1.3.5.1 K00240 dehydrogenase iron- dehydrogenase 3Fe-4S cycle sulfur subunit succinate Dicarboxylate- succinate dehydrogenase AU hydroxybutyrate 1.3.5.1 K00241 heme dehydrogenase cytochrome b556 cycle subunit succinate Dicarboxylate- succinate dehydrogenase AU hydroxybutyrate 1.3.5.1 K00242 heme dehydrogenase membrane anchor cycle subunit Dicarboxylate- succinate succinate semialdehyde Zinc, NADP, AU hydroxybutyrate semialdehyde 1.1.1.- K14465 reductase (NADPH) NAD cycle reductase Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology Dicarboxylate- succinyl-CoA AU hydroxybutyrate 1.2.1.76 K15038 succinyl-CoA reductase reductase cycle Hydroxypropion 3-hydroxyacyl- enoyl-CoA hydratase / ate- AU CoA 1.1.1.35 K15016 3-hydroxyacyl-CoA hydroxybutylate dehydrogenase dehydrogenase cycle

3-hydroxyacyl-CoA Hydroxypropion 3-hydroxyacyl- dehydrogenase / enoyl- ate- AU CoA 1.1.1.35 K01782 CoA hydratase / 3- FAD, NAD hydroxybutylate dehydrogenase hydroxybutyryl-CoA cycle epimerase

3-hydroxyacyl-CoA Hydroxypropion dehydrogenase / enoyl- 3-hydroxyacyl- ate- CoA hydratase / 3- AU CoA 1.1.1.35 K01825 FAD, NAD hydroxybutylate hydroxybutyryl-CoA dehydrogenase cycle epimerase / enoyl-CoA isomerase

Hydroxypropion 3-hydroxyacyl- ate- 3-hydroxyacyl-CoA AU CoA 1.1.1.35 K07516 hydroxybutylate dehydrogenase dehydrogenase cycle Hydroxypropion 3- malonyl-CoA reductase 1.2.1.76; ate- hydroxypropionate / 3-hydroxypropionate AU 1.2.1.75; K14468 hydroxybutylate dehydrogenase dehydrogenase 1.1.1.298 cycle (NADP+) (NADP+) Hydroxypropion 3- 1.2.1.76; 3-hydroxypropionate ate- hydroxypropionate AU 1.2.1.75; K15039 dehydrogenase hydroxybutylate dehydrogenase 1.1.1.298 (NADP+) cycle (NADP+)

acrylyl-CoA reductase Hydroxypropion (NADPH) / 3- ate- acryloyl-coenzyme hydroxypropionyl-CoA AU 1.3.1.84 K14469 hydroxybutylate A reductase dehydratase / 3- cycle hydroxypropionyl-CoA synthetase

Hydroxypropion ate- acryloyl-coenzyme acryloyl-coenzyme A Zinc, NADP, AU 1.3.1.84 K15020 hydroxybutylate A reductase reductase NAD cycle Hydroxypropion malonyl- malonyl-CoA/succinyl- ate- CoA/succinyl-CoA NADP, NAD, AU 1.2.1.75 K15017 CoA reductase hydroxybutylate reductase Mg(2+), Mn(2+) (NADPH) cycle (NADPH) Hydroxypropion succinate succinate semialdehyde ate- Zinc, NADP, AU semialdehyde 1.1.1.- K14465 reductase (NADPH) hydroxybutylate NAD reductase [EC:1.1.1.-] cycle Hydroxypropion ate- succinyl-CoA AU 1.2.1.76 K15038 succinyl-CoA reductase hydroxybutylate reductase cycle Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology Reductive acetyl-CoA carbon-monoxide carbon-monoxide 1.2.99.2; 4Fe-4S, nickel, AU pathway (Wood- K00198 dehydrogenase catalytic dehydrogenase 1.2.7.4 Ni-Fe-S Ljungdahl subunit pathway) Reductive acetyl-CoA carbon-monoxide 1.2.99.2; AU pathway (Wood- no KO dehydrogenase 1.2.7.4 Ljungdahl pathway) Reductive acetyl-CoA 4Fe-4S, 2Fe-2S, formate AU pathway (Wood- 1.2.1.43 K05299 Fe(3+), NADP, dehydrogenase alpha subunit Ljungdahl NAD pathway) Reductive acetyl-CoA formate dehydrogenase formate 4Fe-4S, Fe(3+), AU pathway (Wood- 1.2.1.43 K15022 beta subunit dehydrogenase Flavoprotein Ljungdahl [EC:1.2.1.43] pathway) Reductive methylenetetrahydr acetyl-CoA methylenetetrahydrofol ofolate AU pathway (Wood- 1.5.1.5 K01491 ate dehydrogenase NADP, NAD dehydrogenase Ljungdahl (NADP+) (NADP+) pathway) Reductive acetyl-CoA methylenetetrahydr methylenetetrahydrofol AU pathway (Wood- ofolate reductase 1.5.1.20 K00297 Flavoprotein ate reductase (NADPH) Ljungdahl (NADPH) pathway) 2-oxoglutarate Reductive citrate 2-oxoglutarate ferredoxin AU cycle (Arnon- ferredoxin 1.2.7.3 K00174 oxidoreductase subunit Buchanan cycle) oxidoreductas alpha 2-oxoglutarate Reductive citrate 2-oxoglutarate ferredoxin Mg(2+), AU cycle (Arnon- ferredoxin 1.2.7.3 K00175 oxidoreductase subunit Magnesium Buchanan cycle) oxidoreductas beta 2-oxoglutarate Reductive citrate 2-oxoglutarate ferredoxin AU cycle (Arnon- ferredoxin 1.2.7.3 K00177 oxidoreductase subunit Buchanan cycle) oxidoreductas gamma 2-oxoglutarate Reductive citrate 2-oxoglutarate ferredoxin AU cycle (Arnon- ferredoxin 1.2.7.3 K00176 4Fe-4S oxidoreductase subunit Buchanan cycle) oxidoreductas delta Reductive citrate fumarate reductase Flavoprotein, AU cycle (Arnon- fumarate reductase 1.3.5.4 K00244 flavoprotein subunit heme, Fe(3+) Buchanan cycle) 4Fe-4S, 2Fe-2S, Reductive citrate 3Fe-4S, Iron- fumarate reductase AU cycle (Arnon- fumarate reductase 1.3.5.4 K00245 sulfur, iron-sulfur, iron-sulfur subunit Buchanan cycle) Iron, iron, Metal- binding Reductive citrate fumarate reductase AU cycle (Arnon- fumarate reductase 1.3.5.4 K00246 heme subunit C Buchanan cycle) Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology Reductive citrate fumarate reductase AU cycle (Arnon- fumarate reductase 1.3.5.4 K00247 subunit D Buchanan cycle) Reductive citrate isocitrate isocitrate Mg(2+), Mn(2+, AU cycle (Arnon- 1.1.1.42 K00031 dehydrogenase dehydrogenase NADP, NAD Buchanan cycle) Reductive citrate malate AU cycle (Arnon- 1.1.1.37 K00024 malate dehydrogenase NAD, NADP dehydrogenase Buchanan cycle) Reductive citrate putative pyruvate- putative pyruvate- AU cycle (Arnon- flavodoxin 1.2.7.- K03737 flavodoxin 4Fe-4S Buchanan cycle) oxidoreductase oxidoreductase

Reductive citrate pyruvate pyruvate ferredoxin AU cycle (Arnon- ferredoxin 1.2.7.1 K00169 oxidoreductase, alpha Buchanan cycle) oxidoreductase subunit

Reductive citrate pyruvate pyruvate ferredoxin AU cycle (Arnon- ferredoxin 1.2.7.1 K00170 oxidoreductase, beta 4Fe-4S Buchanan cycle) oxidoreductase subunit

Reductive citrate pyruvate pyruvate ferredoxin AU cycle (Arnon- ferredoxin 1.2.7.1 K00171 oxidoreductase, delta 4Fe-4S Buchanan cycle) oxidoreductase subunit

Reductive citrate pyruvate pyruvate ferredoxin AU cycle (Arnon- ferredoxin 1.2.7.1 K00172 oxidoreductase, gamma 4Fe-4S Buchanan cycle) oxidoreductase subunit Reductive citrate succinate succinate AU cycle (Arnon- 1.3.5.1 K00239 dehydrogenase FAD, Flavoprotein dehydrogenase Buchanan cycle) flavoprotein subunit Reductive citrate succinate succinate 4Fe-4S, 2Fe-2S, AU cycle (Arnon- 1.3.5.1 K00240 dehydrogenase iron- dehydrogenase 3Fe-4S Buchanan cycle) sulfur subunit succinate Reductive citrate succinate dehydrogenase AU cycle (Arnon- 1.3.5.1 K00241 heme dehydrogenase cytochrome b556 Buchanan cycle) subunit succinate Reductive citrate succinate dehydrogenase AU cycle (Arnon- 1.3.5.1 K00242 heme dehydrogenase membrane anchor Buchanan cycle) subunit Reductive glyceraldehyde 3- glyceraldehyde 3- pentose AU phosphate 1.2.1.12 K00134 phosphate NAD, NADP phosphate cycle dehydrogenase dehydrogenase (Calvin cycle) Reductive glyceraldehyde-3- glyceraldehyde-3- NADP, NAD, pentose phosphate phosphate AU 1.2.1.59 K00150 Mg(2+), phosphate cycle dehydrogenase dehydrogenase Magnesium (Calvin cycle) (NAD(P)) (NAD(P)) glyceraldehyde-3- glyceraldehyde-3- Reductive phosphate phosphate pentose AU dehydrogenase 1.2.1.13 K05298 dehydrogenase NADP, NAD phosphate cycle (NADP+) (NADP+) (Calvin cycle) (phosphorylating) (phosphorylating) Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

Cytochrome c type Cytochrome c type D Denitrification no EC K02569 Heme protein NapC protein NapC

Ferredoxin-Type Ferredoxin-Type D Denitrification no EC K02573 Ferredoxin protein NapG protein NapG

Ferredoxin-Type Ferredoxin-Type D Denitrification no EC K02574 Ferredoxin protein NapH protein NapH

assimilatory nitrate D Denitrification nitrate reductase 1.7.99.4 K00360 reductase electron transfer subunit

nitrate reductase alpha molybdopterin, D Denitrification nitrate reductase 1.7.99.4 K00370 subunit 4Fe-4S

nitrate reductase beta D Denitrification nitrate reductase 1.7.99.4 K00371 4Fe-4S, 3Fe-4S subunit assimilatory nitrate molybdopterin, D Denitrification nitrate reductase 1.7.99.4 K00372 reductase catalytic 4Fe-4S subunit nitrate reductase D Denitrification nitrate reductase 1.7.99.4 K00374 heme gamma subunit

periplasmic nitrate molybdopterin, D Denitrification nitrate reductase 1.7.99.4 K02567 reductase NapA 4Fe-4S

cytochrome c-type D Denitrification nitrate reductase 1.7.99.4 K02568 heme protein NapB nitric oxide nitric oxide reductase D Denitrification reductase 1.7.2.5 K04561 heme subunit B (cytochrome c) nitric oxide D Denitrification reductase 1.7.5.2 no KO (menaquinol) nitrite reductase nitrite reductase D Denitrification (cytochrome; 1.7.2.2 K03385 heme (cytochrome c-552) ammonia-forming)

nitrite reductase nitrite reductase D Denitrification (cytochrome; 1.7.2.2 K05904 (cytochrome c-552) ammonia-forming)

nitrite reductase nitric oxide reductase D Denitrification (cytochrome; 1.7.2.2 K02305 heme subunit C ammonia-forming)

nitrite reductase nitrite reductase 4Fe-4S, heme, D Denitrification 1.7.1.15 K00362 (NADH) (NADH) large subunit flavoprotein

nitrite reductase nitrite reductase D Denitrification 1.7.1.15 K00363 2Fe-2S, NAD (NADH) (NADH) small subunit

nitrite reductase cytochrome c nitrite D Denitrification 1.7.1.15 K15876 heme (NADH) reductase small subunit Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

nitrite reductase nitrite reductase (NO- Cu(2+), FAD, D Denitrification 1.7.2.1 K00368 (NO-forming) forming) Flavoprotein nitrite reductase (NO- nitrite reductase forming) / D Denitrification 1.7.2.1 K15864 heme (NO-forming) nitrous-oxide D Denitrification 1.7.2.4 K00376 nitrous-oxide reductase copper reductase Fatty acid acyl-CoA acyl-CoA H 1.3.8.7 K00249 FAD, Flavoprotein degradation dehydrogenase dehydrogenase long-chain acyl- Fatty acid long-chain-acyl-CoA H CoA 1.3.8.8 K00255 FAD, Flavoprotein degradation dehydrogenase dehydrogenase very-long-chain Fatty acid very long chain acyl- H acyl-CoA 1.3.8.9 K09479 FAD, Flavoprotein degradation CoA dehydrogenase dehydrogenase Fatty acid 3-hydroxyacyl- 3-hydroxyacyl-CoA H degradation/Tolu CoA 1.1.1.35 K00022 NAD dehydrogenase ene degradation dehydrogenase

3-hydroxyacyl-CoA Fatty acid 3-hydroxyacyl- dehydrogenase / enoyl- H degradation/Tolu CoA 1.1.1.35 K01782 CoA hydratase / 3- FAD, NAD ene degradation dehydrogenase hydroxybutyryl-CoA epimerase

3-hydroxyacyl-CoA dehydrogenase / enoyl- Fatty acid 3-hydroxyacyl- CoA hydratase / 3- H degradation/Tolu CoA 1.1.1.35 K01825 FAD, NAD hydroxybutyryl-CoA ene degradation dehydrogenase epimerase / enoyl-CoA isomerase

enoyl-CoA hydratase / Fatty acid 3-hydroxyacyl- 3-hydroxyacyl-CoA H degradation/Tolu CoA 1.1.1.35 K07514 dehydrogenase / 3,2- NAD ene degradation dehydrogenase trans-enoyl-CoA isomerase

Fatty acid 3-hydroxyacyl- 3-hydroxyacyl-CoA H degradation/Tolu CoA 1.1.1.35 K07516 dehydrogenase ene degradation dehydrogenase

2- Fatty acid 3-hydroxyacyl- [hydroxy(phenyl)methy H degradation/Tolu CoA 1.1.1.35 K07547 l]-succinyl-CoA ene degradation dehydrogenase dehydrogenase BbsC subunit 2- Fatty acid 3-hydroxyacyl- [hydroxy(phenyl)methy H degradation/Tolu CoA 1.1.1.35 K07548 l]-succinyl-CoA ene degradation dehydrogenase dehydrogenase BbsD subunit Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

3-hydroxyacyl-CoA Fatty acid 3-hydroxyacyl- dehydrogenase / 3- H degradation/Tolu CoA 1.1.1.35 K08683 hydroxy-2- NAD ene degradation dehydrogenase methylbutyryl-CoA dehydrogenase

Fatty acid 3-hydroxyacyl- enoyl-CoA hydratase/3- H degradation/Tolu CoA 1.1.1.35 K10527 hydroxyacyl-CoA NAD ene degradation dehydrogenase dehydrogenase

3-hydroxyacyl-CoA Fatty acid 3-hydroxyacyl- dehydrogenase / H degradation/Tolu CoA 1.1.1.35 K12405 3a,7a,12a-trihydroxy- NAD ene degradation dehydrogenase 5b-cholest-24-enoyl- CoA hydratase

Fatty acid 3-hydroxyacyl- enoyl-CoA hydratase / H degradation/Tolu CoA 1.1.1.35 K15016 3-hydroxyacyl-CoA ene degradation dehydrogenase dehydrogenase

Glycerophosphol H reductase 1.1.1.21 K00011 aldehyde reductase NADP, NAD ipid metabolism glycerol 2- glycerol 2- Glycerophosphol H dehydrogenase 1.1.1.156 K18097 dehydrogenase NADP, NAD ipid metabolism (NADP+) (NADP+) Glycerophosphol glycerol H 1.1.1.6 K00005 zinc, NAD ipid metabolism dehydrogenase glycerol-3- Glycerophosphol phosphate glycerol-3-phosphate H 1.1.1.8 K00006 NAD ipid metabolism dehydrogenase dehydrogenase (NAD+) (NAD+) Glycerophosphol H glycolate oxidase 1.1.3.15 K00104 glycolate oxidase FAD, Flavoprotein ipid metabolism

Glycerophosphol (S)-2-hydroxy-acid Flavoprotein, H glycolate oxidase 1.1.3.15 K11517 ipid metabolism oxidase FMN FAD, Glycerophosphol thioredoxin- Flavoprotein, H 1.8.1.9 K00384 ipid metabolism reductase (NADPH) NADP, NAD, Selenocysteine alcohol Glycolysis / NADP, NAD, H dehydrogenase 1.1.1.2 K00002 Gluconeogenesis (NADP+) Zinc (NADP+) glyceraldehyde 3- Glycolysis / glyceraldehyde-3- H 1.2.1.12 K00134 phosphate NAD, NADP Gluconeogenesis P-dehydrogenase dehydrogenase glyceraldehyde-3- Glycolysis / glyceraldehyde-3- phosphate H 1.2.1.12 K10705 NAD Gluconeogenesis P-dehydrogenase dehydrogenase, spermatogenic glyceraldehyde-3- glyceraldehyde-3- phosphate NADP, NAD, Glycolysis / phosphate H dehydrogenase 1.2.1.59 K00150 Mg(2+), Gluconeogenesis dehydrogenase (NAD(P)) Magnesium (NAD(P)) (phosphorylating) Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

malonate-semialdehyde glyceraldehyde-3- dehydrogenase phosphate Glycolysis / (acetylating) / H dehydrogenase 1.2.1.59 K00140 NAD Gluconeogenesis methylmalonate- (NAD(P)) semialdehyde (phosphorylating) dehydrogenase

NAD-reducing Glycolysis / hydrogen Ni(2+), FMN, H 1.12.1.2 K00436 large Gluconeogenesis dehydrogenase NAD subunit Glycolysis / L-lactate L-lactate H 1.1.1.27 K00016 NAD Gluconeogenesis dehydrogenase dehydrogenase Glycolysis/Gluc oneogenesis/Fatt alcohol H 1.1.1.1 K00001 alcohol dehydrogenase Zinc, NAD y acid dehydrogenase degradation

Glycolysis/Gluc S- oneogenesis/Fatt alcohol (hydroxymethyl)glutath H 1.1.1.1 K00121 Zinc, NAD, FAD y acid dehydrogenase ione dehydrogenase / degradation alcohol dehydrogenase

Glycolysis/Gluc acetaldehyde oneogenesis/Fatt alcohol H 1.1.1.1 K04072 dehydrogenase / Iron, NAD y acid dehydrogenase alcohol dehydrogenase degradation Glycolysis/Gluc oneogenesis/Fatt alcohol H 1.1.1.1 K11440 NAD y acid dehydrogenase degradation Glycolysis/Gluc oneogenesis/Fatt alcohol alcohol dehydrogenase H 1.1.1.1 K13951 Zinc, NAD y acid dehydrogenase 1/7 degradation Glycolysis/Gluc oneogenesis/Fatt alcohol alcohol dehydrogenase H 1.1.1.1 K13952 Zinc, NAD y acid dehydrogenase 6 degradation Glycolysis/Gluc oneogenesis/Fatt alcohol alcohol dehydrogenase, H 1.1.1.1 K13953 Zinc, NAD y acid dehydrogenase propanol-preferring degradation Glycolysis/Gluc oneogenesis/Fatt alcohol H 1.1.1.1 K13954 alcohol dehydrogenase NAD, Fe(2+), zinc y acid dehydrogenase degradation Glycolysis/Gluc oneogenesis/Fatt alcohol alcohol dehydrogenase H 1.1.1.1 K13980 Zinc, NAD y acid dehydrogenase 4 degradation Glycolysis/Gluc oneogenesis/Fatt alcohol alcohol dehydrogenase H 1.1.1.1 K18857 y acid dehydrogenase class-P degradation Glycolysis/Gluc aldehyde NAD, NADP, aldehyde H oneogenesis/Fatt dehydrogenase 1.2.1.3 K00128 Potassium, dehydrogenase (NAD+) y acid (NAD+) Mg(2+), Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology degradation Magnesium

Glycolysis/Gluc aldehyde aldehyde oneogenesis/Fatt H dehydrogenase 1.2.1.3 K00149 dehydrogenase family 9 NAD y acid (NAD+) member A1 degradation Glycolysis/Gluc aldehyde aldehyde oneogenesis/Fatt H dehydrogenase 1.2.1.3 K14085 dehydrogenase family 7 NAD y acid (NAD+) member A1 degradation methanol Glycolysis/Gluc quinone, Metal- H oneogenesis/Met dehydrogenase 1.1.2.7 K14028 (cytochrome c) subunit binding hane metabolism (cytochrome c) 1 methanol Glycolysis/Gluc methanol dehydrogenase H oneogenesis/Met dehydrogenase 1.1.2.7 K14029 (cytochrome c) subunit hane metabolism (cytochrome c) 2 glyceraldehyde-3- glyceraldehyde-3- Glycolysis/Gluc phosphate phosphate H oneogenesis/Pent 1.2.1.9 K00131 NADP, NAD dehydrogenase dehydrogenase ose Phosphate (NADP+) (NADP+) Glycolysis/Gluc FAD, dihydrolipoyl dihydrolipoamide H oneogenesis/TC 1.8.1.4 K00382 Flavoprotein, dehydrogenase dehydrogenase A Cycle NAD, quinone pyruvate thiamine Glycolysis/Gluc E1 diphosphate, H oneogenesis/TC 1.2.4.1 K00161 dehydrogenase component alpha Mg(2+), A Cycle subunit Magnesium Glycolysis/Gluc pyruvate Pyruvate thiamine H oneogenesis/TC 1.2.4.1 K00162 dehydrogenase E1 dehydrogenase diphosphate A Cycle component beta subunit Mg(2+), Glycolysis/Gluc pyruvate Pyruvate Magnesium, H oneogenesis/TC 1.2.4.1 K00163 dehydrogenase E1 dehydrogenase thiamine A Cycle component diphosphate Glycolysis/Gluc oneogenesis/TC pyruvate ferredoxin Pyruvate H A 1.2.7.1 K00169 oxidoreductase, alpha Oxidoreductase Cycle/Methane subunit Metabolism Glycolysis/Gluc oneogenesis/TC pyruvate ferredoxin Pyruvate H A 1.2.7.1 K00170 oxidoreductase, beta 4Fe-4S Oxidoreductase Cycle/Methane subunit Metabolism Glycolysis/Gluc oneogenesis/TC pyruvate ferredoxin Pyruvate H A 1.2.7.1 K00171 oxidoreductase, delta 4Fe-4S Oxidoreductase Cycle/Methane subunit Metabolism Glycolysis/Gluc oneogenesis/TC pyruvate ferredoxin Pyruvate H A 1.2.7.1 K00172 oxidoreductase, gamma 4Fe-4S Oxidoreductase Cycle/Methane subunit Metabolism Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology glucose-6- Pentose glucose-6-phosphate 1- H phosphate 1.1.1.49 K00036 NADP, NAD Phosphate dehydrogenase dehydrogenase isocitrate isocitrate Mg(2+), Mn(2+), H TCA Cycle dehydrogenase 1.1.1.41 K00030 dehydrogenase (NAD+) NAD (NAD+) isocitrate-- isocitrate-- Mg(2+), Mn(2+), H TCA Cycle homoisocitrate 1.1.1.286 K17753 homoisocitrate NAD dehydrogenase dehydrogenase malate malate dehydrogenase quinone, FAD, H TCA Cycle dehydrogenase 1.1.5.4 K00116 (quinone) Flavoprotein (quinone) thiamine oxoglutarate 2-oxoglutarate diphosphate, dehydrogenase H TCA Cycle 1.2.4.2 K00164 dehydrogenase E1 Metal-binding, (succinyl- component Mg(2+), transferring) Magnesium oxoglutarate probable 2-oxoglutarate dehydrogenase thiamine H TCA Cycle 1.2.4.2 K15791 dehydrogenase E1 (succinyl- diphosphate component DHKTD1 transferring) TCA succinate Cycle/Oxidative quinone, succinate dehydrogenase H Phosphorylation/ 1.3.5.1 K00234 ubiquinone, FAD, dehydrogenase (ubiquinone) Reverse TCA Flavoprotein flavoprotein subunit Cycle TCA succinate Cycle/Oxidative 4Fe-4S, 2Fe-2S, succinate dehydrogenase H Phosphorylation/ 1.3.5.1 K00235 3Fe-4S, quinone, dehydrogenase (ubiquinone) iron- Reverse TCA ubiquinone sulfur subunit Cycle TCA succinate Cycle/Oxidative dehydrogenase succinate heme, quinone, H Phosphorylation/ 1.3.5.1 K00236 (ubiquinone) dehydrogenase ubiquinone Reverse TCA cytochrome b560 Cycle subunit TCA succinate Cycle/Oxidative succinate dehydrogenase heme, quinone, H Phosphorylation/ 1.3.5.1 K00237 dehydrogenase (ubiquinone) membrane ubiquinone Reverse TCA anchor subunit Cycle TCA succinate Cycle/Oxidative succinate dehydrogenase / H Phosphorylation/ 1.3.5.1 K00239 FAD, Flavoprotein dehydrogenase fumarate reductase, Reverse TCA flavoprotein subunit Cycle TCA succinate Cycle/Oxidative succinate dehydrogenase / 4Fe-4S, 2Fe-2S, H Phosphorylation/ 1.3.5.1 K00240 dehydrogenase fumarate reductase, 3Fe-4S Reverse TCA iron-sulfur subunit Cycle TCA succinate Cycle/Oxidative succinate dehydrogenase / H Phosphorylation/ 1.3.5.1 K00241 heme dehydrogenase fumarate reductase, Reverse TCA cytochrome b subunit Cycle Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology TCA succinate Cycle/Oxidative dehydrogenase / succinate H Phosphorylation/ 1.3.5.1 K00242 fumarate reductase, heme dehydrogenase Reverse TCA membrane anchor Cycle subunit TCA succinate Cycle/Oxidative succinate dehydrogenase / H Phosphorylation/ 1.3.5.1 K18859 dehydrogenase fumarate reductase, Reverse TCA subunit D Cycle TCA putative succinate Cycle/Oxidative succinate dehydrogenase / H Phosphorylation/ 1.3.5.1 K18860 dehydrogenase fumarate reductase, Reverse TCA subunit D Cycle 2-oxoglutarate TCA 2-oxoglutarate ferredoxin H Cycle/Reverse 1.2.7.3 K00174 oxidoreductase subunit TCA Cycle alpha 2-oxoglutarate TCA 2-oxoglutarate ferredoxin Mg(2+), H Cycle/Reverse 1.2.7.3 K00175 synthase oxidoreductase subunit Magnesium TCA Cycle beta 2-oxoglutarate TCA 2-oxoglutarate ferredoxin H Cycle/Reverse 1.2.7.3 K00176 4Fe-4S synthase oxidoreductase subunit TCA Cycle delta 2-oxoglutarate TCA 2-oxoglutarate ferredoxin H Cycle/Reverse 1.2.7.3 K00177 synthase oxidoreductase subunit TCA Cycle gamma succinate TCA dehydrogenase / H Cycle/Reverse fumarate reductase 1.3.5.4 K00239 FAD, Flavoprotein fumarate reductase, TCA Cycle flavoprotein subunit succinate TCA dehydrogenase / 4Fe-4S, 2Fe-2S, H Cycle/Reverse fumarate reductase 1.3.5.4 K00240 fumarate reductase, 3Fe-4S TCA Cycle iron-sulfur subunit TCA FAD, fumarate reductase H Cycle/Reverse fumarate reductase 1.3.5.4 K00244 Flavoprotein, flavoprotein subunit TCA Cycle heme, Fe(3+) TCA fumarate reductase 4Fe-4S, 2Fe-2S, H Cycle/Reverse fumarate reductase 1.3.5.4 K00245 iron-sulfur subunit 3Fe-4S TCA Cycle TCA isocitrate isocitrate Mg(2+), Mn(2+), H Cycle/Reverse dehydrogenase 1.1.1.42 K00031 dehydrogenase NADP, NAD TCA Cycle (NADP+) TCA Cycle/Reverse malate H TCA 1.1.1.37 K00024 malate dehydrogenase NAD, NADP dehydrogenase Cycle/Methane metabolism TCA Cycle/Reverse malate H TCA 1.1.1.37 K00025 malate dehydrogenase NAD dehydrogenase Cycle/Methane metabolism Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology TCA Cycle/Reverse malate H TCA 1.1.1.37 K00026 malate dehydrogenase NAD dehydrogenase Cycle/Methane metabolism TCA Cycle/Reverse malate H TCA dehydrogenase no EC no KO Cycle/Methane [NAD(P)+] metabolism [NiFe] hydrogenase 4Fe-4S, Hydrogen hydrogen HO 1.12.1.2 K18005 diaphorase moiety large Flavoprotein, Oxidation dehydrogenase subunit FMN, NAD

[NiFe] hydrogenase 4Fe-4S, Hydrogen hydrogen HO 1.12.1.2 K18006 diaphorase moiety Flavoprotein, Oxidation dehydrogenase small subunit FMN, NAD NAD-reducing 4Fe-4S, 2Fe-2S, Hydrogen hydrogen HO 1.12.1.2 K18007 hydrogenase small 3Fe-4S, Ni(2+), Oxidation dehydrogenase subunit FMN, NAD hydrogen NADP-reducing Hydrogen HO dehydrogenase 1.12.1.3 K17992 hydrogenase subunit Oxidation (NADP+) HndB hydrogen Hydrogen Ni(2+), iron, HO dehydrogenase 1.12.1.3 K17993 Oxidation subunit alpha NADP, NAD (NADP+) hydrogen 4Fe-4S, 3Fe-4S, Hydrogen sulfhydrogenase HO dehydrogenase 1.12.1.3 K17994 Nickel, Ni(2+), Oxidation subunit delta (NADP+) NADP, NAD hydrogen NADP-reducing Hydrogen HO dehydrogenase 1.12.1.3 K18330 hydrogenase subunit Oxidation (NADP+) HndA hydrogen NADP-reducing Hydrogen HO dehydrogenase 1.12.1.3 K18331 hydrogenase subunit Oxidation (NADP+) HndC hydrogen NADP-reducing Hydrogen HO dehydrogenase 1.12.1.3 K18332 hydrogenase subunit Oxidation (NADP+) HndD hydrogen Hydrogen sulfhydrogenase Ni(2+), iron, HO dehydrogenase 1.12.1.5 K17993 Oxidation subunit alpha NADP, NAD [NAD(P)+] hydrogen 4Fe-4S, 3Fe-4S, Hydrogen sulfhydrogenase HO dehydrogenase 1.12.1.5 K17994 Nickel, Ni(2+), Oxidation subunit delta [NAD(P)+] NADP, NAD NADH:ubiquinone Intra Na Translocating reductase (Na+- 1.6.5.8 no KO transporting) heme, NADP, Intra Other 1.11.1.6 K03781 catalase NAD heme, NADP, Intra Other catalase- 1.11.1.21 K03782 catalase-peroxidase NAD eosinophil heme, NADP, Intra Other 1.11.1.18 K10788 peroxidase NAD heme, NADP, Intra Other 1.11.1.7 K12550 lactoperoxidase NAD Intra Other peroxidase 1.11.1.7 K00430 peroxidase heme, NADP, Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology NAD

6, 1- 1.11.1.7 1.11. peroxiredoxin 6, 1-Cys Intra Other K11188 Cys peroxiredoxin 1.15 peroxiredoxin caldariellaquinol Oxidative Intra oxidase (H+- 1.10.3.13 no KO Phosphorylation transporting) Oxidative cytochrome-c cytochrome c heme, Zinc, Zinc- Intra 1.11.1.5 K00428 Phosphorylation peroxidase peroxidase finger

menaquinol cytochrome aa3-600 Oxidative Intra oxidase (H+- 1.10.3.12 K02826 menaquinol oxidase Phosphorylation transporting) subunit II

menaquinol cytochrome aa3-600 Oxidative Intra oxidase (H+- 1.10.3.12 K02827 menaquinol oxidase heme, Cu(2+) Phosphorylation transporting) subunit I

menaquinol cytochrome aa3-600 Oxidative Intra oxidase (H+- 1.10.3.12 K02828 menaquinol oxidase heme, Cu(2+) Phosphorylation transporting) subunit III

menaquinol cytochrome aa3-600 Oxidative Intra oxidase (H+- 1.10.3.12 K02829 menaquinol oxidase Phosphorylation transporting) subunit IV Flavoprotein, Oxidative NADH Intra 1.6.99.3 K00356 NADH dehydrogenase NADP, FMN, Phosphorylation dehydrogenase NAD FAD, Oxidative NADH Flavoprotein, Intra 1.6.99.3 K03885 NADH dehydrogenase Phosphorylation dehydrogenase NAD, quinone, Ubiquinone

NADH dehydrogenase 4Fe-4S, 2Fe-2S, Oxidative NADH Intra 1.6.99.3 K03934 (ubiquinone) Fe-S quinone, Phosphorylation dehydrogenase protein 1 Ubiquinone, NAD NADH dehydrogenase Oxidative NADH 4Fe-4S, quinone, Intra 1.6.99.3 K03935 (ubiquinone) Fe-S Phosphorylation dehydrogenase Ubiquinone, NAD protein 2 NADH dehydrogenase iron-sulfur, Oxidative NADH Intra 1.6.99.3 K03936 (ubiquinone) Fe-S quinone, Phosphorylation dehydrogenase protein 3 Ubiquinone, NAD NADH dehydrogenase Oxidative NADH 4Fe-4S, quinone, Intra 1.6.99.3 K03940 (ubiquinone) Fe-S Phosphorylation dehydrogenase Ubiquinone, NAD protein 7 NADH dehydrogenase Oxidative NADH 4Fe-4S, quinone, Intra 1.6.99.3 K03941 (ubiquinone) Fe-S Phosphorylation dehydrogenase Ubiquinone, NAD protein 8

4Fe-4S quinone, NADH dehydrogenase Oxidative NADH ubiquinone, Intra 1.6.99.3 K03942 (ubiquinone) Phosphorylation dehydrogenase Flavoprotein, flavoprotein 1 FMN, NAD

NADH dehydrogenase Oxidative NADH 2Fe-2S, quinone, Intra 1.6.99.3 K03943 (ubiquinone) Phosphorylation dehydrogenase ubiquinone, NAD flavoprotein 2 Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology NADH Oxidative NADH dehydrogenase 4Fe-4S, quinone, Intra dehydrogenase 1.6.99.5 K05903 Phosphorylation (quinone) Ubiquinone, NAD (quinone) NADH:ubiquinone Oxidative Intra reductase (H+- 1.6.5.3 K00329 NADH dehydrogenase Phosphorylation translocating)

NADH:ubiquinone NADH-quinone Oxidative quinone, Intra reductase (H+- 1.6.5.3 K00330 oxidoreductase subunit Phosphorylation ubiquinone, NAD translocating) A

NADH:ubiquinone NADH-quinone 4Fe-4S, quinone, Oxidative Intra reductase (H+- 1.6.5.3 K00331 oxidoreductase subunit Ubiquinone, Phosphorylation translocating) B NAD, FAD

NADH:ubiquinone NADH-quinone Oxidative quinone, Intra reductase (H+- 1.6.5.3 K00332 oxidoreductase subunit Phosphorylation ubiquinone, NAD translocating) C

NADH:ubiquinone NADH-quinone Oxidative quinone, Intra reductase (H+- 1.6.5.3 K00333 oxidoreductase subunit Phosphorylation ubiquinone, NAD translocating) D

NADH:ubiquinone NADH-quinone Oxidative 2Fe-2S, quinone, Intra reductase (H+- 1.6.5.3 K00334 oxidoreductase subunit Phosphorylation ubiquinone, NAD translocating) E

NADH:ubiquinone NADH-quinone 4Fe-4S, quinone, Oxidative Intra reductase (H+- 1.6.5.3 K00335 oxidoreductase subunit Ubiquinone, Phosphorylation translocating) F NAD, FAD, FMN

NADH:ubiquinone NADH-quinone 4Fe-4S, 2Fe-2S, Oxidative Intra reductase (H+- 1.6.5.3 K00336 oxidoreductase subunit quinone, Phosphorylation translocating) G Ubiquinone, NAD

NADH:ubiquinone NADH-quinone 4Fe-4S, quinone, Oxidative Intra reductase (H+- 1.6.5.3 K00337 oxidoreductase subunit Ubiquinone, Phosphorylation translocating) H NAD, FAD

NADH:ubiquinone NADH-quinone Oxidative 4Fe-4S, quinone, Intra reductase (H+- 1.6.5.3 K00338 oxidoreductase subunit Phosphorylation Ubiquinone, NAD translocating) I

NADH:ubiquinone NADH-quinone Oxidative quinone, Intra reductase (H+- 1.6.5.3 K00339 oxidoreductase subunit Phosphorylation ubiquinone, NAD translocating) J

NADH:ubiquinone NADH-quinone Oxidative quinone, Intra reductase (H+- 1.6.5.3 K00340 oxidoreductase subunit Phosphorylation ubiquinone, NAD translocating) K

NADH:ubiquinone NADH-quinone Oxidative quinone, Intra reductase (H+- 1.6.5.3 K00341 oxidoreductase subunit Phosphorylation ubiquinone, NAD translocating) L Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

NADH:ubiquinone NADH-quinone Oxidative quinone, Intra reductase (H+- 1.6.5.3 K00342 oxidoreductase subunit Phosphorylation ubiquinone, NAD translocating) M

NADH:ubiquinone NADH-quinone Oxidative quinone, Intra reductase (H+- 1.6.5.3 K00343 oxidoreductase subunit Phosphorylation ubiquinone, NAD translocating) N

NADH:ubiquinone Oxidative NADH-ubiquinone quinone, Intra reductase (H+- 1.6.5.3 K03878 Phosphorylation oxidoreductase chain 1 ubiquinone, NAD translocating)

NADH:ubiquinone Oxidative NADH-ubiquinone quinone, Intra reductase (H+- 1.6.5.3 K03879 Phosphorylation oxidoreductase chain 2 ubiquinone, NAD translocating)

NADH:ubiquinone Oxidative NADH-ubiquinone quinone, Intra reductase (H+- 1.6.5.3 K03880 Phosphorylation oxidoreductase chain 3 ubiquinone, NAD translocating)

NADH:ubiquinone Oxidative NADH-ubiquinone quinone, Intra reductase (H+- 1.6.5.3 K03881 Phosphorylation oxidoreductase chain 4 ubiquinone, NAD translocating)

NADH:ubiquinone NADH-ubiquinone Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03882 oxidoreductase chain Phosphorylation ubiquinone, NAD translocating) 4L

NADH:ubiquinone Oxidative NADH-ubiquinone quinone, Intra reductase (H+- 1.6.5.3 K03883 Phosphorylation oxidoreductase chain 5 ubiquinone, NAD translocating)

NADH:ubiquinone Oxidative NADH-ubiquinone quinone, Intra reductase (H+- 1.6.5.3 K03884 Phosphorylation oxidoreductase chain 6 ubiquinone, NAD translocating) 4Fe-4S, 2Fe-2S, NADH:ubiquinone NADH dehydrogenase quinone, Oxidative Intra reductase (H+- 1.6.5.3 K03934 (ubiquinone) Fe-S ubiquinone, Phosphorylation translocating) protein 1 NAD, iron-sulfur, iron NADH:ubiquinone NADH dehydrogenase Oxidative 4Fe-4S, quinone, Intra reductase (H+- 1.6.5.3 K03935 (ubiquinone) Fe-S Phosphorylation Ubiquinone, NAD translocating) protein 2

NADH:ubiquinone NADH dehydrogenase iron-sulfur, Oxidative Intra reductase (H+- 1.6.5.3 K03936 (ubiquinone) Fe-S quinone, Phosphorylation translocating) protein 3 ubiquinone, NAD

NADH:ubiquinone NADH dehydrogenase iron-sulfur, Oxidative Intra reductase (H+- 1.6.5.3 K03937 (ubiquinone) Fe-S quinone, Phosphorylation translocating) protein 4 ubiquinone, NAD Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

NADH:ubiquinone NADH dehydrogenase iron-sulfur, Oxidative Intra reductase (H+- 1.6.5.3 K03938 (ubiquinone) Fe-S quinone, Phosphorylation translocating) protein 5 ubiquinone, NAD

NADH:ubiquinone NADH dehydrogenase iron-sulfur, Oxidative Intra reductase (H+- 1.6.5.3 K03939 (ubiquinone) Fe-S quinone, Phosphorylation translocating) protein 6 ubiquinone, NAD

NADH:ubiquinone NADH dehydrogenase Oxidative 4Fe-4S, quinone, Intra reductase (H+- 1.6.5.3 K03940 (ubiquinone) Fe-S Phosphorylation Ubiquinone, NAD translocating) protein 7

NADH:ubiquinone NADH dehydrogenase Oxidative 4Fe-4S, quinone, Intra reductase (H+- 1.6.5.3 K03941 (ubiquinone) Fe-S Phosphorylation Ubiquinone, NAD translocating) protein 8

NADH:ubiquinone NADH dehydrogenase 4Fe-4S, quinone, Oxidative Intra reductase (H+- 1.6.5.3 K03942 (ubiquinone) Ubiquinone, Phosphorylation translocating) flavoprotein 1 NAD, FMN

NADH:ubiquinone NADH dehydrogenase Oxidative 2Fe-2S, quinone, Intra reductase (H+- 1.6.5.3 K03943 (ubiquinone) Phosphorylation ubiquinone, NAD translocating) flavoprotein 2

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03944 (ubiquinone) Phosphorylation ubiquinone, NAD translocating) flavoprotein 3

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03945 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 1

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03946 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 2

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03947 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 3

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03948 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 4

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03949 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 5

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03950 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 6

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03951 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 7 Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

NADH:ubiquinone NADH dehydrogenase quinone, Oxidative Intra reductase (H+- 1.6.5.3 K03952 (ubiquinone) 1 alpha ubiquinone, NAD, Phosphorylation translocating) subcomplex subunit 8 iron-sulfur

quinone, NADH:ubiquinone NADH dehydrogenase Oxidative ubiquinone, FAD, Intra reductase (H+- 1.6.5.3 K03953 (ubiquinone) 1 alpha Phosphorylation Flavoprotein, translocating) subcomplex subunit 9 NAD quinone, NADH:ubiquinone NADH dehydrogenase Oxidative ubiquinone, FAD, Intra reductase (H+- 1.6.5.3 K03954 (ubiquinone) 1 alpha Phosphorylation Flavoprotein, translocating) subcomplex subunit 10 NAD NADH dehydrogenase NADH:ubiquinone Oxidative (ubiquinone) 1 quinone, Intra reductase (H+- 1.6.5.3 K03955 Phosphorylation alpha/beta subcomplex ubiquinone, NAD translocating) 1

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03956 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 11

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K11352 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 12

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K11353 (ubiquinone) 1 alpha Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 13

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03957 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 1

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03958 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 2

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03959 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 3

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03960 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 4

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03961 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 5

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03962 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 6

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03963 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 7 Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03964 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 8

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03965 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 9

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03966 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 10

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K11351 (ubiquinone) 1 beta Phosphorylation ubiquinone, NAD translocating) subcomplex subunit 11

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03967 (ubiquinone) 1 subunit Phosphorylation ubiquinone, NAD translocating) C1

NADH:ubiquinone NADH dehydrogenase Oxidative quinone, Intra reductase (H+- 1.6.5.3 K03968 (ubiquinone) 1 subunit Phosphorylation ubiquinone, NAD translocating) C2

NADH:ubiquinone NAD(P)H-quinone Oxidative quinone, NADP, Intra reductase (H+- 1.6.5.3 K05572 oxidoreductase subunit Phosphorylation NAD translocating) 1

NADH:ubiquinone NAD(P)H-quinone Oxidative quinone, NADP, Intra reductase (H+- 1.6.5.3 K05573 oxidoreductase subunit Phosphorylation NAD translocating) 2

NADH:ubiquinone NAD(P)H-quinone Oxidative quinone, NADP, Intra reductase (H+- 1.6.5.3 K05574 oxidoreductase subunit Phosphorylation NAD translocating) 3

NADH:ubiquinone NAD(P)H-quinone Oxidative quinone, NADP, Intra reductase (H+- 1.6.5.3 K05575 oxidoreductase subunit Phosphorylation NAD translocating) 4

NADH:ubiquinone NAD(P)H-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K05576 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) 4L NADP

NADH:ubiquinone NAD(P)H-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K05577 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) 5 NADP

NADH:ubiquinone NAD(P)H-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K05578 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) 6 NADP

NADH:ubiquinone NAD(P)H-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K05579 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) H NADP Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

4Fe-4S, Iron- NADH:ubiquinone NAD(P)H-quinone sulfur, Iron, Oxidative Intra reductase (H+- 1.6.5.3 K05580 oxidoreductase subunit Quinone, quinone, Phosphorylation translocating) I NADP, Metal- binding, NAD

NADH:ubiquinone NAD(P)H-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K05581 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) J NADP

NADH:ubiquinone NAD(P)H-quinone Oxidative 4Fe-4S, quinone, Intra reductase (H+- 1.6.5.3 K05582 oxidoreductase subunit Phosphorylation NADP, NAD translocating) K

NADH:ubiquinone NAD(P)H-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K05583 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) L NADP

NADH:ubiquinone NAD(P)H-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K05584 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) M NADP

NADH:ubiquinone NAD(P)H-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K05585 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) N NADP

NADH:ubiquinone bidirectional [NiFe] Oxidative Intra reductase (H+- 1.6.5.3 K05586 hydrogenase diaphorase Phosphorylation translocating) subunit

NADH:ubiquinone bidirectional [NiFe] Oxidative Intra reductase (H+- 1.6.5.3 K05587 hydrogenase diaphorase Phosphorylation translocating) subunit

NADH:ubiquinone bidirectional [NiFe] Oxidative Intra reductase (H+- 1.6.5.3 K05588 hydrogenase diaphorase Phosphorylation translocating) subunit

NADH:ubiquinone NADH-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K13378 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) C/D NADP

NADH:ubiquinone NADH-quinone quinone, Oxidative Intra reductase (H+- 1.6.5.3 K13380 oxidoreductase subunit ubiquinone, NAD, Phosphorylation translocating) B/C/D NADP

NADH:ubiquinone NADH-quinone Oxidative Intra reductase (H+- 1.6.5.3 K15863 oxidoreductase subunit Phosphorylation translocating) L/M

quinol--- ubiquinol-cytochrome c Oxidative Intra cytochrome-c 1.10.2.2 K00410 reductase cytochrome heme Phosphorylation reductase b/c1 subunit Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

quinol--- ubiquinol-cytochrome c Oxidative Intra cytochrome-c 1.10.2.2 K00411 reductase iron-sulfur 2Fe-2S Phosphorylation reductase subunit

quinol--- ubiquinol-cytochrome c Oxidative Intra cytochrome-c 1.10.2.2 K00412 reductase cytochrome b heme Phosphorylation reductase subunit

quinol--- ubiquinol-cytochrome c Oxidative Intra cytochrome-c 1.10.2.2 K00413 reductase cytochrome heme Phosphorylation reductase c1 subunit quinol--- ubiquinol-cytochrome c Oxidative Intra cytochrome-c 1.10.2.2 K00414 reductase core subunit Phosphorylation reductase 1 quinol--- ubiquinol-cytochrome c Oxidative Intra cytochrome-c 1.10.2.2 K00415 reductase core subunit Phosphorylation reductase 2 quinol--- Oxidative ubiquinol-cytochrome c Intra cytochrome-c 1.10.2.2 K00416 heme Phosphorylation reductase subunit 6 reductase quinol--- Oxidative ubiquinol-cytochrome c Intra cytochrome-c 1.10.2.2 K00417 Phosphorylation reductase subunit 7 reductase quinol--- Oxidative ubiquinol-cytochrome c quinone, Intra cytochrome-c 1.10.2.2 K00418 Phosphorylation reductase subunit 8 ubiquinone reductase quinol--- Oxidative ubiquinol-cytochrome c Intra cytochrome-c 1.10.2.2 K00419 heme Phosphorylation reductase subunit 9 reductase quinol--- Oxidative ubiquinol-cytochrome c Intra cytochrome-c 1.10.2.2 K00420 Phosphorylation reductase subunit 10 reductase Oxidative Intra (electrogenic, non 1.10.3.14 no KO Phosphorylation H+-transporting)

Oxidative ubiquinol oxidase Intra 1.10.3.10 no KO Phosphorylation (H+-transporting) 5,10- 5,10- methenyltetrahydro M 1.12.98.2 K13942 methenyltetrahydromet methanopterin hanopterin hydrogenase hydrogenase 5,10- 5,10- methylenetetrahydr M Methanogenesis 1.5.98.2 K00320 methylenetetrahydrome omethanopterin thanopterin reductase reductase

carbon-monoxide carbon-monoxide 4Fe-4S Nickel, M Methanogenesis dehydrogenase 1.2.99.2 K00198 dehydrogenase catalytic Ni-Fe-S (acceptor) subunit

carbon-monoxide carbon-monoxide M Methanogenesis dehydrogenase 1.2.99.2 K03518 dehydrogenase small 2Fe-2S (acceptor) subunit Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

carbon-monoxide carbon-monoxide M Methanogenesis dehydrogenase 1.2.99.2 K03519 dehydrogenase medium FAD, Flavoprotein (acceptor) subunit

carbon-monoxide carbon-monoxide molybdopterin, M Methanogenesis dehydrogenase 1.2.99.2 K03520 dehydrogenase large Copper (acceptor) subunit

carbon-monoxide acetyl-CoA 4Fe-4S, Nickel, M Methanogenesis dehydrogenase 1.2.7.4 K00192 decarbonylase/synthase Ni-Fe-S (ferredoxin) complex subunit alpha

carbon-monoxide carbon-monoxide 4Fe-4S, Nickel, M Methanogenesis dehydrogenase 1.2.7.4 K00198 dehydrogenase catalytic Ni-Fe-S (ferredoxin) subunit

CoB-CoM 4Fe-4S, FAD, heterodisulfide M Methanogenesis heterodisulfide 1.8.98.1 K03388 Flavoprotein, reductase subunit A reductase Selenocysteine CoB-CoM heterodisulfide M Methanogenesis heterodisulfide 1.8.98.1 K03389 reductase subunit B reductase CoB-CoM heterodisulfide M Methanogenesis heterodisulfide 1.8.98.1 K03390 4Fe-4S reductase subunit C reductase CoB-CoM heterodisulfide M Methanogenesis heterodisulfide 1.8.98.1 K08264 4Fe-4S reductase subunit D reductase CoB-CoM heterodisulfide M Methanogenesis heterodisulfide 1.8.98.1 K08265 reductase subunit E reductase coenzyme F420 Iron-sulfur, coenzyme F420 M Methanogenesis 1.12.98.1 K00440 hydrogenase subunit Ni(2+), FAD, hydrogenase alpha Flavoprotein coenzyme F420 coenzyme F420 4Fe-4S, Ni(2+), M Methanogenesis 1.12.98.1 K00441 hydrogenase subunit hydrogenase FAD, heme beta coenzyme F420 coenzyme F420 4Fe-4S, Ni(2+), M Methanogenesis 1.12.98.1 K00443 hydrogenase subunit hydrogenase FAD, heme gamma formylmethanofuran Formylmethanofur M Methanogenesis 1.2.99.5 K00200 dehydrogenase subunit inc an Dehydrogenase A formylmethanofuran Formylmethanofur tungsten, M Methanogenesis 1.2.99.5 K00201 dehydrogenase subunit an Dehydrogenase selenocysteine B formylmethanofuran Formylmethanofur , M Methanogenesis 1.2.99.5 K00202 dehydrogenase subunit an Dehydrogenase tungsten C formylmethanofuran Formylmethanofur M Methanogenesis 1.2.99.5 K00203 dehydrogenase subunit an Dehydrogenase D formylmethanofuran Formylmethanofur M Methanogenesis 1.2.99.5 K11261 dehydrogenase subunit an Dehydrogenase E Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

Formylmethanofur M Methanogenesis 1.2.99.5 K00205 4Fe-4S ferredoxin an Dehydrogenase

Formylmethanofur M Methanogenesis 1.2.99.5 K11260 4Fe-4S ferredoxin an Dehydrogenase

Formylmethanofur M Methanogenesis 1.2.99.5 K00204 4Fe-4S ferredoxin an Dehydrogenase

methylenetetrahydr methylenetetrahydrome M Methanogenesis omethanopterin 1.5.98.1 K00319 thanopterin dehydrogenase dehydrogenase Methane MO 1.1.3.13 K17066 alcohol oxidase FAD, Flavoprotein oxidation methane methane MO monooxygenase 1.14.13.25 K16157 iron, NADP, NAD oxidation component A alpha (soluble) chain methane methane Methane monooxygenase MO monooxygenase 1.14.13.25 K16158 NADP, NAD oxidation component A beta (soluble) chain methane methane Methane monooxygenase MO monooxygenase 1.14.13.25 K16159 NADP, NAD oxidation component A gamma (soluble) chain methane methane 2Fe-2S, FAD, Methane MO monooxygenase 1.14.13.25 K16161 monooxygenase Flavoprotein, oxidation (soluble) component C NADP, NAD methane methane Methane MO monooxygenase 1.14.13.25 K16162 monooxygenase oxidation (soluble) component D methane/ammonia Methane methane/ammonia 1.14.18.3 MO K10944 monooxygenase oxidation monooxygenase or 1.14.99.39 subunit A methane/ammonia Methane methane/ammonia 1.14.18.3 MO K10945 monooxygenase Cu(2+), NAD oxidation monooxygenase or 1.14.99.39 subunit B methane/ammonia Methane methane/ammonia 1.14.18.3 MO K10946 monooxygenase oxidation monooxygenase or 1.14.99.39 subunit C N Annamox R10471 no EC no KO

hydroxylamine hydroxylamine N Nitrification 1.7.2.6 K10535 heme dehydrogenase dehydrogenase hydroxylamine N Nitrification oxidase 1.7.3.6 no KO (cytochrome) methane/ammonia methane/ammonia 1.14.18.3 N Nitrification K10944 monooxygenase monooxygenase or 1.14.99.39 subunit A methane/ammonia methane/ammonia 1.14.18.3 N Nitrification K10945 monooxygenase Cu(2+), NAD monooxygenase or 1.14.99.39 subunit B methane/ammonia methane/ammonia 1.14.18.3 N Nitrification K10946 monooxygenase monooxygenase or 1.14.99.39 subunit C Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology delta NF N-fixation nitrogenase 1.18.6.1 K00531 subunit nitrogenase Molybdenum, NF N-fixation nitrogenase 1.18.6.1 K02586 molybdenum-iron iron-sulfur protein alpha chain nitrogenase iron protein NF N-fixation nitrogenase 1.18.6.1 K02588 4Fe-4S NifH nitrogenase Molybdenum, NF N-fixation nitrogenase 1.18.6.1 K02591 molybdenum-iron iron-sulfur protein beta chain NF N-fixation nitrogenase 1.19.6.1 no KO nitrogenase(flavodoxin) Oxygenic Cytochrome b6f OP 1.10.9.2 K02635 cytochrome b6 heme Photosynthesis complex cytochrome b6-f Oxygenic Cytochrome b6f OP 1.10.9.2 K02636 complex iron-sulfur 2Fe-2S, quinone Photosynthesis complex subunit Oxygenic Cytochrome b6f cytochrome b6-f OP 1.10.9.2 K02637 Photosynthesis complex complex subunit 4 Oxygenic Cytochrome b6f OP 1.10.9.2 K02634 apocytochrome f heme Photosynthesis complex Oxygenic Cytochrome b6f cytochrome b6-f OP 1.10.9.2 K02642 Photosynthesis complex complex subunit 6

Oxygenic Cytochrome b6f cytochrome b6-f OP 1.10.9.2 K02643 Photosynthesis complex complex subunit 7

Oxygenic Cytochrome b6f cytochrome b6-f OP 1.10.9.2 K03689 Photosynthesis complex complex subunit 8

Oxygenic Cytochrome b6f cytochrome b6-f OP 1.10.9.2 K02640 Photosynthesis complex complex subunit 5 FAD, Oxygenic ferredoxin-NADP+ ferredoxin--NADP+ OP 1.18.1.2 K02641 Flavoprotein, Photosynthesis reductase reductase NADP, NAD photosystem II P680 manganese, Oxygenic OP Photosystem II 1.10.3.9 K02703 reaction center D1 magnesium, Iron, Photosynthesis protein quinone, heme photosystem II P680 Oxygenic magnesium, iron, OP Photosystem II 1.10.3.9 K02706 reaction center D2 Photosynthesis quinone, heme protein Oxygenic photosystem II CP43 OP Photosystem II 1.10.3.9 K02705 Manganese Photosynthesis chlorophyll apoprotein

Oxygenic photosystem II CP47 OP Photosystem II 1.10.3.9 K02704 Photosynthesis chlorophyll apoprotein photosystem II Oxygenic OP Photosystem II 1.10.3.9 K02707 cytochrome b559 heme Photosynthesis subunit alpha photosystem II Oxygenic OP Photosystem II 1.10.3.9 K02708 cytochrome b559 heme Photosynthesis subunit beta Oxygenic photosystem II PsbL OP Photosystem II 1.10.3.9 K02713 Photosynthesis protein OP Oxygenic Photosystem II 1.10.3.9 K02711 photosystem II PsbJ Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology Photosynthesis protein Oxygenic photosystem II PsbK OP Photosystem II 1.10.3.9 K02712 Photosynthesis protein Oxygenic photosystem II PsbM OP Photosystem II 1.10.3.9 K02714 Photosynthesis protein

Oxygenic photosystem II PsbH OP Photosystem II 1.10.3.9 K02709 Photosynthesis protein Oxygenic photosystem II PsbI OP Photosystem II 1.10.3.9 K02710 Photosynthesis protein photosystem II - Oxygenic OP Photosystem II 1.10.3.9 K02716 evolving enhancer Manganese Photosynthesis protein 1 photosystem II oxygen- Oxygenic OP Photosystem II 1.10.3.9 K02717 evolving enhancer Photosynthesis protein 2 photosystem II oxygen- Oxygenic OP Photosystem II 1.10.3.9 K08901 evolving enhancer Photosynthesis protein 3 Oxygenic photosystem II 10kDa OP Photosystem II 1.10.3.9 K03541 Photosynthesis protein

Oxygenic photosystem II 22kDa OP Photosystem II 1.10.3.9 K03542 Photosynthesis protein Oxygenic photosystem II PsbT OP Photosystem II 1.10.3.9 K02718 Photosynthesis protein Oxygenic photosystem II PsbU OP Photosystem II 1.10.3.9 K02719 Photosynthesis protein

Oxygenic photosystem II OP Photosystem II 1.10.3.9 K02720 heme Photosynthesis cytochrome c550

Oxygenic photosystem II PsbW OP Photosystem II 1.10.3.9 K02721 Photosynthesis protein Oxygenic photosystem II PsbX OP Photosystem II 1.10.3.9 K02722 Photosynthesis protein Oxygenic photosystem II PsbY OP Photosystem II 1.10.3.9 K02723 Manganese Photosynthesis protein Oxygenic photosystem II PsbZ OP Photosystem II 1.10.3.9 K02724 Photosynthesis protein Oxygenic photosystem II Psb27 OP Photosystem II 1.10.3.9 K08902 Photosynthesis protein

Oxygenic photosystem II 13kDa OP Photosystem II 1.10.3.9 K08903 Photosynthesis protein

Oxygenic photosystem II Psb28-2 OP Photosystem II 1.10.3.9 K08904 Photosynthesis protein P700 Oxygenic Magnesium, 4Fe- OP Photosytem I 1.97.1.12 K02689 chlorophyll a Photosynthesis 4S, quinone apoprotein A1 photosystem I P700 Oxygenic Magnesium, 4Fe- OP Photosytem I 1.97.1.12 K02690 chlorophyll a Photosynthesis 4S, quinone apoprotein A2 Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02691 4Fe-4S Photosynthesis VII Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02692 Photosynthesis II Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02693 Photosynthesis IV Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02694 Photosynthesis III Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K08905 Photosynthesis V Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02695 Photosynthesis VI Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02696 Photosynthesis VIII Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02697 Photosynthesis IX Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02698 Photosynthesis X Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02699 Photosynthesis XI Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02700 Photosynthesis XII Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K02701 Photosynthesis PsaN Oxygenic photosystem I subunit OP Photosytem I 1.97.1.12 K14332 Photosynthesis PsaO Oxygenic photosystem I 4.8kDa OP Photosytem I 1.97.1.12 K02702 Photosynthesis protein Sulfide sulfide:quinone SDO 1.8.5.4 no KO Oxidation reductase Thiosulfate Thiosulfate SDO 1.8.2.2 no KO Oxidation dehydrogenase thiosulfate thiosulfate Thiosulfate SDO dehydrogenase 1.8.5.2 K16936 dehydrogenase Oxidation (quinone) [quinone] small subunit Thiosulfate Thiosulfate SDO no EC K08738 cytochrome c heme Oxidation Oxidation (SOX)

Thiosulfate Thiosulfate sulfur-oxidizing protein SDO no EC K17222 Heme, Cu(2+) Oxidation Oxidation (SOX) SoxA

Thiosulfate Thiosulfate sulfur-oxidizing protein SDO no EC K17223 heme Oxidation Oxidation (SOX) SoxX

Thiosulfate Thiosulfate sulfur-oxidizing protein SDO no EC K17224 Oxidation Oxidation (SOX) SoxB

Thiosulfate Thiosulfate sulfane dehydrogenase SDO no EC K17225 Oxidation Oxidation (SOX) subunit SoxC

Thiosulfate Thiosulfate sulfur-oxidizing protein SDO no EC K17226 Oxidation Oxidation (SOX) SoxY

Thiosulfate Thiosulfate sulfur-oxidizing protein SDO no EC K17227 Oxidation Oxidation (SOX) SoxZ Sulfur sulfite SO 1.8.2.1 K05301 Metabolism dehydrogenase Sulfur molybdopterin, SO 1.8.3.1 K00387 sulfite oxidase Metabolism heme Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology sulfhydrogenase Sulfur H2:polysulfide 2Fe-2S, FAD, SR 1.12.98.4 K17995 subunit gamma ( oxidoreductase Flavoprotein, reductase) sulfhydrogenase Sulfur H2:polysulfide SR 1.12.98.4 K17996 subunit beta (sulfur 4Fe-4S Metabolism oxidoreductase reductase) hydrogen sulfhydrogenase Iron, Ni(2+), SR Sulfydrogenase dehydrogenase 1.12.1.5 K17993 subunit alpha NADP, NAD [NAD(P)+] hydrogen 4Fe-4S, 3Fe-4S, sulfhydrogenase SR Sulfydrogenase dehydrogenase 1.12.1.5 K17994 Ni(2+), NADP, subunit delta [NAD(P)+] NAD adenylyl- adenylylsulfate STR Sulfate reduction 1.8.99.2 K00394 reductase reductase, subunit A

adenylyl-sulfate adenylylsulfate STR Sulfate reduction 1.8.99.2 K00395 reductase reductase, subunit B adenylyl-sulfate adenylyl-sulfate STR Sulfate reduction reductase 1.8.4.9 K05907 4Fe-4S reductase () (glutathione) adenylyl-sulfate STR Sulfate reduction reductase 1.8.4.10 no KO (thioredoxin) alpha STR Sulfite reduction sulfite reductase 1.8.99.1 K11180 4Fe-4S, heme subunit (and 1.8.99.3)

sulfite reductase beta STR Sulfite reduction sulfite reductase 1.8.99.1 K11181 4Fe-4S, heme subunit (and 1.8.99.3) phosphoadenylyl- phosphoadenosine Sulfur STR sulfate reductase 1.8.4.8 K00390 phosphosulfate NADP, NAD assimilation (thioredoxin) reductase Sulfur sulfite reductase sulfite reductase STR 1.8.7.1 K00392 4Fe-4S, heme assimilation (ferredoxin) (ferredoxin) FAD, sulfite reductase Sulfur sulfite reductase Flavoprotein, STR 1.8.1.2 K00380 (NADPH) flavoprotein assimilation (NADPH) NADP, FMN, alpha-component NAD

sulfite reductase Sulfur sulfite reductase 4Fe-4S, heme, STR 1.8.1.2 K00381 (NADPH) hemoprotein assimilation (NADPH) NADP, NAD beta-component

Arsenate Ex arsenate reductase 1.20.4.1 K00537 reduction

Arsenate Ex arsenate reductase 1.20.4.1 K03741 reduction

Selenate Putative selenate Ex 1.97.1.9 K12527 reduction reductase Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology

Ferric iron Ex Iron Reduction K13255 reductase

Mercuric Ex Mercuric reductase 1.16.1.1 K00520 NAD, FAD reductase

Supplemental Table 2. List of the taxa presented in Figure 1 (main text) and the Figure 2.1 and the sources used to survey their physiology and metabolism.

Domain Phylum Class Reference

Euryarchaeota (6, 9, 15, 18, 21) Archaea Crenarchaeota (6, 8, 18, 21, 24)

Gammaproteobacteria

Betaproteobacteria

Proteobacteria Alphaproteobacteria (6, 18, 21) Epsilonproteobacteria Deltaproteobacteria Chlorobi (6, 18, 21) Bacteria Nitrospirae (6, 16, 18, 21)

Cyanobacteria

Chloroflexi (6, 18, 21) Firmicutes Aquificae

Thermodesulfobacteria (6, 12, 18, 21) Redox Center Midpoint Enzyme Name Organism Reference (or couple) Potential

Selenate reductase Thauera selenatis [Fe3S4] +118 (7)

Formylmethanofuran Methanobacterium Molybdopterin -530 (2) dehydrogenase thermoautotrophicum dinucleotide Formate Methanobacterium (1) Mo(V)/Mo(IV) -470 dehydrogenase formicicum Center II (Fe S APS reductase Desulfovibrio gigas 4 4 -400 (14) Ferredoxin) Sulfide-quinone Acidithiobacillus FAD Semiquinone -139 (25) reductase ferrooxidans p870 (primary e- Rhodopseudomonas Bacteriochlorophyll -45 (5) acceptor) spheroides reaction center

Cytochrome C oxidase mitochondrial Cu +340 (17)

Nitrate reductase Rhodobacter sphaeroides Mo(VI)/Mo(V) +570 (4)

Assimilatory nitrate Escherichia coli Mo(V)/Mo(VI) +250 (19) reductase p700 Synechocystis sp. PCC 6803 p700 +260 (10) p680 generic p680 +1200 (11)

Arsenate reductase Synechocystis sp. PCC 6803 Single disulfide -165 (13)

Ferric iron reductase Geobacter sulfurreducens Heme (Cytochrome) -167 (22)

Nitrite reductase Rhodobacter sphaeroides Type I (Cu) +247 (20)

Nitric oxide reductase Paracoccus denitrificans Low-spin b heme +345 (3)

Carbon monoxide Ni-X-[Fe S ] (C- Rhodospirillum rubrum 4 4 -110 (23) dehydrogenase center) Supplemental References

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