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 redox reactions of biogeochemical interest. Pathway Enzyme Complex KEGG Process EC number KEGG Enzyme Name Cofactors Abbreviation Name Orthology Cytochrome c type Cytochrome c type A Ammonification no EC K02569 heme 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 reductase alpha molybdopterin, A Ammonification nitrate reductase 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 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 sulfur 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 oxidase AR 1.9.3.1 K00404 heme, copper Phosphorylation oxidase cbb3-type subunit I Oxidative cytochrome-c cytochrome c oxidase 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 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-coenzyme A 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- succinate dehydrogenase 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 isomerase 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