Multiple alignements used to produce the consensus sequences shown in figure 2.

First Transmembrane regions of TolQ and ExbB.
TolQ Sequences
E.coli ASLLVKLIMLILIGFSIAS-WAIIIQR
H.influenzae ASIVVQLVIVILISFSIIS-WAIIIQR
V.cholerae ......MVMLTLLGMSVAS-WAAIIKR
X.fastidiosa ASIPVKIIVLLLLLGSFTS-WVIIFRK
P.aeruginosa ASIVVQLVMLTLVAASVTS-WIMIFQR
R.capsulatus ASLTVKLVMILLTLASFWS-WSIMIRK
H.pylori LDSIVYFFNKSGFVTTLVLVWISLYLV
C.jejuni ..MNFEAIFHFFNSSSIIT-YIVLLWL
C.trachomatis ADLFGKVIFFSLFALSICT-WTVLHQK
C.pneumoniae ADFFGKSIFFCLLILSVCT-WTVLHQK
C.tepidum SGPVVVMVLLVLILFSIIS-WAIIAWK
TolQ Consensus a...v..v...l...S..s*W..i...

ExbB Sequences
E.coli ADIVVKCVMIGLILASVVT-WAIFFSK
S.typhi ADIVVKCVMIGLILASVVT-WAIFFSK
S.paratyphi PFLGTVGSISPYIGLFGTV-WGIMHAF
S.typhimurium ASLLVKLIMLILIGFSIAS-WAIIIQR
H.influenzae QQYSDYFIIGLLLLMSIIM-LAMVIER
V.cholerae ......MVMLTLLGMSVAS-WAAIIKR
V.cholerae2 LQAGGVIGNVILVLLGVGLIIALYRGA
X.fastidiosa EFAVSWAVLIILVTMSSLS-WYWTVIN
Y.pestis QGRVMKGVMVLLLATGLASHAQAAPGN
P.aeruginosa2 LESVEGAVIWLLVGFSVVT-WGLALVK
P.aeruginosa3 LLLTSLICLGLLAPASASA-WWQDDWQ
P.aeruginosa ........MMLPIILSSIAATAIVAER
B.pertusis NLLREAGWPIWPLLATSILGLALIVER
B.pertusis2 SDFVGKTLFIILIVMSLVT-WYLIVVK
B.bronchiseptica NLLREAGWPIWPLLATSILGLALIVER
N.gonnohreae GDPVLIGVFVLMLLMSTVT-WCLVVLR
A.actinomycetemcomitans QNYSDYIIIGLLLFMSVLM-LTMVIER
P.multocida QQYIDYIILGLLAFMSFIMVW-LVIER
P.multocida2 ASIVVQFVIVILIIFSIMS-WAIIIQR
S.putrefaciens2 TLHGQLGSLTWPLLICAFLALMICLER
S.putrefaciens ........MFTLLGLSIMS-WTVILQR
T.ferrooxidans21
T.ferrooxidans LAAVSGGILYLMPLLLLVV-LFVALER
R.capsulatus ADILVQGVMLGLLAASVLA-WAIWAGK
R.prowazekii ADIIGKSVMLMLLFASIWS-WSIILHK
H.pylori KEMVDYGIIGFLIFLSVIV-IAIAIER
H.pylori2 KDYVDIFVFAVLGVASFLALWF-AIER
C.jejuni2 ADEVVKGVIYILVLFSILA-WAVFISK
C.jejuni KDYIDLIIFLILGIMAFIAFWC-VVER
P.gingivalis .MKKLFATIACVAFMSVGF-MTQAFAQ
Synecho1 EFLKGGVVMFPLLLLSILA-LTTAFER
Synecho2 LMQKGGVAMWPLLLLSILS-VSTIIER
Synecho3 ..MAGGIVAVPLLGFSLLA-VALIIER
A.aeolicus WIEKGGIVMYPLILLSILS-WYVIIER
A.aeolicus2 KELIDYGIMGTLLFMSFVA-LAVGIER
D.radiodurans LARAAGPLLWVLLALSLYV-VYLTVAR
M.thermoautotrophicum MFRSGGVITYLIAAIGIYG-FITALEK
ExbB Consensus ...........l...s.i.*w....er

Notes
1This T.ferroxidans ORF does contains only 2 predicted transmembrane helices homologous to the TolQ-II and TolQ-III helices.

C terminal Transmembrane helical hairpin of TolQ, ExbB and MotA
TolQ Sequences
E.coli PFL-GTVGSISPYIGLFGTVWGIMHAFIALGA-VKQATLQ---MVAPGIAEALIATAIGLFAAIPAVMAY-NRL
H.influenzae PFL-ATVASVSPYIGLFGTVWGIMHAFMALSG-AKQATLQ---MVAPGIAEALIATAIGLFAAIPAVMAY-NRL
V.cholerae PFL-ATVGSISPYIGLFGTVWGIMHAFIALGE-VKQATLA---MVAPGIAEALIATAIGLFAAIPAVMAY-NRL
X.fastidiosa -ELLANIGSTAPYVGLVGTVFGIMVTMHDMISSGDQAGIA---AVAPGISEALFATAVGLFVAIPAVWAY-NRF
P.aeruginosa PFL-ATVGSTSPYVGLFGTVWGIMNSFRGLAT-VQQATLA---TVAPGIAEALIATAIGLFAAIPAVIAY-NRF
R.capsulatus SFL-ATVGSTAPFVGLFGTVWGIKVAFEEIAI-SQNTSLA---VVAPGISEALVATAIGLVAAIPAVIAY-NKL
H.pylori VVL-SIISSTAPFIGLFGTVVEILEAFNNLGT-LGQASFG---VIAPIISKALIATAAGILAAIPAYSFY-LIL
C.jejuni TWL-SIIASTSPFIGLFGTVISILETFGGLGT---QNSLS---IIAPKISEALVATGCGILVAIPAYTFH-LII
C.trachomatis -FIPATTISLAPFLGLLGTVWGILLAFAHIST--GQANGT---IMMEGLATALGTTIVGLFVAIPSLVGF-NYL
C.pneumoniae -FIPATTISLAPFLGLLGTVWGILVAFTHISS--GSSGNS---AIMEGLATALGTTIIGLFVAIPSLIAF-NYL
C.tepidum PFL-ATVGNTAPFIGLFGTVWGIMSSFQNIGL-MKSASLA---AVAPGISEALVATATGLVAAIPAVMGY-NY-
TolQ Consensus .fL-atvgS.aP.iGLfGTVwgIm.aF.....-..qa.l.---.vaPGI.eAL.aTaiGlfaAIPav.ay-n.l
ExbB Sequences
E.coli GYL-ATIGAISPFVGLFGTVWGIMNSFIGIAQ-TQTTNLA---VVAPGIAEALLATAIGLVAAIPAVVIY-NVF
S.typhi GYL-ATIGAISPFVGLFGTVWGIMNSFIGIAQ-TQTTNLA---VVAPGIAEALLATAIGLVAAIPAVVIY-NIF
S.paratyphi PFL-GTVGSISPYIGLFGTVWGIMHAFIALGA-VKQATLQ---MVAPGIAEALIATAIGLFAAIPAVMAY-NRL
S.typhimurium PFL-GTVGSISPYIGLFGTVWGIMHAFIALGP-VKQATLQ---MVAPGIAEALIATAIGLFAAIPAVMAY-NRL
H.influenzae TVI-STIGANAPYVGLLGTVIGILLTFYQIGH-GGGDIDP--SVIMLHLSLALKATALGILVAIPSMVFY-NGL
V.cholerae PFL-ATVGSISPYIGLFGTVWGIMHAFIALGE-VKQATLA---MVAPGIAEALIATAIGLFAAIPAVMAY-NRL
V.cholerae2 SML-KLLAALAPMLGLLGTVTGMIETFQVITQ-FGNGDPK---VMAGGISMALVTTVEGLIAAIPLLLAH-NIL
Y.pestis GFL-ATIGAISPFVGLFGTVWGIMNSFIGIAH-SQTTNLA---VIAPGIAEALLATALGLVAAIPAVVIY-NIF
X.fastidiosa TLL-ATVGATAPFVGLLGTVWGIYNALITIGA-TGSASID---AVAGPVGEALIMTAIGLFVAIPAVFAF-NFF
P.aeruginosa2 AVL-ASIGSTSPFIGLFGTVWGIMEALKGISA-AGSASLE---TVAGPIGSALIATGVGIAVAVPAVLVY-NYF
P.aeruginosa3 SSL-SNAIAGGPYIGLLGTVLGIMVVFLGTAM-AGDVNIN---AIAPGMAAALLATAMGLFVAIPALFGY-NRL
P.aeruginosa NAL-GTIAAMAPLLGLLGTVFGMIQIFGAFMD-NGMANSP---MLAAGISKALITTAAGLLVAIPAVFFH-RYL
B.pertusis SAI-GTIAVVAPLMGLFGTVVGMIEIFGSYA--PGASDPA---QLARGISIALYNTGFGILIAIPAMIVH-RYL
B.pertusis2 TVL-ASVGSTAPFVGLFGTVWGVYHALVGIGL-SDGVTIN---RIAGPVGEALIMTGLGLAVAIPAVLAY-NAF
B.bronchiseptica SAI-GTIAVVAPLMGLFGTVVGMIEIFGSYA--PGASDPA---QLARGISIALYNTGFGILIAIPAMIVH-RYL
A.actinomycetemcomitans TIV-STVGANAPYVGLLGTVIGILLTFYQIGQSGGEVDAG---EIMLHLSLALKATALGILVAIPSMIFY-NAL
P.multocida TAI-STIGSNAPYVGLLGTVIGILLTFYELGHSGGDIDAA---AIMVHLSLALKATAVGILVAIPAMVCY-NGL
P.multocida2 PFL-ATVASISPYIGLFGTVWGIMHAFMALSG-AKQATLQ---MVAPGIAEALIATAIGLFAAIPAVMAY-NRL
S.putrefaciens2 KIL-QVIGIISPLLGLLGTVLGLIDMFAQLGQSQGPVTPA---QLSAGLGLAMNTTAAGLIIAVPTITAA-HLF
S.putrefaciens PLL-ATIGSTSPYIGLFGTVWGIMNSFIAIGS-MENATLA---MVAPGIAEALIATAMGLFAAIPAVIAY-NRF
T.ferrooxidans2 NFL-GSIAGVAPLLGLLGTVFGIMHAFAAIGM-VGAGDPK---ALASGIAEALITTASGLIVAIPSLMFY-RYF
T.ferrooxidans WIL-DTAVTLAPLLGLLGTIIGMFNAFQILGN--PDTAPT---AITGHVAEALVATATGLAIAIVGLVLF-NGL
R.capsulatus TAV-GSIGSTAPFVGLFGTVWGIMNAFVGIAE-SGSSNLA---VVAPGIAEALMATALGLVAAIPAVLLY-NHL
R.prowazekii NVL-ATIGSSAPFIGLFGTVWGIMHSFQSIAS-SKNTSLA---VVAPGIAEALLATAIGLFVAIPAVIFY-NYL
H.pylori TLV-ATIGSNAPYIGLLGTVMGIMLTFMDLGSASGIDTKA----IMTNLALALKATGMGLLVAIPAIVIY-NLL
H.pylori2 TIL-YVIFSNAPYVGLLGTVLGIMVIFYDMGVSGGMDAKT----IMVGLSLALKATALGLAVAIPTLIAY-NSL
C.jejuni2 SLL-ASIGASAPFIGLFGTVWGIMNAFIGIAN-LGNASLA---VVAPGIAEALFATAFGLIAAIPAVLFY-NYL
C.jejuni TTI-YIIYSNAPYIGLLGTVIGIMVTFYEMGL-AGNIDVK---SIVVGLSLALKATALGLLVAIPALMAY-NAL
P.gingivalis SWITLFIA-MAPSLGFLGTVVGMVMAFDKIER-VGDISPT---VVAGGMKVALITTIGGLIVALILQVFY-NYI
Synecho1 KLL-ETIIALAPLLGLLGTVTGLIRTFNNLNI-GGGGSSAEATQAASGIGEALITTAAGMMVAIFALLVF-RVL
Synecho2 KIL-EAIIALSPLLGLLGTVLGLIQSLSSIQISDLGTAST--AGVTLGIGEALISTAAGLIIAIVSLAFY-RVF
Synecho3 TLF-QTIITVSPLLGLLGTILGLMRSFSSMSL--GSTTAANASGVTGGISEALVSTVMGLVVAIATLLFA-NVF
A.aeolicus PIL-STTASVAPLLGLFGTITGLIKVFQAYAI-TTQGEAM--NLLAKGISEVLVAAATGLGVAIPALLAY-WVY
A.aeolicus2 YII-ATVASNAPYVGLLGTVLGILLTFYIIGE-KGI-VNT--KEIMVGLALALKATALGLIVAIPSTILY-NFL
D.radiodurans SAL-GTAAQIAPLLGLLGTVVGMVRSFLVFSA-TNNPTPT---ELAQGISEALINTAAGLIVAIVAYVAR-NAL
M.thermoautotrophicum GTL-RTIIEVAPMLGLIGTVIGIWYTFRAL---GVNADPA---AMAEGIYVALITTILGLAVAIILMPLY-SYI
ExbB Consensus ..l-.tia..aPllGllGTV.Gi...F.....*.g.....--*..a.gi..AL..ta.Gl.vAIpa...y-n.l
MotA Sequences
E.coli ANSLALVGDSLPAFGIVAAVMGVVHALGSADR-PAAE-------LGALIAHAMVGTFLGILLAYGFISPLATVL
P.aeruginosa SHAVTKVADALPGFGIVAAVLGIVITMALLGEGSQAE-------IGHHVAAALVGTFLGILAAYGFVGPLAGAL
P.aeruginosa2 AKVFESMGGYAPTIGIIGAVMGLIHVMGNLAN-PAQ--------LGSGIAVAFVATIYGVGFANLLLLPIGNKL
R.meliloti YHAMTTMGDALPAIGIVAAVLGVIKAMGAISEAPEV--------LGAKIAAALVGTLLGVFLSYSIVGPLVANI
R.sphaeroides QGAVKAWIDIGPAMGMVGTLIGLVLMLGNMSD-PKS--------IGPAMAVALLTTLYGALMANVIFAPILNKL
C.crescentus AHALTQLSDGLPALGIVAAVLGVIKTMGSITEPPAV--------LGTMIGGALVGTFMGVFMAYGLVGPMATRL
H.pylorii -HYWETAGETAPTMGLVGAVMGLMLALQKLDN-PAE--------MAAGIAGAFTATVTGIMCSYAIFGPFGHKL
B.burgdorferi SDLFKTWAKLAPAFGMTGTLIGLVALLGNLED-KSA--------LGSSMAVALITTLYGTIMANLMFTPVQLKL
T.pallidum -SLLNSWAALAPGYGMLGTVMGLIGMLATLED-KSS--------LGSNMATALITTFYGSLVQNWFITPVATKL
B.subtilis --IFTQAGTYAPTLGVLGAVIGLIAALSHMDN-TDE--------LGHAISAAFVATLLGIFTGYVLWHPFANKL
A.aolicus -AVWEKLADLFPAFGMIGTLIGLIQMLRNLND-PSA--------LGPGMAVALITTLYGAILANAFAIPVANKL
MotA Consensus ...........P..G..gav.Gl...l.....-p..*-------lG...a.Al..T..G...a.....P...kL
Overall Consensus ..........aP..G..gtv.Gi.........-.......--......i..AL..T..G...A........n.l

 

N Terminal transmembrane helix of TolR, ExbD and MotB
TolR sequences
E.coli RGRGRRDLKSEINIVPLLDVLLVLLLIFMATAPIIT
H.influenzae RQRKA--IKSEINIVPFLDVLLVLVLIFMATAPIIS
V.cholerae QTKKREM-KAEINVVPYIDVMLVLLIIFMVTSPFVT
X.fastidiosa RRKRRKL-KSEINVVPYIDVMLVLLVIFMVTAPLLT
P.aeruginosa R-HKRKP-VAEMNVVPYIDVMLVLLVIFMVTAPMLN
R.capsulatus GGKGKHAVMAEINVTPMVDVMLVLLIIFMVAAPMMT
H.pylori YDNYWDEDKPELNITPLVDVMLVLLAILMVTTPTLT
C.jejuni ..MPFDDEKPELNITPLVDIMLVLLAILMVTAPSIT
C.trachomatis VY-EDLEEDPSVSLTPLIDIVFVILMAFMIAMPLIK
C.pneumoniae RFTEEIEEEPLVNLTPLIDIVFVILMAFIVAVPLIK
C.tepidum MTGQKTRLMSEINVTPFVDVMLVLLVIFMVTAPMMT
TolR Consensus ..........e.N..P..DvmlVlL.IFMvtaP..t
ExbD Sequences
V.cholerae ..MNSAFSFLLDYWQPLDEFMAQGGAVLWWLAVVVL
S.typhi ENLDDNGEMHEINVTPFIDVMLVLLIIFMVAAPLAT
S.paratyphi RGRGRRELKSEINIVPLLDVLLVLLLIFMATAPIIT
S.typhimurium RGRGRRELKSEINIVPLLDVLLVLLLIFMATAPIIT
Y.pestis DSLDESGELHEINVTPFIDVMLVLLIIFMVAAPLAT
X.fastidiosa SNGNSNGPMADINVTPLVDVMLVLLIIFIITAPLMS
X.fastidiosa2 SSGSNRGPMADINVTPLVDVMLVLLIIFIVTAPIMT
B.pertusis NKGSXSHTXSEINMVPLIDVMLVLLVIFIITAPLLA
B.bronchiseptica RDGRASQDELEINLIPLIDVLLVILIFLAATTSFAR
S.putrefaciens2 AGISALEPLPSVDLTALIDIIFIVLVFLLLTANSRL
S.putrefaciens YQRKRRRPVAEINVVPYIDVMLVLLIIFMVTAPIVT
T.ferrooxidans2 NLRQRVSEEPEINVISMVDIVLVLLLFFMVTSSFVH
T.ferrooxidans .MRYFEARKGRIEIIPMIDIMLFLLVFFIMITLRMI
P.multocida .....MKKFDEINIIPFIDIMLVLLAIVLITASFIS
P.multocida2 YRRKRRDVKSEINIVPFLDVLLVLLLIFMATAPIIS
R.prowazekii NRKSKKAVVSDINVTPLVDVMLVLLIIFMVTSPMLV
M.thermoautotrophicum RYRNKIHGKPRFNMVPFIDILFTILIFLVVTATFSG
Synecho1 RLRFREEERAYIDVVPLVDTLLAVFLFLAILAFQSP
Synecho2 RLPDEFEAQGEINIIPMIDVIFSILAFFIISSLYLS
R.capsulatus SDGEDLTPEAAINITPFIDVMLVLLIIFMVAAPLST
E.coli ENLDDNGEMHDINVTPFIDVMLVLLIIFMVAAPLAT
H.influenzae .....MKKFDEINIIPFIDIMLVLLTVVLITASFIS
P.aeruginosa2 STQDSDEVLSEINVTPLVDVMLVLLVVFIVTAPLLT
P.aeruginosa3 HDDDDDGAVDSINITPLVDVLMVVLVMFILTATAQV
P.aeruginosa RAGA-AREDVFINLASLIDVIFVLLLFFVVSTTFTR
B.pertusis RA---SQDELEINLIPLIDVLLVILIFLAATTSFAR
H.pylori .....MKKVESMNVVPFIDIMLVLLVIVLTTASFVQ
P.gingivalis MAVTKIRKVSSWTLISIVTISVIVVLAFFFGGNHVE
D.radiodurans RLRD-DVEGVTFDFAPMVDIVLLLLIFFFLTSNLGA
A.aeolicus RSME-EKEISSMNVIPLVDIMLVLLTIVLTTATFIA
ExbD Consensus ............n..p..Dv.lvll..f..t.....
MotB Sequences
E.coli RKAKSHGAAHGSWKIAYADFMTAMMAFFLVMWLISI
P.aeruginosa VKRYAAGHHGGSWKIAFADFATAMMAFFLVLWLLSS
A.hydrophila RR-NSAPKGGGACKVAFADFTLAMMAFFMVLWILAV
C.crescentus KKGGGHGHHGGAWKVAYADFVTAMMAFFLLMWLLNT
H.pylorii KP--TECPAGEKWAVPYADFLSLLLALFIALYAISA
B.burgdorferi KP-SKCDEGSPDYMLTYGDMVTLLLVFFVTMFSLND
T.pallidum R---APRGAAQGWLTTYSDMVTLMLCFFVMLFNPTE
B.subtilis KKKHEDEHVDESWLVPYADILTLLLALFIVLYASSS
C.acetobutylicum RKKHEEPENSERWLLTYSDLITLLMAFFIVMYASST
A.aolicus K---EECPKPPAWLTSFGDLMSLLLTFFILLYSMSI
MotB Consensus k.......a...Wl..yaD..tl..afF......s.
Overall Consensus ...............p..D....ll..f........

For generating the Consensus sequences within groups the sampling rules were: That residues represented in the consensus sequence appear in all three types of sequence. That the distance between any two sequences sampled be greater than .

For generating the overall consensus the additional sampling constraint was that the different types of sequence were equally probable.