#NEXUS [saved by seaview on Thu Nov 13 11:49:19 2014] BEGIN DATA; DIMENSIONS NTAX=29 NCHAR=763; FORMAT DATATYPE=PROTEIN GAP=- ; MATRIX [1] APyrobaculum -------------------------------------MSGKIEYISGPVVKAE----LPG ARLYELVFV--------GE---IKLFGEVVRIQGEKAFIQV-YEDTTGLK-PGEPVERTG EPLS-------AWLGPTIIGKIYDGVQRPLRNIEEISKNPFIARGIGYDKAPPLDLKAEF DFKP--AVKPGEEVYPGDVLGSVKETEPMT-HYILYPPLPEHAPGVV------------- -EWIADGKYKVDD--VIARVKTKRGVVEVKMWHKWPVRRPRPFKEKLPP-VEPLITGVRT VDTMFPIAKGGTAAVPGPFGSGKTVMIRTLSMF--------------------AQSRFII PVLCGERGNEAADALQGLLKLKDPS-------TGR--------PLLERTTIIVNTSNMPV AAREASVYMGTTLGEYFRD-QGYDVLVLADSTSRWAEAMREVALRIGEMPSEEGYPAYLP TRLAEFYERAGRVVLYGSKE----------------------------RVGSLTIAASVS PPGGDFT-EPVTSNTLRFIGAFWPLSPRLAYSRHYPAIDWLVAFSRYVDTVEVWWSKNVS PEWRRIRDALQSILVKEAELQEIVRIL----GTEALSEYEKHILNVAFMIREGFLKQDAY NPVDTPSAPIKQFLLMKAIYTYYEEGLKAIE-------SGVPASVLREL---ETVKRLP- RLRMEVTNDV-----AKEELTKFIESLVAEIRATTNRRG---- [2] ACyanidium ----------------------------MTTVRVNGMKNGIIKKVSGPVVSAE---NMDG AAMYELVRV--------GN---EQLVGEIIRLEGSVATIQV-YEETSGLT-IGDPVLCTG SPLS-------VELGPGLMGNIFDGIQRPLEKIAERSNSVFIPRGVN---VPALDRKKVW EFRPADNLKVGDPITAGDIYGIVPETPLID-HKIMLPP---NQMGKIV------------ -FLAPPGDYTLED--TVLEIDFNGQKKKFSMVHQWPVRLPRPVTEKLRA-DKPLLTGQRV LDALFPSVQGGTCAIPGAFGCGKTVISQALSKF--------------------SNSDGIV YVGCGERGNEMAEVLKDFPELTMTV------GD-REE------SIMKRTLLVANTSNMPV AAREASIYTGITVSEYYRD-MGLNISMMADSTSRWAEALREISGRLAEMPADSGYPAYLA ARLASFYERAGKVSCLGSPN----------------------------RQGSITIVGAVS PPGGDFS-DPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMKALEPYY-EERF PEFLNYQQKAREILQTEDDLMEIVQLV----GKDSLAENDKITLEVAKMIREDFLAQNSF TEYDRFCPFYKSVLMLRNMIHFYELANKAVEGSGE---QHLTLAQIKEQM-GETIYKIS- GMKFLDP--------------------AQGWSLF--------- [3] A1Homo1_Ho ---------------------MDFSKLPKILDEDKESTFGYVHGVSGPVVTAC---DMAG AAMYELVRV--------GH---SELVGEIIRLEGDMATIQV-YEETCGVS-VGDPVLRTG KPLS-------VDVGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVN---VSALSRDIKW DFTPCKNLRVGSHITGGDIYGIVSENSLIK-HKIMLPP---RNRGTVT------------ -YIAPPGNYDTSD--VVLELEFEGVKEKFTMVQVWPARQVRPVTEKLPA-NHPLLTGQRV LDALFPCVQGGTTAIPGAFGCGKTVISQSLSKY--------------------SNSDVII YVGCGERGNEMSEVLRDFPELTMEV-------DGKVE------SIMKRTALVANTSNMPV AAREASIYTGITLSEYFRD-MGYHVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLG ARLASFYERAGRVKCLGNPE----------------------------REGSVSIVGAVS PPGGDFS-DPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYY-DKHF TEFVPLRTKAKEILQEEEDLAEIVQLV----GKASLAETDKITLEVAKLIKDDFLQQNGY TPYDRFCPFYKTVGMLSNMIAFYDMARRAVETTAQSD-NKITWSIIREHM-GDILYKLS- SMKFKDPLKD-GEAKIKSDYAQLLEDMQNAFRSLED------- [4] AGiardia ------------------------------MVTSETTSNGLIQSIAGPVVTAT---NMTG CFMFEVCYV--------GK---ARLIGEIIQLKGDSAVIQV-YEDTSGLE-VNDCVYKSG RLLS-------VHLGPGLLSSIYDGIQRPLEKIAQITNSHFIPRGIS---APALDLERRW TFRP--LVKLGDLLSVGDIFGIVPENDLLE-CKIMLQS---MDSTRLQMRKRTFQAERLL KYVRPTDAYTVKDEEKILVLEYAGQRYYYGLAHYHPVRSPKKVFKKLPC-INPLITGQRT LDGLFPLAIGATAAIPGGFGCGKTVVSQSISKY--------------------GNTDVIV YIGCGERGNEMAEILTDFPEMTFEAKKRVIGPSGQQEIKTVVSDIFSRTVLVANTSNMPV AAREASIYTGITISEFFRD-QGYNVTLLADSTSRWAEALREISGRLGGIPGEGGYPADLT SKLSHFYERAGRVICLGNSNGAWSPENILDPTSGAISSTEQGLLQPGQRIGSVSVIGAVS PAAGDLS-DAVAVSTLAIVQVFWGLSKNLANGKHFPSVDWLISYSRCTETLAPWY-NARD ISFLTNKEKAKTLLQNEVAIQETAQLV----GYDSLDDSEKLILDVCNLIQEGFLQQNSY TVYDKFCPFIKTDLMLRNIVHYYESCKTALG-------QGHSYQELKNSL-EKLITALY- RMKFIDTNTN-GIEYGVTELDKLHAQITAAFDAL--------- [5] AArabidopsis ------------------MPAFYGGKLTTFEDDEKESEYGYVRKVSGPVVVAD---GMAG AAMYELVRV--------GH---DNLIGEIIRLEGDSATIQV-YEETAGLT-VNDPVLRTH KPLS-------VELGPGILGNIFDGIQRPLKTIARISGDVYIPRGVS---VPALDKDCLW EFQP-NKFVEGDTITGGDLYATVFENTLMN-HLVALPP---DAMGKIT------------ -YIAPAGQYSLKD--TVIELEFQGIKKSYTMLQSWPVRTPRPVASKLAA-DTPLLTGQRV LDALFPSVLGGTCAIPGAFGCGKTVISQALSKY--------------------SNSDAVV YVGCGERGNEMAEVLMDFPQLTMTL------PDGREE------SVMKRTTLVANTSNMPV AAREASIYTGITIAEYFRD-MGYNVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLA ARLASFYERAGKVKCLGGPE----------------------------RNGSVTIVGAVS PPGGDFS-DPVTSATLSIVQVFWGLDKKLAQRKHFPSVNWLISYSKYSTALESFY-EKFD PDFINIRTKAREVLQREDDLNEIVQLV----GKDALAEGDKITLETAKLLREDYLAQNAF TPYDKFCPFYKSVWMMRNIIHFYNLANQAVERAAGMDGQKITYTLIKHRL-GDLFYRLV- SQKFEDPAEG--EDTLVEKFKKLYDDLNAGFRALEDETR---- [6] AHalobacterium -----------------------------MSQAEAITDTGEIESVSGPVVTAT---GLD- AQMNDVVYV--------GD---EGLMGEVIEIEGDVTTIQV-YEETSGIG-PGQPVDNTG EPLT-------VDLGPGMLDSIYDGVQRPLDVLEDEMGA-FLDRGVD---APGIDLDTDW EFEP--TVEAGDEVAAGDVVGTVDETVSIE-HKVLVPP---RSDGGEV------------ -VAVESGTFTVDD--TVVELD---TGEEIQMHQEWPVRRQRPTVDKQTP-TEPLVSGQRI LDGLFPIAKGGTAAIPGPFGSGKTVTQQSLAKF--------------------ADADIVV YIGCGERGNEMTEVIEDFPELPDPQ-------TGN--------PLMARTTLIANTSNMPV AGRESCIYTGITIAEYYRD-MGYDVALMADSTSRWAEAMREISSRLEEMPGEEGYPAYLA ARLSEFYERAGYFENFNG------------------------------TEGSISVIGAVS PPGGDFS-EPVTQNTLRIVKTFWALDSDLAERRHFPAINWDESYSLYKDQLDPWFTDNVV DDWAEQRQSAVDILDEESELEEIVQLV----GKDALPEDQQLTLEVARYIREAWLQQNAL HDVDRYCPPEKTYAILSGIKTLHEESFEALD-------AGVPVEEITSIDAAPRLNRLG- TTPDDEHEAE---------VAEIKQQITEQLRELY-------- [7] ANeurospora ------------------------MAPQQNGAEVDGIHTGKIYSVSGPVVVAE---DMIG VAMYELVKV--------GH---DQLVGEVIRINGDQATIQV-YEETAGVM-VGDPVLRTG KPLS-------VELGPGLLNNIYDGIQRPLEKIAEASNSIYIPRGIA---TPALDRKKKW EFTP--TMKVGDHIAGGDVWGTVYENSFISVHKILLPP---RARGTIT------------ -RIAEKGEYTVEE--KILEVEFDGKKTEYPMMQTWPVRVPRPAAEKHSA-NQPFLVGQRV LDALFPSVQGGTVAIPGAFGCGKTVISQSVSKF--------------------SNSDVIV YVGCGERGNEMAEVLKDFPELSIEV-------DGRKE------PIMKRTTLIANTSNMPV AAREASIYTGITVAEYFRD-QGMNVAMMADSSSRWAEALREISGRLGEMPADQGFPAYLG AKLASFYERAGKVQALGSPP----------------------------REGSVSIVGAVS PPGGDFS-DPVTSATLGIVQVFWGLDKKLAQRKHFPSINTSVSYSKYLTILDKWY-EREY PDFPRLRDRIRQLLSDSEELDQVVQLV----GKSALSDPDKITLDMATLIKEDFLQQNGY SDYDQFCPIWKTEWMMKLMMGFHDEAQKAIA-------QGQNWNKVREAT-QDLQAQLK- SLKFEVPSEG--QEKICKKYEAIQQQMLDKFASVIDE------ [8] APlasmodium ----------------------------MTKVAVEKEEPGVVYKVAGSLVIAE---NMSG TRMYELAKV--------GW---NKLVGEIIRLEGNYAYIQV-YEDTSGLS-VGDPVIKTG NALS-------VELGPGILDNIYDGIQRPLERIANVCGDVYIYKGID---MTSLDHDKQW QFYADKKLKLNDIVTGGDIFGFVDENKLFKEHKIMAPP---NAKGRLT------------ -YIAPDGSYTLKD--KIFELEYQGKKYTYGLSHLWPVRDPRPVLEKVTG-DTLLLTGQRV LDSLFPTVQGGTCAIPGAFGCGKTCVSQALSKY--------------------SNSEVII YVGCGERGNEMAEILSDFPELTTKV-------DNEDV------GIMQRTCLVANTSNMPV AAREASIYTGITLCEYFRD-MGYNATMMADSTSRWAEALREISGRLAEMPADSGYPAYLG ARLASFYERAGKVKCIGSPS----------------------------RIGSITIVGAVS PPGGDFS-DPVTTATMSIVQAFWGLDKKLAQRKHFPSVNWSTSFSKYVRQLEQYF-DNFD QDFLSLRQKISDILQQESDLNDIVQLV----GKDSLSEDQKVVMEVAKIIREDFLQQNAF SDYDYMCPLQKTVGMMRIICHFYAQCLRTLQEYDSRE-RKIGWGSIYNTL-RPTINKIT- HMKFENPKNS--DEYFKKYFKALEEEITVGLRNLMEK------ [9] ASulfolobus -----------------------------------MVSEGRVVRVNGPLVIAD---GMRE AQMFEVVYV--------SD---LKLVGEITRIEGDRAFIQV-YESTDGVK-PGDKVYRSG APLS-------VELGPGLIGKIYDGLQRPLDSIAKVSNSPFVARGVS---IPALDRQTKW HFVP--KVKSGDKVGPGDIIGVVQETDLIE-HRILIPP---NVHGTLK------------ -ELAREGDYTVED--VVAVVDMNGDEIPVKMYQKWPVRIPRPYKEKLEP-VEPLLTGIRV LDTVFPIAKGGTAAIPGPFGSGKTVTLQSLAKW--------------------SAAKVVI YVGCGERGNEMTDELRSFPKLKDPW-------TGK--------PLLLRTILVANTSNMPV AARESSIYVGVTMAEYFRD-QGYDVLLVADSTSRWAEALRDLGGRMEEMPAEEGFPSYLP SRLAEYYERAGRVIALGNPE----------------------------RYGSVTIASAVS PPGGDFT-EPVTSNTLRFVRVFWPLDVSLAQARHYPAINWIQGFSAYVDLVAQWWHKNVD PNWKEMRDTMMKVLIREDELRQIVRLV----GPEELAEKDKLVLEAAKLIKDAFLKENAY DDIDAFSSPQKQVRIMRLIYIFYNQSQDLIS-------KGVPLKKILDKV-GPIEPEII- RIKYTIKNDE----------LNKIDEIENKLKATFDSLLKEVS [10] AMethanosarcina -----------------------------------MEVKGEIYRVSGPVVTAI---GLQ- AKMYDLVKV--------GN---EGLMGEVIQILGPKTIIQV-YEETAGIK-PGEPCVSTG SSLS-------VELGPGLLSSIYDGVQRPLHVLLEKMGS-FIQRGVS---ADGLDHKKLW DFKP--IVKKGDSVKGGDVIGVVQETVNIE-HKIMVPP---DI-SGTI------------ -SDIKSGNFTVVD--TICTLT---DGTELQMMQRWPVRRPRPVKAKLTP-TRPLVTGMRI LDGLFPVAKGGTAAIPGPFGSGKTVTQQSLAKW--------------------SDTEIVV YIGCGERGNEMADVLSEFPELEDPQ-------TGR--------PLMERTVLIANTSNMPV AAREASVYTGITIAEYYRD-MGLDVSLMADSTSRWAEAMREISSRLEEMPGEEGYPAYLS ARLAEFYERAGVAESLCG------------------------------ETGSITVIGAVS PPGGDFS-EPVTQNTLRIVKVFWALDAKLSQRRHFPAINWLNSYSLYKDSLNDWFADNVA PDYVPLRERAMEMLQTESELQEIVQLV----GSDALPDDQQLLLEITRMLREIFLQQNAF HPVDAYSPFDQQYKILKAIMKWGDAAMDALK-------SGVPVTEIIKLESKNVLAKVKY EEKFDESMNA------------VLAQMDKEFASLRGR------ [11] alpE.coli -----------MQLNSTEISELIKQRIAQFNVVSEAHNEGTIVSVSDGVIRIH---GLAD CMQGEMISL-------PGN-----RYAIALNLERDSVGAVV-MGPYADLA-EGMKVKCTG RILE-------VPVGRGLLGRVVNTLGAPIDG---------------------------- ------------------------------------------------------------ -----KGPLDHDG--------------------FSAVEAIAPGVIERQSVDQPVQTGYKA VDSMIPIGRGQRELIIGDRQTGKTALAIDAIINQR------------------DSGIKCI YVAIGQKASTISNVVRKLEEH----------------------GALANTIVVVATASESA ALQYLARMPVALMGEYFRD-RGEDALIIYDDLSKQAVAYRQISLLLRRPPGREAFPGDVF YLHSRLLERAARVNAEYVEAFTKGEVKG--------------------KTGSLTALPIIE TQAGDVS-AFVPTNVISITDGQIFLETNLFNAGIRPAVNPGISVSRVGG-------AAQT KIMKKLSGGIRTALAQYRELAAFSQFA------SDLDDATRKQLDHGQKVTE-LLKQKQY APMSVAQQSLVLFAAERGYL------------------ADVELSKIGSFE-AALLAYVD- RDHAPLMQEINQTGGYNDEIEGKLKGILDSFKATQSW------ [12] alpAquifex ----------MATLTYEEALEILRQQIKDFEPEAKMEEVGVVYYVGDGVARAY---GLEN VMAMEIVEF-------QGG-----QQGIAFNLEEDNVGIII-LGSETGIE-EGHIVKRTG RILD-------APVGEGLVGRVIDPLGNPLDG---------------------------- ------------------------------------------------------------ -----KGPIQFEY--------------------RSPVEKIAPGVVKRKPVHEPLQTGIKA IDAMIPIGRGQRELIIGDRATGKTTVAIDTILAQK------------------NSDVYCI YVAVGQKRAAIARLIELLERE----------------------GAMEYTTVVVASASDPA SLQYLAPFVGCTIGEYFRD-NGKHALIIYDDLSKHAEAYRQLSLLMRRPPGREAYPGDVF YLHSRLLERAAKLNDDL-------------------------------GAGSLTALPIIE TKAGDVA-AYIPTNVISITDGQIYLEADLFNKGIRPAINVGLSVSRVGG-------AAQI KAMKQVAGTLRLELAQFRELEAFVQFA------SELDKATQQQINRGLRLVE-LLKQEPY NPIPVEKQIVLIYAGTHGYL------------------DDIPVESVRKFE-KELYAYLD- NERPDILKEISEKKKLDEELEKKIKEALDAFKQKFVP------ [13] alphaGeobacter -----------MEIRAEEISEIIRKQIKEYGKEVEVAETGTIISVGDGIARIH---GLDK AMAGELLEF-------PGG-----VSGMVLNLEEDNVGAAILGEDNENIK-EGTTVKRTG RIVE-------VPVGEALIGRVVNAIGQPIDG---------------------------- ------------------------------------------------------------ -----KGPINTTT--------------------FGKVEVKAPGIVKRKSVHQPMQTGLKA IDSMVPIGRGQRELIIGDRQTGKTAVAIDTIINQK------------------GGDLICI YVAIGQKRSTVAQVVSKLQEY----------------------GAMDYTIVVSASASEPA PLQFIAPYTGVTMGEYFRD-NGKHALIIYDDLSKQAVAYRQLSLLLRRPPGREAYPGDVF YLHSRLLERAAKLSDDC-------------------------------GAGSLTALPIIE TQAGDVS-AYIPTNVISITDGQIYLESDLFYSGVRPAINVGLSVSRVGG-------SAQV KAMKQVAGTLRLNLAQYREMAAFAQFG------SDLDKATQMQLARGERLVE-ILKQPQY RPIPNEKQVLVIFAANNGFV------------------DEYPVSSLRRYE-SELYSFFD- SRKADILAELRDKKAIDDDLKAKMIAALEELKKEFTA------ [14] alpha_Thermoto -----------------------------------------VIQVGDGIARAY---GLNK VMVSELVEF--------VE---TGVKGVAFNLEEDNVGIII-LGEYKDIK-EGHTVRRLK RIIE-------VPVGEELLGRVVNPLGEPLDG---------------------------- ------------------------------------------------------------ -----KGPINAKN--------------------FRPIEIKAPGVIYRKPVDTPLQTGIKA IDSMIPIGRGQRELIIGDRQTGKTAIAIDTIINQK------------------GQGVYCI YVAIGQKKSAIARIIDKLRQY----------------------GAMEYTTVVVASASDPA SLQYIAPYAGCAMGEYFAY-SGRDALVVYDDLSKHAVAYRQLSLLMRRPPGREAYPGDIF YLHSRLLERAVRLNDKL-------------------------------GGGSLTALPIVE TQANDIS-AYIPTNVISITDGQIYLEPGLFYAGQRPAINVGLSVSRVGG-------SAQI KAMKQVAGMLRIDLAQYRELETFAQFA------TELDPATRAQIIRGQRLME-LLKQEQY SPMPVEEQVVVLFAGVRGYL------------------DDLPVEEVRRFE-KEFLRFMH- EKHQDILDDIKTKKELTSETEEKLKKAIEEFKTTFRV------ [15] B_Homo MEIDSRPGGLPGSSCNLGAAREHMQAVTRNYITHPRVTYRTVCSVNGPLVVLD---RVKF AQYAEIVHF-----TLPDG---TQRSGQVLEVAGTKAIVQV-FEGTSGIDARKTTCEFTG DILR-------TPVSEDMLGRVFNGSGKPIDKGP-------------------------- ------------------------------------------------------------ -VVMAEDFLDING------------------QPINPHSRIYP--------EEMIQTGISP IDVMNSIARGQKIPIFSAAGLPHNEIAAQICRQAGLVKKSKAVLDYH------DDNFAIV FAAMGVNMETARFFKSDFEQN----------------------GTMGNVCLFLNLANDPT IERIITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGRRGFPGYMY TDLATIYERAGRVEG---------------------------------RGGSITQIPILT MPNDDIT-HPIPDLTGFITEGQIYVDRQLHNRQIYPPINVLPSLSRLMKSAIGE--GMTR KDHGDVSNQLYACYAIGKDVQAMKAVV----GEEALTSEDLLYLEFLQKFEKNFINQGPY ENRSMFES------------------------------LDLSWKLLRIFP-KEMLKRIP- QAVIDEFYSR----------EGRLQDLAPDTAL---------- [16] B_Cyanidium ----------------MEAFNLHKKAVSRDYIVKPRLEYRTVSAVNGPLIILQ---NVKS PRFAEIVNV-----TLGDG---SVRRGQVLEINQDKAVVQI-FEGTTGIDNKKTVCQFTG EILK-------TPVSLDMLGRVFNGSGKPIDGGP-------------------------- ------------------------------------------------------------ -PILPEAYLDIQG------------------QPINPQSRTYP--------EEMFETGISS IDVMNSIARGQKIPLFSGAGLPHNEVAAQICRQVCLVSTCTLVKRSGKD----EEDFAIV FAAMGVNMETARFFRQDFEEN----------------------GAMERVTLFLNLANDPT IERIITPRLALTFAEYLAYEKGKHVLVILTDMSAYADALREVSAAREEVPGRRGYPGYMY TDLATIYERAGRVEG---------------------------------RPGSITQLPILT MPNDDIT-HPIPDLTGYITEEQIYLDRQLHNRQIYPPINVLPSLSRLMKSAIGE--GMTR KDHSDVSNQLYAAYAMGKDALAMRAVV----GVEALSQEDLLYLEFHDKFERRFVNQGAY ERRDIYTS------------------------------LDMAWDLLRIFP-VQMLRRIP- EKILQEYYHR----------TSNYEHKENKPHSSRS------- [17] B_Arabidopsis --------------MSLSVNMGTNDLDIEEGTLEIGMEYRTVSGVAGPLVILD---KVKG PKYQEIVNI-----RLGDG---STRRGQVLEVDGEKAVVQV-FEGTSGIDNKFTTVQFTG EVLK-------TPVSLDMLGRIFNGSGKPIDNGP-------------------------- ------------------------------------------------------------ -PILPEAYLDISG------------------SSINPSERTYP--------EEMIQTGIST IDVMNSIARGQKIPLFSAAGLPHNEIAAQICRQAGLVKRLEKTVDLLEDHG--EDNFAIV FAAMGVNMETAQFFKRDFEEN----------------------GSMERVTLFLNLANDPT IERIITPRIALTTAEYLAYECGKHVLVILTDMSSYADALREVSAAREEVPGRRGYPGYMY TDLATIYERAGRIEG---------------------------------RKGSITQIPILT MPNDDIT-HPTPDLTGYITEGQIYIDRQLHNRQIYPPINVLPSLSRLMKSAIGE--GMTR KDHSDVSNQLYANYAIGKDVQAMKAVV----GEEALSSEDLLYLEFLDKFERKFVMQGAY DTRNIFQS------------------------------LDLAWTLLRIFP-RELLHRIP- AKTLDQFYSR---------------DSTS-------------- [18] B_Halobacterium -----------------------------------MKEYQTITEVSGPLVYVE---TDEP IGYDEIVEI-----ETPNG---DVKRGQVLESSDGFVAIQV-FEGTEGVG-KDASVRFLG ETLK-------MPVTEDLLGRVLDGSGNPIDGGP-------------------------- ------------------------------------------------------------ -DIVPDDRVDIVG------------------EAINPHAREYP--------EEFIQTGVSG IDGMNTLVRGQKLPIFSGSGLPHSDLALQIARQASVPEEEAETDDDE------GSEFAVV FGAMGITAEEANEFMDDFERT----------------------GALERSVVFMNLADDPA VERTVTPRMALTTAEYLAFEKDYHVLVILTDMTNYCEALRQIGAAREEVPGRRGYPGYMY TDLAQLYERAGRIEG---------------------------------KEGSVTQIPILT MPGDDDT-HPIPDLTGYITEGQIMMNRDLNSQGVTPPVNVLPSLSRLMDDGIGE--GLTR ADHGDVSDQLYAAYAEGEELRDLVNIV----GREALSERDNRYLDFADRFEAEFIDQGFK TNRDIEET------------------------------LDLGWELLSMFP-KTELNRVD- EDLIEDHY---------------VEDVADEATAD--------- [19] B_Methanosarcina ----------------------------------MVKEYKTITQIAGPLIFVE---KTEP VGYNEIVNI-----KMTDG---TVRRGQVLDSSSDIVVVQV-FEGTGGLD-KDCGVIFTG ETLK-------LPASIDLLGRILSGSGDPRDGGP-------------------------- ------------------------------------------------------------ -RIVPDQLLDING------------------AAMNPYARLPP--------KDFIQTGIST IDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGS--------------ESAFAVV FAAMGITNEEAQYFMSDFEKT----------------------GALERAVVFLNLADDPA VERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMY TDLATLYERAGIVKG---------------------------------AKGSVTQIPILS MPGDDIT-HPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGP--GKTR EDHKAVSDQMYAGYAEGRDLRGLVAIV----GKEALSERDTKFLEFADLFEDKFVRQGRN ENRTIEDT------------------------------LEIGWQILTHLP-ENQLGRID- NKYIQKYH-------------------PAHRKAK--------- [20] BPyrobaculum -------------------------------MLTPVVSYTTVREVKGPLIVIE---KTRG VSYGEVGEV-----IGPDG---EPRRVQVIEVGTDYAVAQV-LGGTLGLPAKGSTVRFYG KTLK-------IPVSEQLIGRILDGKGQPRDHMP-------------------------- ------------------------------------------------------------ -LPPPEDFRDVNG------------------EPLNPYSREYP--------EEPIETGISA IDGLYTLVRGQKLPIFSGTGLPHNLMAAQVVRQATVRGS--------------EEEFAVV FVGVGIKTEEALFFMDEFRKT----------------------GALRRAVAVLNLASDPV AERILAPRVGLTIGEYLAWQLGYHVLVVITDMTNYCEGLRELSSGRGELPGRRGYPGYMY TDLATIYERAGRARG---------------------------------RRGSVTQFPILT MPHDDIT-HPIPDLTGYITEGQLVLSRAMWGKGIYPPFDVIMSLSRLAKDAIGE--GKTR EDHKDVANTLIAAYSKALEIRNLATLV----GERNLGWRERRYLRFADAFEQRFIKQGYY ERRSFEET------------------------------LDIGWDVLSILP-EDELTNAR- PQITQKFYRR---------------HIFESVQL---------- [21] BGiardia --------------------MSLATNITPTPKIHPLPCYSSISSINGPIVVVD---KVQR QCYGEIVTL-----RLGNG---EIRTGKVLECHGSQAVLQV-FEGTEGLDIKQTSAKFTG EVMK-------VGVSRALLGRTLSGSGEIIDGGA-------------------------- ------------------------------------------------------------ -PVLAEEIRDIEG------------------SSLNPVSREYP--------KNCLETGIST IDILTSICQGQKILLLSGSGLPYNPLLAQIARNARVCVSWEKAVTGEEIKTSEDDKFMIV FAGIGLSHEQAMFFKTQFEQT----------------------GALNRSVILLNLASDPV VQRISTPRIAVTIAEYFAYTLGYHVLVLLSDIFNYADALRQISSARNEVPGRKGYPPYLY SDLSTIYERAGRVHG---------------------------------IKGSITQIPLIT LPNDDIT-HIIADLSAFITEGQIFQDRKLFNKNIIPAVDPLPSLSRLQKSAIGK--GRTR EDHPDVANQLYASYAIAVEVLSLKSIV----GSEGLSDNDHKYLKFLEVFEEQFLKQDFN TRRSIYES------------------------------LDLAWKCLRVLP-INLLSRIS- DSILEKYYYV-------------QTDAAEQPGAKTK------- [22] BNeurospora ---------------------MADPRVPSSYNVTPRIRYNTVGGVNGPLVILD---NVKF PRYNEIVTL-----TLPDG---TQRSGQVLEARGNRAVVQV-FEGTSGIDVKKTKVEFTG ESLK-------LGVSEDMLGRIFDGSGRAIDKGP-------------------------- ------------------------------------------------------------ -KVLAEEYLDING------------------SPINPYAREYP--------QEMISTGISA IDTMNSIARGQKIPIFSAAGLPHNEIAAQICRQAGLVQRQGITNKGVHDGH--EENFSIV FGAMGVNLETARFFTRDFEEN----------------------GSLGRTTLFLNLANDPT IERIITPRLALTTAEYYAYQLEKHVLVILTDLSSYCDALREVSAAREEVPGRRGFPGYMY TDLSTIYERAGRVAG---------------------------------RNGSITQIPILT MPNDDIT-HPIPDLTGYITEGQIFVDRGLHNRGIYPPINVLPSLSRLMKSAIGE--GMTR KDHGDVSNQLYAKYAIGRDAAAMKAVV----GEEALSNEDKLSLEFLDKFERSFIAQGPY ESRTIFES------------------------------LDLAWSLLRIYR-KDMLNRIP- KKIIDEFYSRSAADRKGKGKDKPTTKDTRDTAAPEEENLIDA- [23] BSulfolobus ------------------------------MSLLNVREYSNISMIKGPLIAVQ---GVSD AAYNELVEI-----EMPDG---SKRRGLVVDSQMGVTFVQV-FEGTTGISPTGSKVRFLG RGLE-------VKISEEMLGRIFNPLGEPLDNGP-------------------------- ------------------------------------------------------------ -PVIGGEKRNING------------------DPINPATREYP--------EEFIQTGISA IDGLNSLLRGSKITDLSGSGLPANTLAAQIAKQATVRGE--------------ESNFAVV FAAIGVRYDEALFFRKFFEET----------------------GAINRVAMFVTLANDPP SLKILTPKTALTLAEYLAFEKDMHVLAILIDMTNYCEALRELSASREEVPGRGGYPGYMY TDLATIYERAGKVIG---------------------------------KKGSITQMPILT MPNDDMT-HPIPDLTGYITEGQIVLDRSLFNKGIYPPINVLMSLSRLMKDGIGE--GKTR DDHKDLSNQLFAAYARAQDIRGLAAII----GEDSLSEVDRKYLLFAEAFERRFVAQGVN ENRSIETT------------------------------VDIGWEVLSILP-ESELSLIR- SEYIKKYHPN--------------------YRGKK-------- [24] betE.coli ------------------------------------MATGKIVQVIGAVVDVEFP-QDAV PRVYDALEV------QNGN---ERLVLEVQQQLGGGIVRTIAMGSSDGLR-RGLDVKDLE HPIE-------VPVGKATLGRIMNVLGEPVDM---------------------------- ------------------------------------------------------------ -----KGEIGEEE--------------------RWAIHRAAPSYEELSNSQELLETGIKV IDLMCPFAKGGKVGLFGGAGVGKTVNMMELIRNIAI-----------------EHSGYSV FAGVGERTREGNDFYHEMTDS----------------------NVIDKVSLVYGQMNEPP GNRLRVALTGLTMAEKFRD-EGRDVLLFVDNIYRYTLAGTEVSALLGRMPSAVGYQPTLA EEMGVLQERITST-----------------------------------KTGSITSVQAVY VPADDLT-DPSPATTFAHLDATVVLSRQIASLGIYPAVDPLDSTSRQLDP------LVVG QEHYDTARGVQSILQRYQELKDIIAIL----GMDELSEEDKLVVARARKIQR-FLSQ-PF FVAEVFTGSPGKYVS-----------------------LKDTIRGFKGIM-EGEYDHLP- EQAFYMVGSI--------------EEAVEKAKKL--------- [25] beta_Thermoto ---------------------------------MVKGSKGFIVSIMGPVVDVKFP-EEEL PDIYNALEV----VNPQTG---QKVVLEVEQLIGDGVVRTVAMDSTDGLT-KGLEVVDTG APIT-------APVGKEVLGRILNVIGEPVDE---------------------------- ------------------------------------------------------------ -----AGEIKAKE--------------------RWPIHRPAPELVEQSTEIEILETGIKV IDLLAPFPKGGKIGFFGGAGVGKTVLVMELIRNIAI-----------------EHKGFSV FAGVGERTREGNELWLEMQES----------------------GVLGNTVLVFGQMNEPP GARFRVALTALTIAEYFRDIEGRDVLLFIDNIFRFGQAGSEVSALLGRMPSAVGYQPTSA TIWENLQERITST-----------------------------------RRGSITSVQAIY VPADDIT-DPAPATTFAHLDATVVLSRRIAELGLYPAVDPLDSSSKILDP------AIVG REHYEVARGVQEVLQRYKDLQDIIAIL----GVEELSPEDKLVVHRARRIQR-FLSQ-PF HVAERFTGRPGRYVP-----------------------IEETIRGFKEIL-DGKLDDVP- EQAFLMAGNI--------------EEVKERAKEIEELKM---- [26] beta_Enteroc ------------------------------------MSSGKIVQVIGPVVDVEFSLDQSL PDINNALVV---YKNDEKK---SKVVLETALELGDGVIRTIAMESTDGLQ-RGMEVIDTG KAIS-------VPVGKDTLGRVFNVLGDTIDLGS-------------------------- ------------------------------------------------------------ -SFPEDAERS-------------------------EIHKKAPSFDELSTSTEILETGIKV IDLLAPYLKGGKVGLFGGAGVGKTVLIQELIHNIAQ-----------------EHGGISV FTGVGERTREGNDLYYEMKDS----------------------GVIEKTAMVFGQMNEPP GARMRVALTGLTIAEYFRDVEGQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLA TEMGQLQERITST-----------------------------------KKGSITSIQAIY VPADDYT-DPAPATAFAHLDATTNLERKLTEQGIYPAVDPLASSSSALAP------EIVG EEHYKVATEVQHVLQRYRELQDIIAIL----GMDELSDQEKVLVSRARRVQF-FLSQN-F NVAEQFTGLPGSYVP-----------------------VEETVKGFREIL-EGKYDDLP- EEAFRSVGRI--------------EDVVEKAKKLGY------- [27] beta_aquifex ---------------------------------MAEVIKGKVVQVIGPVVDVEFEGVKEL PKIKDGLKTIRRAIDDRGNWFEEVLFMEVAQHIGEHRVRAIAMGPTDGLV-RGQEVEYLG GPIK-------IPVGKEVLGRIFNVAGQPIDE---------------------------- ------------------------------------------------------------ -----QGPVEAKE--------------------YWPMFRNPPELVEQSTKVEILETGIKV IDLLQPIIKGGKVGLFGGAGVGKTVLMQELIHNIAR-----------------FHEGYSV VVGVGERTREGNDLWLEMKES----------------------GVLPYTVMVYGQMNEPP GVRFRVAHTGLTMAEYFRDVEGQDVLIFIDNIFRFVQAGAEVSTLLGRLPSAVGYQPTLN TDVGEVQERITST-----------------------------------KKGSITAIQAVY VPADDIT-DPAPWSIFAHLDATTVLTRRLAELGIYPAIDPLESTSKYLAP------EYVG EEHYEVAMEVKRILQRYKELQEIIAIL----GMEELSDEDKAIVNRARRIQK-FLSQ-PF HVAEQFTGMPGKYVK-----------------------LEDTIRSFKEVL-TGKYDHLP- ENAFYMVGTI--------------EDVIEKAKQMGAKV----- [28] flEcoli -----------MTTRLTRWLTTLDNFEAKMAQLPAVRRYGRLTRATGLVLEAT---GLQL P-LGATCVI-----ERQNGSETHEVESEVVGFNGQRLFLMP-LEEVEGVL-PGARVYAKN ISAEGLQSGKQLPLGPALLGRVLDGSGKPLDGLP-------------------------- ------------------------------------------------------------ -----SPDTTETG--------------ALITPPFNPLQRTPI--------EHVLDTGVRP INALLTVGRGQRMGLFAGSGVGKSVLLGMMARY--------------------TRADVIV VGLIGERGREVKDFIENILGA----------------------EGRARSVVIAAPADVSP LLRMQGAAYATRIAEDFRD-RGQHVLLIMDSLTRYAMAQREIALAIGEPPATKGYPPSVF AKLPALVERAGNGIS---------------------------------GGGSITAFYTVL TEGDDQQ-DPIADSARAILDGHIVLSRRLAEAGHYPAIDIEASISRAMT-------ALIS EQHYARVRTFKQLLSSFQRNRDLVSVGAYAKGSDPMLDKAIALWPQLEG----YLQQGIF --------------------------------------ERADWEASLQGL-ERIFPTVS- ------------------------------------------- [29] flAquifex ------------MKGIRRNLQKSYLKRCSEMYLRGLKVSGEIVSAKGIYLEAI----LPF ANIGNEVEI------QSNS---RRIRGEVIGFSGDKVLVMP-YEPVFGLR-KGDKVLLKN ELVS-------TKTGNGVVGKVVDPFGNPLDGGF-------------------------- ------------------------------------------------------------ -----IGFVEEKG---------------LELPQINPLYRERI--------REVFDTGVRS VNALFTLGKGQKIGIFAGAGVGKSTLLGMITRH--------------------SKADVVV LALIGERGREVKEFLEEVLGE----------------------EGLKKSVVVVSTADQSP ILKVKGAISAVVHAHHFAS-QGKDVLLLMDSITRLALAQREIGLAAGEPPTLKGFTPSVF QLLTRIAESCGAF-----------------------------------KKGSITGIFTVL VEGDDISLDPIADSLMGVLDGHIILSRKRAVRGLFPAVDPVRSLSRLMP-------KLVS EEHFMKANFFKEVLSKFEDVEELVRIGLYKGGSNPLVDKVINNLEKVES----FFKQKPE --------------------------------------EKVNFEESLKAL-DEIYSLLK- ------------------------------------------- ; END; BEGIN NOTES; TEXT TAXON=13 TEXT='no comment '; TEXT TAXON=14 TEXT='no comment '; TEXT TAXON=15 TEXT='no comment '; TEXT TAXON=16 TEXT='no comment '; TEXT TAXON=17 TEXT='no comment '; TEXT TAXON=18 TEXT='no comment '; TEXT TAXON=19 TEXT='no comment '; TEXT TAXON=20 TEXT='no comment '; TEXT TAXON=21 TEXT='no comment '; TEXT TAXON=22 TEXT='no comment '; TEXT TAXON=23 TEXT='no comment '; TEXT TAXON=24 TEXT='no comment '; TEXT TAXON=25 TEXT='no comment '; TEXT TAXON=26 TEXT='no comment '; TEXT TAXON=27 TEXT='no comment '; TEXT TAXON=29 TEXT='gi|3913671|sp|O67531|FLII_AQUAE Flagellum-specific ATP synthase '; END; begin mrbayes; prset aamodelpr=fixed(jones) [this sets the substititution matrix to JTT, a mdern version of PAM]; lset rates=gamma [this selects the gamma distribution to describe ASRV - this makes the program run a lot slower, you might not want to execute this option]; mcmcp samplefreq=100 printfreq=100 [this sets the frequency with which the "robot" reports results to the screen and to the files (different files for parameters (.p) and trees (.t))]; mcmcp savebrlens=yes [mcmcp sets parameters for the chain. savebrlens tells it to save the trees with branchlengths]; [mcmcp filename=ATPaseSUplus.nexus] [if you use this command, it tells the program to save the files under a certain name. This is handy, if you want to read in data from a previous run, but it usually is easier to go with the default] mcmcp ngen=5000 [this sets the number of generations to run the chain for to 5000 generations]; END;