Additional File 1. Sequence Alignment of 2TM-Fragments of C Subunits of F-Type Atpases

Additional File 1. Sequence alignment of 2TM-fragments of c subunits of F-type ATPases and c/K subunits of V-type ATPases

1. F- type ATPase c subunits

Phylum, class / Organism namea / gi numberb / Residues / 2TM sequence (aligned)c / Iond / Fig.4e / Fig.5f
PDB: 1YCE / Ilyobacter tartaricus / 66360700 / 14-85 / SAVGAGTAMIAGIGPGVGQGYAAGKAVESVARQPEAKGDIISTMVLGQAVAESTGIYSLVIALILLYANPFV / Na+ / Y / Y
Archaea
Euryarchaeota / Methanosarcina acetivorans / 20091267 / 15-86 / IATSGLTIGIGVLGPAIGEGRAVATALSSLAQQPDASATITRTLFVGLAMIESLSIYCFVVSMILIFANPFW / H+ / Y / Y
Methanosarcina barkeri / 73670553 / 15-86 / IATAGITIGIGVIGPAIGEGRAVATALSSLAQQPDASATITRTLFVGLAMIESLAIYCFVVSMILIFANPFW / H+ / Y / Y
Bacteria
Acidobacteria / Acidobacteria bacterium 345 / 94968328 / 38-104 / PIAAGIGFGIAVGLAALGQGRVAASACESMARNPAGRAGIQLFLIFGLAFIESLVLFAFVIVFIKVV----- / H+ / Y / ─
Solibacter usitatus / 116619895 / 35-101 / PISAGFSMAIASGMCGLAQAKAVAAAAEGMARNPGAAAAIRFALLLGLVLIESLALYTLVIIFVKVT----- / H+ / Y / ─
Actinobacteria / Mycobacterium tuberculosis / 15608445 / 10-81 / LIGGGLIMAGGAIGAGIGDGVAGNALISGVARQPEAQGRLFTPFFITVGLVEAAYFINLAFMALFVFATPVK / H+ / Y / Y
Corynebacterium diphtheriae / 38233641 / 15-79 / GSIATVGYGIATIGPGLGIGILVGKALEGMARQPEMAGQLRTTMFLGIAFVEALALIGLVAGFIL------/ H+ / Y / ─
Streptomyces lividans / 405796 / 10-76 / GSLGSIGYGLAAIGPGVGVGIIFGNGTQAMARQPEAAGLIRANQILGFAFCEALALIGLVMPFVYGY----- / H+ / Y / Y
Aquificae / Aquifex aeolicus / 3913149 / 32-100 / YLGAGLAIGLAGLGAGVGMGHAVRGTQEGVARNPNAGGRLQTLMFIGLAFIETIALYGLLIAFILLFVV--- / H+ / Y / Y
Bacteroidetes / Bacteroides fragilis / 53713464 / 18-85 / KLGAALGAGLAVIGAGIGIGKIGGSAMEGIARQPEASGDIRMNMIIAAALVEGVALLALVVCLLVLFL---- / H+ / Y / Y
Cytophaga hutchinsonii / 110279286 / 12-79 / LAGAGIGAGVAALAAGLGIGRIGSSAVESIARQPSESGKIQTAMLIAAALIEGVALFGVVVCLLIALA---- / H+ / Y / ─
Salinibacter ruber / 83758190 / 8-76 / YLAAGLGAGISAVGAAIGIGRLASSSMDGAARQPEAAGDIRGLMIVSAGLIEGVALFALIICLLLVLFV--- / H+ / Y / ─
Chlamydiae / Protochlamydia amoebophila / 46447307 / 29-98 / ALSAPFAVGLAALGSGLGLGRAVSSAMEAIGRQPEASGKILTTMIIGAALIEALTIYALIVFFVVLEKMA-- / H+ / Y / ─
Chlorobi / Chlorobium tepidum / 21672861 / 7-73 / YLGAGIGAGLAAIGAGLGIGNAAASAAEGTARQPEAASDIRTTMIIAAALIEGVALFGEVICVLLALK---- / H+ / Y / Y
Pelodictyon luteolum / 78187939 / 8-75 / YLGAGLGAGLAVIGAGLGIGNIAASAAEGTARQPEATSDIRTTMIIAAALIEGVALFGEVICVLLALK---- / H+ / Y / ─
Prosthecochloris vibrioformis / 145220543 / 8-75 / YLGAGIGAGLAVIGAGLGIGNIAASAAEGTARQPEATSDIRTTMIIAAALIEGVALFGEVICVLLALK---- / H+ / Y / ─
Chloroflexi / Chloroflexus aurantiacus / 163848590 / 6-76 / LVATALAVGLGAIGPGVGIGIIVSGAVQAIGRNPEIENRVVTYMFIGIAFTEALAIFGLVIAFLIGFGVLQ- / H+ / Y / ─
Dehalococcoides sp. CBDB1 / 73660114 / 8-76 / LLAAGLAMGLGAIGPGIGVGILGFGALQAIGRNPEAKGSIFTNMILLVAFAESIAIFALVISIVLIFVA--- / H+ / Y / ─
Herpetosiphon aurantiacus / 159900580 / 8-77 / LLAAALAIGLAAIGPGIGVGLLVAGALQAIARNPETEGSIRTNMFVGIALTEGLAIFGLVISLLIGFGVL- / H+ / Y / ─
Cyanobacteria / Gloeobacter violaceus / 37522478 / 10-81 / VIAAALAVGLAAIGPGIGQGNAASKAAEGIARQPEAEGKIRGTLLLSLAFMESLTIYGLLVSIVLLFANPFR / H+ / Y / ─
Prochlorococcus marinus / 33241057 / 10-81 / VVAAGLAVGLGAIGPGIGQGSAAQGAVEGIARQPEAEGKIRGTLLLSFAFMESLTIYGLVVALVLLFANPFA / H+ / Y / ─
Synechocystis sp. PCC6803 / 114677 / 10-81 / VIAAALAVGLGAIGPGIGQGNASGQAVSGIARQPEAEGKIRGTLLLTLAFMESLTIYGLVIALVLLFANPFA / H+ / Y / ─
Firmicutes
Bacilli / Bacillus subtilis / 16080739 / 3-70 / LIAAAIAIGLGALGAGIGNGLIVSRTVEGIARQPEAGKELRTLMFMGIALVEALPIIAVVIAFLAFFG---- / H+ / Y / ─
Bacillus pseudofirmus / 114665 / 3-69 / FLGAAIAAGLAAVAGAIAVAIIVKATIEGTTRQPELRGTLQTLMFIGVPLAEAVPIIAIVISLLILF----- / H+ / N / Y
Bacillus PS3 / 114678 / 5-72 / VLAAAIAVGLGALGAGIGNGLIVSRTIEGIARQPELRPVLQTTMFIGVALVEALPIIGVVFSFIYLGR---- / H+ / N / Y
Enterococcus faecalis / 29377098 / 6-73 / FIAAAIAIFGSAIGAAIGNGQVISKTIESMTRQPEMSGQLRTTMFIGVALIEAVPILGVVVSLLLLFR---- / H+ / N / Y
Enterococcus hirae / 114669 / 3-71 / YIAAAIAIMGAAIGAGYGNGQVISKTIESMARQPEMSGQLRTTMFIGVALVEAVPILGVVIALILVFAV--- / H+ / Y / Y
Lactobacillus plantarum / 28378943 / 3-70 / AIAAGIAMFGAALGAGIGNGLVISKMLEGMARQPELSGQLRTNMFIGVGLIESMPIISFVVALMVMNK---- / H+ / Y / ─
Lactococcus lactis / 15674249 / 6-71 / AALGAIAIGLAALGAAIGDGLIVSNFLQAVARQPELEGKLRGSMFMGIAFVEGTFFIALAMAFLFR------/ H+ / N / Y
Clostridia / Acetobacterium woodii / 4713918 / 11-82 / SAIGAGIAMIAGVGPGIGQGFAAGKGAEAVGRQPEAQSDIIRTMLLGAAVAETTGIYGLIVALILLFANPFF / Na+ / Y / Y
Acetobacterium woodii / 6014714_1 / 23-99 / SALGIGLAMVAGVGPGIGQGFAAGKGAEAVGKNPTKSNDIVMIMLLGAAVAETSGIFSLVIALILLFANPFI / Na+ / N / Y
Acetobacterium woodii / 6014714_2 / 110-182 / SAMASGIAMIAGIGPGTGQGYAAGKGAEAVGIRPEMKSAILRVMLLGQAVAQTTGIYALIVALILMYANPFL / N
Alkaliphilus metalliredigens / 150388188 / 14-85 / SAIGAGLAMIAGIGPGIGQGYAAGKGAEGVGRQPEAQGDIVRTMLLGAAVAETTGIYGLIIALILLFANPLV / Na+ / N / ─
Alkaliphilus metalliredigens / 150388187_1 / 27-98 / TAIAAGLAMIAGIGPGIGQGFAAGKGAEAASLNPKSAKSASMVMLLGAAVAETSGILSLVVALIMLYANPLV / Na+ / N / ─
Alkaliphilus metalliredigens / 150388187_2 / 110-181 / SVIGAGLAMIAGIGPGIGQGYAAGKGTEMVGKRPQYQPMIVRTMFLGQAVAQTTGIYALIIALVLMFANPLV / N
Carboxydothermus hydrogenof. / 78043573 / 13-82 / AIGAGIAVGFGAIGSGIGQGIAAGKAFEAMARQPEVRGTVQTFLIIALAFMETLTIYGLVIAFMLLNKMS-- / H+ / Y / ─
Clostridium acetobutylicum / 5915735 / 13-81 / QYLGAGLAAIGCIGGGVGIGTVTGKAVEAIGRQPESASKVMPTMIMGLAFAEVTSLYALFVAIMLLFVK--- / H+ / N / Y
Clostridium difficile / 115252533 / 10-81 / SAIGAGIAVATGIGAGIGQGIAAAKAAEAVGNQPEAKGDITSTLLLGVAIAESSAIYGLVISIILLFVNPFF / Na+ / Y / ─
Clostridium paradoxum / 77964176 / 10-81 / SAIGAGLAMIAGIGPGIGQGFAAGKGAEAVGKQPEAQGDILRTMLLGAAVAESTGIYALVVALILLFANPLL / Na+ / Y / Y
Ruminococcus albus / 2662061 / 12-83 / SALGAGLAMIAGIGPGIGEGYAVGKTIESIARQPEAQGDCTRTMFIGVAMAESTGIYAFVVALILMFGNPFI / Na+ / Y / Y
Symbiobacterium thermophilum / 51891224 / 8-77 / ALAAALSISVAAIGATVAQGKATTAAMDAIWRQPEAANDVRGALIVSLALMEAIAIYGLLIGLLIIFMLG-- / H+ / Y / ─
Mollicutes / Mycoplasma genitalium / 12045266 / 32-102 / AYIGAGVTMIAGSTVGIGQGYIFGKAVEAIARNPEVEKQVFKLIFIGSAVSESTAIYGLLISFILIFVAGA- / Na+ / N / ─
Spiroplasma citri / 110004061 / 31-109 / SLLGAGLAAIGCCGSGIGQGYTGGKAVEAIARNPEVESKVRTQYIIAAAITESGSIYALVIAIILAFVTG-- / H+ / Y / ─
Ureaplasma parvum / 13357693 / 41-109 / KYIGTGITMLAAGAVGLMQGFSTANAVQAVARNPEAQPKILSTMIVGLALAEAVAIYALIVSILIIFVA--- / H+ / Y / ─
Fusobacteria / Fusobacterium nucleatum / 19703705 / 14-85 / SAVGAGLAMIAGLGPGIGEGYAAGKAVESVARQPEARGSIISTMILGQAVAESTGIYSLVIALILLYANPFL / Na+ / Y / ─
Propionigenium modestum / 114672 / 14-85 / SAVGAGLAMIAGLGPGIGEGYAAGKAVESVARQPEARGSIISTMILGQAVAESTGIYSLVIALILLYANPFL / Na+ / Y / Y
Planctomycetes / Rhodopirellula baltica / 32473397 / 33-104 / IIMAGLTTAIGSIGPAFAEGRAVAQALNSIAQQPDSSNTITRTLFVGLAMIESTAIYCFVVSMILLFANPFW / Na+ / Y / ─
Kuenenia stuttgartiensis / 91201494 / 7-78 / LAIAVSLLAIAAFGCGIGQGIAVYGAANGMARQPDMAGKIQLVMFVGLAFIESLTIYSLMVSFILLGKLPKT / H+ / Y / ─
Kuenenia stuttgartiensis / 91202299 / 12-83 / IIVAGFTIAVGSIGPALGEARAAAQALSSIAQQPDEANTITRTLFVSMAMIESTAIYCFVVAMIVIFANPFW / Na+ / Y / ─
Proteobacteria
Alpha / Bradyrhizobium sp. BTAi1 / 148252982 / 8-79 / IIGAVIAVSIGSIGPALAEGRSVAAAMDAIARQPEAAGTISRTLFVGLAMIETMAIYCLVVALLLLFANPYA / H+ / Y / ─
Gluconobacter oxydans / 58040600 / 9-80 / IVSAAMAVSFGSIGPALAEGRAVAAAMDAIARQPESAGTISRTLFVGLAMIETMAIYCLVIALLLLFANPLL / H+ / Y / ─
Paracoccus denitrificans / 119385603 / 9-77 / QYLGAGLACVGMAGAAMGVGNVAGNYLAGALRNPSAAASQTATLFIGMAFAEALGIFSFLVALLLLFAV--- / H+ / N / Y
Rhodobacter capsulatus / 75340080 / 10-78 / AYIGAGLACTGMGGAAVGVGHVVGNFISGALRNPSAAASQTATMFIGIAFAEALGIFSFLVALLLMFAV--- / H+ / N / ─
Rhodobacter sphaeroides / 77464618 / 10-78 / KFIGAGLATIGLGGAGIGVGHVAGNFLAGALRNPSAAPGQMANLFVGIAFAEALGIFSFLIALLLMFAV--- / H+ / Y / ─
Rhodobacter sphaeroides / 126464839 / 11-79 / ILGAAFAVGIGSLGPALGEGRAVAAAMEAIARQPEAAGTLSRTLFVGLAMIETMAIYCLVIALLLLFANPFT / H+ / Y / ─
Rhodospirillum rubrum / 114673 / 7-75 / KMIGAGLAAIGMIGSGIGVGNIWANLIATVGRNPAAKSTVELYGWIGFAVTEAIALFALVVALILLFAA--- / H+ / N / Y
Beta / Burkholderia mallei / 53716788 / 10-81 / IAAAALAVSFGAIGPALAEGRAVGAAMDAIARQPDASGTVSRTLFVGLAMIETMAIYCLVVALLLLFANPFV / H+ / Y / ─
Neisseria meningitidis / 15793512 / 5-76 / AIACGLIVALGALGASIGIAMVGSKYLESSARQPELIGPLQTKLFLIAGLIDAAFLIGVAIALLFAFVNPFA / H+ / N / Y
Nitrosomonas eutropha / 114331984 / 12-83 / IFTAGLTIAIGSLGPALGEGRAAAAAIAAIAQQPDAAPTLSRTLFVSLAMIESTAIYCFVVAMILIFANPFW / Na+ / Y / ─
Nitrosospira multiformis / 82702780 / 12-83 / ILTAGLTISIGVIGPALGEGKAVATALTSLAQQPDVAGTIARTLFVGLAIIESLAIYCFVVSMILIFANPFW / H+ / Y / ─
Polaromonas naphthaleni / 121605230 / 12-83 / IVIAGLTTGFGCMGPAFAEGRAVATALTALAQQPDASATITRTLFVGLAMIESTAIYCFVVSMILIFANPFW / Na+ / Y / ─
Rhodoferax ferrireducens / 89899962 / 12-83 / IVIAGITTGFGCMGPALAEGRAVATALTALSQQPDASATITRTLFVGLAMIESTAIYCFVVSMILIFANPFW / Na+ / Y / ─
Gamma / Escherichia coli / 16131605 / 10-79 / YMAAAVMMGLAAIGAAIGIGILGGKFLEGAARQPDLIPLLRTQFFIVMGLVDAIPMIAVGLGLYVMFAVA-- / H+ / Y / Y
Azotobacter vinelandii / 67157244 / 10-81 / ILGAALAVSFGALGPALAEGRAVAAAMDAIARQPEAAGTLSRTLFVGLAMIETMAIYCLVVAVLLLFANPFV / H+ / Y / ─
Hahella chejuensis / 83643799 / 12-83 / TVAAIIGIALGAMLPALAMGKAISSALDALARQPEAEKSITRTLFIGLAMIESLAIYVLVIVLIVLFRNPLL / H+ / Y / ─
Legionella pneumophila / 54298274 / 12-83 / TVIAAIAIAIGTIGPALAMGRAISHALDALARQPEAEKSITRTLFIGLAMIESLAIYCLVIVLIILFRNPLL / H+ / Y / ─
Pseudoalteromonas atlant / 109898984 / 12-83 / IITAGLTIGIGVLGPSLAEGSAVASALKALAQQPDASSTITRTLFVGLAMIESTAIYCFVVSMILLFSNPFW / Na+ / Y / ─
Psychromonas ingrahamii / 119944244 / 12-83 / IIIAGLTTGFGTMGPALAEGRAVAAAMASLAQQPDASSTITRTLFVGLAMIESTAIYCFVVSMIILFANPFW / Na+ / Y / ─
Shewanella frigidimarina / 114564217 / 12-83 / IITAGFTITIGVIGPSLGEGKAVATALSSLAQQPDASATITRTLFVGLAMIESTAIYCFVVTMILLFANPFW / Na+ / Y / ─
Vibrio alginolyticus / 60391833 / 9-80 / AIAVGIIVGLASLGTAIGFALLGGKFLEGAARQPEMAPMLQVKMFIIAGLLDAVPMIGIVIALLFTFANPFV / H+ / N / Y
Vibrio cholerae / 9657371 / 9-80 / AIAVAIIVGLCAVGTAIGFAVLGGKFLEGAARQPEMAPMLQVKMFIIAGLLDAVPMIGIVIALLFTFANPFV / H+ / Y / Y
Delta / Desulfovibrio vulgaris / 46579330 / 10-81 / CLAAAIGMAIAAAGCGIGQGMGLKAACEGTARNPEAGGKIMVTLILGLAFVESLAIYALVVNLILLFANPFM / H+ / Y / Y
Geobacter sulfurreducens / 39995442 / 8-79 / MLAAGFGMAIGAFGTGIGQGLAVKNAVEGVSRNPGASGKILTTMMIGLAMIESLAIYVLVVCLIILFANPYK / H+ / Y / Y
Lawsonia intracellularis / 94987500 / 44-115 / IFGCAIGMALAALGCGIGQGLGLKGACEGIARNPEASGKIQVALILGLAFIESLAIYALVINLIILFANPFV / H+ / Y / ─
Syntrophus aciditrophicu / 85860963 / 12-83 / IVTAGLCMAVGSIGPALGEGNAVKQALTAIAQQPDERNSITRTLFVGLAMIESIAIYCFVISMILIFANPFW / H+ / Y / ─
Epsilon / Campylobacter jejuni / 15792265 / 38-109 / VLAAGLGLGVAALGGAIGMGNTAAATIAGTARNPGLGPKLMTTMFIALAMIEAQVIYALVIALIALYANPFI / H+ / Y / ─
Helicobacter pylori / 15645826 / 32-103 / ILGAMIGLGIAAFGGAIGMGNAAAATITGTARNPGVGGKLLTTMFVAMAMIEAQVIYTLVFAIIAIYSNPFL / H+ / Y / Y
Sulfurimonas denitrificans / 78776630 / 32-103 / MIAAGLGLGLAALGGAIGMGHTAAATIAGTARNPGLGAKLMTTMFIALAMIEAQVIYALVIALIALYANPYL / H+ / Y / ─
Spirochaetes / Leptospira borgpetersenii / 116328618 / 7-78 / YIGVGIAAGVAILGAALGIGRIGGSATEGISRQPEAGGKIQTAMIIAAALIEGAALFALVIAFQAAGTLNEG / H+ / Y / ─
Leptospira interrogans / 24215482 / 16-87 / YIGVGIAAGVAILGAALGIGRIGGSATEGISRQPEAGGKIQTAMIIAAALIEGVSLFALVIAFQAAGTLNEG / H+ / Y / Y
Thermotogae / Thermotoga maritima / 15644363 / 17-85 / YLGAGLCMGIGAIGPGIGEGNIGAHAMDAMARQPEMVGTITTRMLLADAVAETTGIYSLLIAFMILLVV--- / Na+ / Y / ─
Thermotoga neapolitana / 24298785 / 17-85 / YLGAGLCMGIGAIGPGIGEGNIGAHAMDAMARQPEMVGTITTRMLLADAVAETTGIYSLLIAFMILLVV--- / Na+ / Y / ─
Petrotoga mobilis / 145622881 / 27-96 / LLGAGVAMGIGAIGPGVGEGNIGAHAMDAMARQPEMSGNLTTRMLLAMAVTESTGLYSLVVALILLFVLP-- / Na+ / Y / ─
Eukaryota
Fungi / Saccharomyces cerevisiae M / 48428795 / 8-76 / KYIGAGISTIGLLGAGIGIAIVFAALINGVSRNPSIKDTVFPMAILGFALSEATGLFCLMVSFLLLFGV--- / H+ / N / ─
Mycetozoa / Dictyostelium discoideumM / 5915722 / 21-88 / KKVGAGLAAIGLTGAGAGVGIVFAAFILAVGMNPNLRGELFKLAMLGFALSEAVGLLALMMSFLILYS---- / H+ / N / Y
Metazoa / Drosophila melanogaster M / 23172756 / 70-138 / KFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMMAFLLLFAF--- / H+ / N / Y
Bos taurus M / 416684 / 68-136 / KFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM--- / H+ / N / Y
Viridiplantae / Arabidopsis thalianaC / 6685247 / 10-81 / VIAAGLAVGLASIGPGVGQGTAAGQAVEGIARQPEAEGKIRGTLLLSLAFMEALTIYGLVVALALLFANPFV / H+ / N / Y
Arabidopsis thalianaM / 114152776 / 17-85 / KLIGAGAATIALAGAAIGIGNVFSSLIHSVARNPSLAKQLFGYAILGFALTEAIALFALMMAFLILFVF--- / H+ / N / Y
Porphyra purpurea C / 1703750 / 10-81 / VIAAGLAVGLAAIGPGIGQGSAAANAVEGIARQPEVEGKIRGTLLLSLAFMESLTIYGLVVALSLLFANPYV / H+ / N / ─

a Eukaryotic F-ATPase subunits are indicated as M (mitochondrial) or C (chloroplast).

b Gene identification numbers are linked to the corresponding sequences in the NCBI protein database

c Active site residues are indicated indicated in boldface and colored as follows: conserved ion-binding acidic (Glu/Asp) residue - red; other Na+ ligands (see Fig. 3) are in purple.. The hydrophobic residue corresponding to Val63 of Ilyobacter tartaricus c subunit is shaded yellow. The conserved small (Pro, Gly, Ala, Ser) residue, corresponding to Pro28 of I. tartaricus c subunit (see text) is shaded green.

d Predicted cation specificity of the c/K subunit. Ions whose binding has been experimentally studied are shown in bold and colored as in Fig. 5.

e Sequences used to construct sequence logos (Fig. 4) are marked with Y.

f Subunits that have been used to assign cation specificity on Fig. 5 are marked with Y.

2. V- type ATPase c/K subunits

Phylum, class / Organism namea / gi numberb / Residues / 2TM sequence (aligned)c / Iond / Fig.4e / Fig.5f
PDB: 2BL2 / Enterococcus hirae / 66361544_1 / 16-83 / VLAMATATIFSGIGSAKGVGMTGEAAAALTTSQPE----KFGQALILQLLPGTQGLYGFVIAFLIFINLGSD / Na+ / ─ / Y
PDB: 2BL2 / Enterococcus hirae / 66361544_2 / 92-156 / FLGASLPIAFTGLFSGIAQGKVAAAGIQILAKKPE----HATKGIIFAAMVETYAILGFVISFLLVLNA--- / ─
Archaea
Nanoarchaeota / Nanoarchaeum equitans / 41615011 / 3-69 / ALASALAIGLAAFGSAIAQGLAASAAAAATSEKPD----LFGKMLIFAALPETQAIYGLVIAYLLSKIV--- / Na+ / Y / Y
Crenarchaeota / Aeropyrum pernix / 118431830 / 38-102 / AIGAGLAVGLAGIGGGYAVGVAGAAATSSITEKPE----MFGRSLLFVVLGEGIAIYGLLIALLLLLVV--- / H+ / Y / Y
Caldivirga maquilingensis / 159042457 / 43-103 / YLGAGLAFGLAAGGAGIGMGIAGAAIASASIEKR-----DLLIFFLVLAFVETIALYGFVALILLR------/ H+ / Y / Y
Cenarchaeum symbiosum / 118195146 / 36-99 / LLGAGLAFGLAAGGAGIGLGYVGSAGLAVISENPA----LQSKVFIFIGMVESIAIYGIVMMFIILGQ---- / H+ / Y / Y
Hyperthermus butylicus / 124027658 / 55-119 / AIAAALAMGLSAIGAGIALGRTGSAASAAVAEKPE----VSGKLLIYLVLGEGIAIYGLLVAILIIFTG--- / H+ / Y / ─
Ignicoccus hospitalis / 156937475 / 49-113 / AVGAGLALLGGTIGAGYALGATGAAGIAVISEKPE----EFGRVLLFIGIAETPAIYGIAIAIVILFAI--- / H+ / Y / ─
Pyrobaculum aerophilum / 18312157 / 26-87 / YIGAGLAVGLAGLGAGIGVGIAGAAAMSALVEKPQ----ERVWYLIFLALAEAIAIYGLLVSILLI------/ H+ / Y / Y
Staphylothermus marinus / 126466069_1 / 10-77 / YAGAAFALMGGLIGSSIGMGKAGSAGSATLAEDPK----QFRNVFLLASLPMTQTFYGLIILIQYIGYINGH / H+ / ─ / ─
Staphylothermus marinus / 126466069_2 / 89-155 / ILGLGLAVAGAELFSAWFQGVICASGISELPRTKGA---VTFSTMILAVYVELIGILGMVFGFLGLSLIG-- / ─
Sulfolobus acidocaldarius / 74053555 / 36-101 / NIGAGLAVGLAAIGAGVAVGTAAAAGIGVLTEKRE----MFGTVLIFVAIGEGIAVYGIIFAVLMLFAGI-- / H+ / Y / Y
Euryarchaeota
Archaeoglobi / Archaeoglobus fulgidus / 11498760 / 11-75 / AVGAGLAVGLAGIGAGLGESGIGAAAVGATAEDRG----FFGLGILFTVIPETIVIFGLVIAFILMFAF--- / H+ / Y / Y
Halobacteria / Haloarcula marismortui / 55379717 / 26-86 / SAGAALAVGLAALGSGYAERGIGAAAVGAIAEDES----MFGRGLILTVLPETLVILALVVVFVV------/ H+ / Y / ─
Halobacterium salinarum / 1487875 / 25-89 / KAAAALAVGLAALAAGYAERGIGSAAVGAIAEDPD----LFGTGLILTVLPETLVILALVVVFVVPTPF--- / H+ / Y / ─
Methanobacteria / Methanobrevibacter smithii / 148642499_1 / 12-79 / AIGAGVAIGFAGLGSGLGQGMAAAGSVGAVAEDND----MFARGIIFSALPETQAIYGFLIAILLLVFSGLL / Na+ / ─ / ─
Methanobrevibacter smithii / 148642499_2 / 93-160 / AIGVGAAIGFAGLGSGMGQGIAASSSVGAIVEDND----MFARGIIFSALPETQAIYGFLIAILLMVFGGIL / ─
Methanosphaera stadtmanae / 84489931_1 / 13-80 / AIGAGVAVGFAALGSGIGQGIASSASVGAVAEDSS----MFAQGLVFTAIPETQAIYGFLIAILLLVFSGIM / Na+ / ─ / Y
Methanosphaera stadtmanae / 84489931_2 / 93-160 / AIGAGAAVGFGGLGSGMGQGIASSASVGAVVEEPG----MFAQGLVFTAIPETQAIYGFLIAILLLVFGGIL / ─
Methanothermobacter thermauto. / 15678977_1 / 12-79 / AIGAGVAVGFAGLGSGLGQGIAAAESVGAVAENSD----MFARGIIFSTLPETQAIYGFLIAILLLMVFSGL / Na+ / ─ / Y
Methanothermobacter thermauto. / 15678977_2 / 93-159 / AVGAGAAIGFAGLGSGMGQGITSASSVGAVVEDPD----MFARGIIFSALSETQAIYGFLIAILL-MVFGGI / ─
Methanococci / Methanocaldococcus jannaschii / 15668394_1 / 9-76 / AVGAGLAVGIAGLGSGIGAGITGASGAGVVAEDPN----KFGTAIVFQALPQTQGLYGFLVAILILFVFKTV / Na+ / ─ / Y
Methanocaldococcus jannaschii / 15668394_2 / 80-147 / AMFAAGLAAGLAGLSAIGQGIAASAGLGAVAEDNS----IFGKAMVFSVLPETQAIYGLLIAILLLVGVFKG / ─
Methanocaldococcus jannaschii / 15668394_3 / 155-220 / AALGAGFAVGFAGLSGIGQGITAAGAIGATARDPD----AMGKGLVLAVMPETFAIFGLLIAILIMLMIK-- / ─
Methanococcus maripaludis / 45358603_1 / 11-78 / AIGAGLAVGIAGLGSGIGAGITGASGAGVVAEDPN----KFGTAIVFQALPQTQGLYGFLVAILILFVFKSA / Na+ / ─ / Y
Methanococcus maripaludis / 45358603_2 / 82-149 / AMLAAGIGTGLAGLSAIGQGIASAAGLGAVAEDDG----IFGKAMVFSVLPETQAIYGLLVAILLLVGVFAS / ─
Methanococcus maripaludis / 45358603_3 / 156-222 / AALGAGLAVGFAGLSGIGQGITAAGAIGATARDPD----AMGKGLVLAVMPETFAIFGLLIAILIMLGIMF- / ─
Methanomicrobia / Methanococcoides burtonii / 91773219 / 18-79 / AIGAGLAVGLTGLASGIAEKDIGAAAIGAMAENES----LFGKGLILTVIPETIVIFGLVVALLIK------/ H+ / Y / Y
Methanosaeta thermophila / 116754902 / 14-81 / AVGAGLATGLAGIGAGVGEQGIGAAVVGVVAEEPG----FLGKGLFLMLLPETLIIFGLAVSLILMFAWSPF / H+ / Y / Y
Methanosarcina acetivorans / 20092947 / 19-82 / ALGAALAITVTGLASAWAEKEIGTAAIGAMAENEG----LFGKGLILTVIPETIVIFGLVVALLINSA---- / H+ / Y
Methanosarcina barkeri / 72395089 / 18-81 / AVGASIAIALTGIASAIAEKDIGTAAIGAMAENEG----LFGKGLILTVIPETIVIFGLVVALLINSA---- / H+ / ─ / Y
Methanosarcina mazei / 21226886 / 18-80 / ALGAAIAIAVTGLASAIAEKDIGTAAIGAMAENEG----LFGKGLILTVIPETIVIFGLVVALLINQ----- / H+ / ─ / Y
Methanospirillum hungatei / 88603036_1 / 2-69 / AIGAGIAVGCSAIGSGIGVGIVGSAASGVISERSE----KFGMALVFTAIPQTQAIYGLLIAILILQAGGFL / Na+ / ─ / ─
Methanospirillum hungatei / 88603036_2 / 83-150 / VAVAAGLAVGLAGFSAIGQGIAASSGVANTAEKPE----MFGKGVVFSAVCETQAIYGLLIAVLMLALTGIL / ─
Methanospirillum hungatei / 88603036_3 / 162 230 / GLVGAGLAVGLAGFSAIGQGITCSSGIAATARNPG----AIGRSLVFAAMSETFAIFGLLVAILILFGLGLF / ─
Methanopyri / Methanopyrus kandleri / 20094449_1 / 9-77 / AIGAGLAAGVAGVGSGIGQGIAAAAGAGAVAEDEA----TFGKAIVFSVLPETQAIYGLLTAILIMVGIGLL / Na+ / Y / ─
Methanopyrus kandleri / 20094449_2 / 90-157 / AALGAGLAVGLAGISGIGQGIAAASGIGAVLKDEA----LFGRAIVYAVLPETQAIYGLLVAIIIMVGSGLL / Y
Methanopyrus kandleri / 20094449_3 / 171-238 / AAMGAGLAVGLAGTSGIGQGIAAASGIHGVLRKEE----LFGRLIVFSVLPETQAIYGLLTAILIANFVGLL / Y
Methanopyrus kandleri / 20094449_4 / 251-318 / AAMGAGLAVGLAGTSGIGQGIAAASGIKSLIEEEG----VFGRAIVFSVLPETQAIYGLLVAILTLFSLLKP / Y
Methanopyrus kandleri / 20094449_5 / 327-394 / AALGMGLAVGIAGTSGIGQGIAAASGIAGVLRKEE----LFGRLIVFSVLPETQAIYGLLTAILAMFFLGAG / Y
Methanopyrus kandleri / 20094449_6 / 402-470 / AAVGAGLAVGFGGTSGIGQGIAAASGIRAMIERAE----LFVRGMVLSVLPETRAIYGLLIAILALFMMKSG / Y
Methanopyrus kandleri / 20094449_7 / 477-544 / ALIGAGLAVGLVGVSGIGQGFTAATGAATLVKNEG----FFGRAIIFSVLPETQAIYGLLTAILIMMFAGIL / Y
Methanopyrus kandleri / 20094449_8 / 558-625 / AAVGAGLAVGLAGSSAIGQGIAAAAGVGASAEKEE----LFGRSVVFSILPETQSIYGLLIGILLAVFAMKA / Y
Methanopyrus kandleri / 20094449_9 / 634-701 / AALGAGLAVGIAGFSGIGQGIAAAAGIGALKRDPG----SFGRSLIFSILPETRSIYGLLVAILVMVGLGLM / Y
Methanopyrus kandleri / 20094449_10 / 714-781 / AALGAGLAIGLAGLSGVGQGVTAATGISNVVKDPG----MFGRSLLFSVFPETQAIYGLLIAILIMMFAGIL / Y
Methanopyrus kandleri / 20094449_11 / 794-861 / AALGAGIAVGMAGTSGIGQGISAAAGARATAEDPG----NFGRSIVFSILPETQSIYGLLAGILALTPVLTG / Y
Methanopyrus kandleri / 20094449_12 / 873-940 / IGIGAGLAVGVAGTSGIGQGIAAAGGTGALAERTE----MFARSLILSILPETRSIYGLLIAILSMSLTGVL / Y
Methanopyrus kandleri / 20094449_13 / 953-1020 / AAVAAGIAVGFAGLSGIGQGITAARGSASMVRREQ----VFGKSLVFSVLPETQAIYGLLTAILIVFAALAA / Y
Thermococci / Pyrococcus horikoshii / 3258424_1 / 11-79 / SLGMALGAGLAGAASSFGVGIAGAAAAGAVAEDER----NFRNALILEGLPMTQSIYGLITLFLIGMAAGII / Na+ / ─ / Y
Pyrococcus horikoshii / 3258424_2 / 98-162 / ILFGAGLLVGLTGFSAIPQGIIAGSGIGAVSKNPR----TFTQNLIFAAMAETMAIFGLVGAIILIMSL--- / ─
Thermococcus kodakarensis / 57641533_1 / 8-75 / VLGAALAAGIAGIASAFGIGIAGAAAAGAVAEDEK----NFKNALILEGLPMTQSIYGLITLFLIMLSAGII / Na+ / ─ / Y
Thermococcus kodakarensis / 57641533_2 / 90-161 / ILFGAGLTVGLTGLSAIPQGIIASAGIGAAAKNPK----TFTQGVIFAAMAETTAIFGLVGALIMIATGVGF / ─
Thermoplasmata / Ferroplasma acidarmanus / 126008295 / 10-75 / ALAASIAIAGGLIGTGMAQQGIGAAGMGIIAEKPE----KFGQVLFFFVIPETLWIIGFVLGIILLLHVI-- / H+ / ─ / Y
Picrophilus torridus / 48477566 / 11-76 / AVAASIAIAGGLIGTGMAQQGIGAAGMGIIAEKPE----KFGQVLFFFVIPETLWIIGFILGIILLLHVI-- / H+ / ─ / Y
Bacteria
Bacteroidetes / Bacteroides fragilis / 52216885_1 / 9-76 / YIGIAVMVGLSGIGSAYGVTIAGNAAIGALKKNDS----AFGNFLVLTALPGTQGLYGFAGYFMFQTIFGIL / Na+ / ─ / Y
Bacteroides fragilis / 52216885_2 / 88-153 / VLGAGIALGLVALFSAIRQGQVCANGIAAIGQGHN----VFSNTLILAVFPELYAIVALAATFLIGSALA-- / ─
Porphyromonas gingivalis / 34541427_1 / 7-74 / YLGIALMVALTGIGSAIGVTICGNTTVGAMKKNPD----SLGLYIGLSALPSSQGLYGFVGFFMASGLITKL / Na+ / ─ / ─
Porphyromonas gingivalis / 34541427_2 / 88-155 / IFFAGLALGVVGLMSAIRQAQVCANGIQAIGGGHN----VFGATMVMAVFPELYAILALLVSILIFGSVPGM / ─
Chlamydiae / Chlamydia trachomatis / 15605025_1 / 6-73 / VVGPVLAMALAMIGSAVGCGMAGVASHAVMSRIDE----GHGKIIGLSAMPSSQSIYGLIFMLLLNDAIKDG / Na+ / ─ / Y
Chlamydia trachomatis / 15605025_2 / 80-141 / GIVMGIAVGSALLLSAFMQGKCCVSAIQAYARSSA----IYGKSFASIGIVESFALFAFVFALLLF------/ ─
Chlamydophila pneumoniae / 15835627_1 / 6-73 / VVGPALVLGLAMIGSAIGCGMAGVASHAVMSRIDE----GHGKLIGMSAMPSSQSIYGFILMLLMQAAIKNG / Na+ / ─ / ─
Chlamydophila pneumoniae / 15835627_2 / 80-141 / GIAIGLSVGAALLVSSVMQGKCCVSGIQAYARSSS----IYGKCYAAIGIVESFSLFAVVFALLLL------/ ─
Protochlamydia amoebophila / 46447310_1 / 5-72 / MVGPAMALGLSSMGCSIGCWIAGSASHAAMSRTEE----GHGKFIGMAAAPSSQVIYGFLLMLQMSRAIQAG / Na+ / ─ / ─
Protochlamydia amoebophila / 46447310_2 / 79-140 / AIAIGIFSGLAIGLSSIYQGKVCATGIQASLKQPS----VYGKCFAAIGIIESFALFAFVFALLII------/ ─
Deinococcus-Thermus / Deinococcus geothermalis / 94986150 / 41-102 / AIGAGLALGLGALGTGVAQARIGSSLVGAVAEDPS----KAGSLLLYFLIPETLVIFGFLALFILA------/ H+ / Y / ─
Deinococcus radiodurans / 15805723 / 40-101 / AIGKGLALGLGALGTGVAQARIGSSLVGAAAEDPS----KLGQLLLVFLLPETLVIFGFLALFLIR------/ H+ / Y / Y
Thermus thermophilus / 1510114 / 35-99 / AVGMGLAVGLAALGTGVAQARIGAAGVGAIAEDRS----NFGTALIFLLLPETLVIFGLLIAFILNGRL--- / H+ / Y / Y
Firmicutes
Bacilli / Enterococcus faecalis / 29376061_1 / 16-83 / VLGMAMATIFAGIGSAKGVGFTGEAAAALTTEQPE----KFGQALILQLLPGTQGLYGFVIAFLIYINLGND / Na+ / ─ / Y
Enterococcus faecalis / 29376061_2 / 92-157 / YFVAALPIAFAGLFSGIAQGRVAAAGIQILAKKPE----HATKGIIYAAMVETYAILGFVISFLLVLNVK-- / ─
Streptococcus pneumoniae / 15901175_1 / 18-85 / ALGIVLAVGLSGMGSAYGVGKAGQSAAALLKEQPE----KFASALILQLLPGTQGLYGFVIGILIWLQLTPE / Na+ / ─ / ─
Streptococcus pneumoniae / 15901175_2 / 94-158 / YFFVALPIAIVGYFSAKHQGNVAVAGMQILAKRPK----EFMKGAILAAMVETYAILAFVVSFILTLRV--- / ─
Clostridia / Caloramator fervidus / 87082843_1 / 21-88 / LLGAALAALMAGIGSAKGVGIVGQSAAGLITEEPE----KFGQSLILQVIPGTQGFYGFITALIVLSRIGLL / Na+ / ─ / Y
Caloramator fervidus / 87082843_2 / 103-169 / LLMACLPMAFVGYSSAISQGKTAAAGIQILAKRPE----KMFNGVIYAVMVETYAVVALITSILMIVNIKI- / ─
Clostridium perfringens / 18310624_1 / 19-86 / AFGIALAVGMSGIGSAKGVGIVGEAAAGLVTEEPE----KFGKALVLELLPGTQGLYGFVIGFLVFNQISNG / Na+ / ─ / Y
Clostridium perfringens / 18310624_2 / 96-163 / LLFACLPIAIAGLWSGISQGKAAAAGIQILAKRPE----HNTKGIIFAAMVETYALLGFVISFLLVNGASVI / ─
Thermoanaerobacter ethanolicus / 76588877_1 / 11-78 / LLGAAMAVFLPGIGSAKGVGMVGEAAAGVVTEDPS----KFSQTLILQALPGTQGIYGLLTGFVVMQRIGIL / Na+ / ─ / Y
Thermoanaerobacter ethanolicus / 76588877_2 / 93-160 / VFAACLPIAIVGLLSAISQARAAAAGVGIVAKRPE----ELAKGITYAAMVETYAVLALLASILMLFGLKLA / ─
Mollicutes / Acholeplasma laidlawii / 162448015 / 82-149 / YLGAAISTGASALGAGIAVAAAAPAAIGAISENPK----NLGKSLIFVALGEGVAIYGMLISILILNTIPAI / H+ / Y / ─
Fusobacteria / Fusobacterium nucleatum / 19705061_1 / 18-85 / VLGAVIAVLLSGIGSAKGVGIAGQAAAGLIIDEPE----KFGKAMVLQLLPGTQGLYGFVIGLLIMFRLTSQ / Na+ / ─ / ─
Fusobacterium nucleatum / 19705061_2 / 94-160 / LLMAGLPVGLVGLKSALYQGQVAVAGINILAKNEA----HQTKGIVLAVMVETYAVLAFVMSLLLLNQVQF- / ─
Proteobacteria
Alpha / Stappia aggregata / 118434482_1 / 9-77 / WFGLFAPVALGAIGSAWGCALGGSAAIGAMLDSDG----GYGRFIGVSLMPSSQVIYGIVIMFSLQQPTIDA / H+ / ─ / ─
Stappia aggregata / 118434482_2 / 83-149 / LFGIGLLSGVTMLYTGIRQGEVLASAIHASKAKPE----IFGISLAPAAVLEGFSVFALVFALVLSGSIPA- / ─
Gamma / Beggiatoa sp. PS / 153870236 / 84-148 / IIGIGIPTAFASLGAAIAVGPVGAASLAVIAEKPE----MFGRTLVYLGLAEGIAIYGLVVTILLLGKL--- / H+ / Y / ─
Nitrosococcus oceani / 77165551 / 87-148 / LLAIGLPTAVATVAAGLAVGAVGSSALAAISEKPE----LFGRTLIYLGLAEGIAIYGVVVTILMLGKI--- / H+ / Y / ─
Delta / Anaeromyxobacter dehalogenans / 86157624 / 7-71 / TLAAALAVGVTALATAWVQSRIGSAGAGALAEKPE----VRGAVIVMLAIPETLVILGFVVAVLILTGG--- / H+ / Y / ─
Geobacter uraniumreducens / 148262502 / 7-70 / GFAAALAIGLPAIATGWAQSKIGSAGAGAVAEKPE----LTGTMLIMLAIPETMVILGFVVAAMILYL---- / H+ / Y
Spirochaetes / Borrelia burgdorferi / 2687983_1 / 5-76 / LIGVNSALTISAIGSALGMGAAGSAAIGAWKRCYMQPAPFGKLLIVFVSAPLTQIIYGYILMNTLYEVMMQT / Na+ / ─ / Y
Borrelia burgdorferi / 2687983_2 / 81-144 / LLGAGIGGGFAIAVSGFAQGKAAAGACDAFSETGKG----FATYLLVLGLIESVALFVMVFLMIFKFV---- / ─
Treponema pallidum / 15639421_1 / 5-76 / MFGAAAVLGISAVGSALGLALAGQGTIGSWKRCYLNPAPFNKILLAFAGAPLTQTIYGFLLMKAMFSSEKDP / Na+ / ─ / Y
Treponema pallidum / 15639421_2 / 79-140 / LLGAGVACGLGIAASALSQGRAAAAGADALAETGKG----FSQYLTIVGLCETVALLVMVFGIINC------/ ─
Thermotogae / Thermotoga neapolitana / 24298772 / 79-143 / LLAVALSTGLAAVGAGVAVGMTGAASIGAISEKPEM----LGRTLIYVGLGEGIVIYGLIISIIILGRL--- / H+ / Y / ─
Thermotoga sp. RQ2 / 161405925 / 78-142 / LMAVALSTGLAAVGAGIAVGMTGAASVGAISEKPEL----LGRTLIYVGLAEGIVIYGLIVSIMILGRL--- / H+ / Y / ─
Eukaryota
Fungi / Saccharomyces cerevisiae / 137481_1 / 14-81 / AIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDL----LFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQK / H+ / ─ / Y
Saccharomyces cerevisiae / 137481_2 / 90-157 / QLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRL----FVGMILILIFAEVLGLYGLIVALLLNSRATQD / ─
Mycetozoa / Dictyostelium discoideum / 1718094_1 / 33-100 / AMGVTAALVFTVMGAAYGTAKASVGISNMGVMKPDL----VIKAFIPVIFAGVIAIYGLIICVILVGGIKPN / H+ / ─ / Y
Dictyostelium discoideum / 1718094_2 / 111-178 / DLGAGLTVGLCGLAAGMAIGIVGDSGVRAFGQQPKL----YVIMMLILIFSEALGLYGLIIGILLSSVSDTY / ─
Metazoa / Drosophila melanogaster / 137478_1 / 18-85 / VMGAASAIIFSALGAAYGTAKSGTGIAAMSVMRPEL----IMKSIIPVVMAGIIAIYGLVVAVLIAGALEEP / H+ / ─ / Y
Drosophila melanogaster / 137478_2 / 96-159 / HLGAGLAVGFSGLAAGFAIGIVGDAGVRGTAQQPRL----FVGMILILIFAEVLGLYGLIVAIYLYTK---- / ─
Bos taurus / 137477_1 / 16-83 / VMGASAAMVFSALGAAYGTAKSGTGIAAMSVMRPEM----IMKSIIPVVMAGIIAIYGLVVAVLIANSLNDG / H+ / ─ / Y
Bos taurus / 137477_2 / 92-155 / QLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRL----FVGMILILIFAEVLGLYGLIVALILSTK---- / ─
Viridiplantae / Arabidopsis thaliana / 27923954_1 / 17-84 / FLGAAAALVFSCMGAAYGTAKSGVGVASMGVMRPEL----VMKSIVPVVMAGVLGIYGLIIAVIISTGINPK / H+ / ─ / Y
Arabidopsis thaliana / 27923954_2 / 96-163 / HLSSGLACGLAGLSAGMAIGIVGDAGVRANAQQPKL----FVGMILILIFAEALALYGLIVGIILSSRAGQS / ─

a Eukaryotic F-ATPase subunits are indicated as M (mitochondrial) or C (chloroplast).

bGene identification numbers are linked to the corresponding sequences in the NCBI protein database

d Predicted cation specificity of the c/K subunit. Ions whose binding has been experimentally studied are shown in bold and colored as in Fig. 5.

e Sequences used to construct sequence logos (Fig. 4) are marked with Y.

f Subunits that have been used to assign cation specificity on Fig. 5 are marked with Y.