Web document 6.1. Example of a benchmark database for multiple sequence alignment: the HOMSTRAD entry for globins.

 

This entry is available at:

http://www-cryst.bioc.cam.ac.uk/cgi-bin/homstrad/showpage.cgi?family=glob&disp=str

 

Key to JOY

alpha helix                                                        red                   x

beta strand                                                       blue                  x

310 helix                                                            maroon x

solvent accessible                                             lower case        x

solvent inaccessible                                           UPPER CASE X

hydrogen bond to main-chain amide                  bold                 x

hydrogen bond to main-chain carbonyl  underline           x

disulfide bond                                                   cedilla               ç

positive phi torsion angle                                   italic                x

 

                           10        20        30        40        50  
1bina  (   1 )             vaFtekqdalVsssfeaFka--nipqySvvFYtSIlekApa
1lh1   (   1 )             gaLtesQAalVksSweeFna--nipkhThrFFiLVleiapa
1hlm   (   1 )    gatqsfqSvgdLtpaekdlIrstWdqlmt--hrtgfVAdVFiriFhndpt
1hlb   (   1 )    ggtlaiqaqgdLtlaqkkiVrkTWhqLmr--nktsFvtdVFirIFaydps
2mm1   (   1 )              gLsdgeWqlVlnVWgkVea--dipgHGqeVLirLFkghpe
1pmba  (   1 )              gLsdgewqlVlnVWgkVea--dvagHGqeVLirLFkghpe
1ymb   (   1 )              gLsdgeWqqVlnVWgkVea--diagHGqeVLIrLFtghpe
1mbs   (   1 )              glsdgewhlVlnvwgkVet--dlagHGQeVLIrLFkshpe
1emy   (   1 )              gLsdgeWelVlkTWgkVea--dipgHGetVFvrLFtghpe
1lht   (   1 )              gLsddeWnhVlgiWakVep--dlsaHGqeVIirLFqlhpe
1myt   (   5 )                  adfdaVlkcWgpVea--dyttmGglVLtrLFkehpe
2pghb  (   1 )             vhLsaeekeaVlglwgkV----nvdeVGGeALGrLLvvypw
2hhbb  (   1 )             vhLtpeeksaVtaLwgkV----nvdeVGgeALGrLLvvypw
1hdab  (   2 )              mLtaeekaaVtaFWgkV----kvdeVGGeALGrLLvvypw
2mhbb  (   1 )             vqLsgeekaaVlalWdkV----neeeVGGeALGrLLvvypw
1hdsb  (   1 )              mltaeekaaVtgfwgkV----dvdvVGaqALGrLLvvypw
1fdhg  (   1 )             ghFteedkatItsLwgkV----nvedaGGeTLGrLLvvypw
1spgb  (   1 )             vdWtdaeraaIkaLwgkI----dvgeIGpqALsrLLivypw
1hbhb  (   1 )             veWtdkersiIsdIFshM----dyddIGpkALsrCLivypw
1outb  (   1 )             veWtdaekstIsaVwgkV----nideIGplALArVLivypw
1spga  (   1 )              sLsatDkarVkaLwdkIeg--ksaeLGaeALGrMLvsfpq
1pbxa  (   1 )              slsdkdkaaVraLwskIgk--sadaIGndALsrMIvvypq
1hdaa  (   1 )              vLsaadkgnVkaawgkVgg--haaeygaeALerMflsfpt
2hhba  (   1 )              vLspadktnVkaAwgkVga--hageyGaeALerMflsfpt
2mhba  (   1 )              vLsaadktnVkaawskVgg--haGeYGaeALerMFlgfpt
2pgha  (   1 )              vLsaadkanVkaAwgkVgg--qagaHGaeALerMFlgfpt
1hdsa  (   1 )              vlsaanksnVkaAWgkVgg--nApayGAqALqrMFlsfpt
1outa  (   1 )              sLtakDksvVkaFwgkIsg--kadvVgaeALGrMLtaypq
2lhb   (   1 )     pIvdtgsvapLsaaektkIrsaWapvys--tyetsGvdILvkFFtstpa
2hbg   (   1 )              gLsaaqrqvIaatwkdIagadnGagVGkkCLikFLsahpq
3sdha  (   2 )       svydaAaqLtadvkkdLrdSwkviGs--dkkgnGvalMttLFadnqe
1mba   (   1 )              sLsaaeadlAgkSWapVfa--nknanGldFLvaLFekfpd
1itha  (   1 )              gLtaaqikaIqdhWflnIkg-clqaAAdSIFfkYLtaypg
1ecd   (   1 )               LsadqistVqasFdkVkg------dpvgILyaVFkadps
1a4fa  (   1 )              vlsaadktnVkgVFskIsg--haeeYGaeTLerMFtaypq
1a4fb  (   1 )             vhWsaeekqlItgLwgkV----nvadCGAeaLArLLivypw
1a9we  (   1 )             vhFtaeekaaVtslwskM----nveeAGgeALGrLLvvypw
1hbra  (   1 )              mLtaedkklIqqAwekAas--hqeeFGaeALtrMFttypq
1a6m   (   1 )              vLsegeWqlVlhVWakVea--dvagHGqdILIrLFkshpe
1cg5a  (   1 )              vLssqnkkaIeelGnlIka--nAeawGAdALarLFelhpq
1cg5b  (   1 )             vkLsedqehyIkgVwkdV----dhkqiTAkALerVFvvypw
                               aaaaaaaaaaaaa      aaaaaaaaaaaaaaa   
 
                           60        70        80        90        100 
1bina  (  40 )    AkdlFsFLa--n---gvdptnpkLtghAekLFalVrdSAgqLkasgtVvA
1lh1   (  40 )    AkdlFsFLkgts---eVpqnnpeLqaHAgkVFklVyeAAiqlevtgvVvt
1hlm   (  49 )    AqrkFpqMagl--spaelrtsrqMhaHAirVSalmttyidemdte---vl
1hlb   (  49 )    AqnkFpqMagm--sasqLrsSrqMqaHAirVssimseyVeeLdSd---iL
2mm1   (  39 )    TlekFdrFk-hlksedeMkasedLkkHGatVLtaLggILkkkg-----hH
1pmba  (  39 )    TlekFdkFk-hlksedeMkasedLkkhGntVLtaLggILkkkg-----hH
1ymb   (  39 )    TlekFdkFk-hLkteaeMkaSedLkkHGtvVLtaLggILkkkg-----hH
1mbs   (  39 )    TLekFdkFk-hlkseddmrrsedLrkHGntVLtaLggILkkkg-----hh
1emy   (  39 )    TlekFdkFk-hlktegeMkasedLkkQGvtVLtaLggILkkkg-----hH
1lht   (  39 )    TqerFakFk-nlttidaLksseeVkkhGttVLtaLgrILkqkn-----nH
1myt   (  39 )    TqklFpkFa-gia-qadIagnaaIsahGatVLkkLGeLLkakg-----sH
2pghb  (  38 )    TqrfFesfg-dLsnadaVmgnpkVkahGkkVLqsFsdGLkhld-----nL
2hhbb  (  38 )    TqrfFesfg-dlstpdaVmgnpkVkaHGkkVLgaFsdGlahld-----nL
1hdab  (  38 )    TqrfFesFg-dLstadaVmnnpkVkaHGkkVLdsFsnGMkhLd-----dL
2mhbb  (  38 )    TqrfFdsFg-dLsnpgaVmgnpkVkahGkkVLhsFGeGVhhld-----nL
1hdsb  (  37 )    TqrfFqhFg-nLssagaVmnnpkVkaHGkrVLdaFTqglkhld-----dl
1fdhg  (  38 )    TqrfFdsfg-nlssasaImgnpkVkahGkkVLtsLgdAikhLd-----dl
1spgb  (  38 )    TqrhFkgfg-nistnaaIlgnakVaehGktVMgGLdrAVqnMd-----nI
1hbhb  (  38 )    TqrhFsgfg-nlynaeaIignanVaaHGikVLhGLdrGvknmd-----nI
1outb  (  38 )    TqryFgsfg-nvstpaaImgnpkVaaHGkvVcgaLdkAVknMg-----nI
1spga  (  39 )    TkiyFsewgqdLg-----pqtpqVrnhGavIMaaVgkAVksId-----nl
1pbxa  (  39 )    TktyFshwp-dvt-----pgSphIkaHGkkVMgGIalAvskId-----dl
1hdaa  (  39 )    TktyFphf--dls-----hgsaqvkgHGakVAaaLtkAvehLd-----dL
2hhba  (  39 )    TktyFphf--dls-----hgsaqvkgHGkkVAdaLtnAvahVd-----dM
2mhba  (  39 )    TktyFphf--dls-----hgsaqVkaHGkkVGdaLtlAvghLd-----dL
2pgha  (  39 )    TktyFphf--nls-----hgsdqVkaHGqkVAdaLtkAvghLd-----dL
1hdsa  (  39 )    TktyFphf--dls-----hgsaqQkaHGqkVAnaLtkAqghLn-----dL
1outa  (  39 )    TktyFshwa-dls-----pgsgpVkkHGgiImgaIgkAvglMd-----dL
2lhb   (  48 )    AqefFpkFkg-lttadeLkksadVrwHAerIInaVddAvasMd--dtekm
2hbg   (  41 )    MaaVF-gfs--------gasdpgVaaLGakVLaqIgvAVshlg--degkM
3sdha  (  47 )    TigyFkrLg----nVsqgmandkLrgHSitlmyAlqnFIdqLd--npddL
1mba   (  39 )    SanfFadFkg--ksvadIkaspkLrdvSsrIFtrLneFVnnAa--nagkM
1itha  (  40 )    dlafFhkFssv--plygLrsnpaYkaqTltVInyLdkVVdaLg----gnA
1ecd   (  34 )    ImakFtqFag--kdlesikgtapFethAnrIvgfFskIIgeLp-----nI
1a4fa  (  39 )    TktyFphF--dlq-----hgsaqIkaHGkkVVaaLveAVnhId-----dI
1a4fb  (  38 )    TqrfFssFg-nLssptaIlgnpmVrahGkkvLtsFgdAVknLd-----ni
1a9we  (  38 )    TqrfFdsfg-nlsspsaIlgnpkVkahGkkvLtsFgdAiknMd-----nl
1hbra  (  39 )    TktyFphf--dls-----pgsdqVrgHGkkVLgaLgnAvknvd-----nL
1a6m   (  39 )    TlekFdrFk-hLkteaeMkaSedLkkHGvtVLtaLGaILkkkg-----hH
1cg5a  (  39 )    TktyFskfs-gfe-----acneqVkkHGkrVMnaLAdAThhLd-----nl
1cg5b  (  38 )    TtrlFskLqglfs-----andigVqqHAdkVqrALgeAIddLk-----kV
                   33                  aaaaaaaaaaaaaaaaaa           
 
                           110       120       130       140       150 
1bina  (  85 )    d---aalGsvHaqk---avtdpqFvvVkeALlkTIkaAVgd-kwsdelsr
1lh1   (  87 )    datlknLGsvHvsk---gVadahFpvVkeAIlkTIkeVVga-kwseeLns
1hlm   (  94 )    pelLatltrtHdkn---hVgkknYdlFGkvLmeaikaelgv-gftkqvhd
1hlb   (  94 )    pellatLartHdln---kVgadhynlFakVLmeaLqaelgs-dfnektrd
2mm1   (  83 )    eaeIkplAqsHAtkh--kIpvkyLefIseAIiqVLqskhpg-dFgadaqg
1pmba  (  83 )    eaeLtplAqsHAtkh--kIpvkyLefIseAIiqVLqskhpg-dFgadaqg
1ymb   (  83 )    eaeLkplAqsHAtkh--kIpikyLefIsdAIihVLhskhpg-dFgadaqg
1mbs   (  83 )    eaelkplAqshatkH--kiPikylefIseaiihvLhskhpa-efgadaqa
1emy   (  83 )    eaeiqplAqsHAtkh--kIpikyLefIsdaIihVLqskhpa-eFgadaqg
1lht   (  83 )    eqeLkpLAesHAtkh--kIpvkyLefICeIIvkVIaekhps-dFgadsqa
1myt   (  83 )    aaiLkpLAnsHAtkh--kIpinnFklIseVLVkVMhekA---gLdaggqt
2pghb  (  82 )    kgtFaklSelHCdql--hVdpenFrlLGnvIVvVLarrlgh-dFnpdvqa
2hhbb  (  82 )    kgtFatlSelHcdkl--hVdpenFrlLgnvLvcVLahhfgk-eFtppvqa
1hdab  (  82 )    kgtFaalSelHcdkl--hVdpenFkllgnvLvvVLarnfgk-eFtpvlqa
2mhbb  (  82 )    kgtFaalSelHcdkl--hVdpenFrlLGnvLVvVLarhfgk-dFtpelqa
1hdsb  (  81 )    kgaFaqlSglHcnkl--hVnpqnFrlLGnVLalVVarnfgg-qFtpnvqa
1fdhg  (  82 )    kgtFaqlSelHcdkl--hVdpenFklLgnvLvtVLaihFgk-eFtpevqa
1spgb  (  82 )    knvYkqLsikHSeki--hVdpdnFrlLGeiItmCVgakfgpsaftpeihe
1hbhb  (  82 )    aatYadLStlHsekl--hVdpdNFklLsdCItiVLaakmgh-aFtaetqg
1outb  (  82 )    latYkslSetHAnkl--fVdpdnFrvLAdVLtiVIaakfga-sFtpeiqa
1spga  (  79 )    vggLsqlSelHAfkl--rVdpaNFkiLahNIilVIsmyfpg-dFtpevhl
1pbxa  (  78 )    ktgLmelSeqHAykl--rVdpaNFkiLnhCIlvVIstmfpk-eFtpeahv
1hdaa  (  77 )    pgaLselSdlHAhkl--rVdpvNFklLshSLlvTLashlps-dftpavha
2hhba  (  77 )    pnaLsalSdlHAhkl--rVdpvnFklLshCLlvTLaahLpa-eftpavha
2mhba  (  77 )    pgaLsdlsnlHAhkl--rVdpvNFklLshCLlsTLavhlpn-dftpavha
2pgha  (  77 )    pgaLsalSdlHAhkl--rVdpvnFklLshCLlvTLaahhpd-dfnpsVha
1hdsa  (  77 )    pgtLsnlsnlHAhkl--rVnpvnFklLshSLlvTLashlpt-nFtpavha
1outa  (  78 )    vggMsalSdlHAfkl--rVdpgnFkiLshNIlvTLaihfps-dftpevhi
2lhb   (  95 )    smkLrnlSgkHAksf--qVdpeyFkvLAavIAdtVaa----------gda
2hbg   (  80 )    vaqMkaVGvrHkgyGnkhIkaqyFepLgasLlsAMehrIgg-kMnaaAkd
3sdha  (  91 )    vcvVekfAvnHitr---kIsaaeFgkIngPikkvlaskn----fgdkyan
1mba   (  85 )    samlsqFAkeHvgf---gVgsaqFenVrsMFpgfVasva---appagAda
1itha  (  84 )    galMkakvpsHdam---gItpkhFgqLLklVggVFqeefs---AdptTva
1ecd   (  77 )    eadVntFvasHkpr---gVthdqLnnFraGFvsYMkaht---dFa-gaea
1a4fa  (  77 )    agaLsklSdlHAqkl--rVdpvNFkfLghCFlvVVaihhps-altaevha
1a4fb  (  82 )    kntFaqlSelHCdkl--hVdpenFrlLGdILiiVLaahfak-eFtpdCqa
1a9we  (  82 )    kpaFaklSelHcdkl--hVdpenFklLGnVMviILathfgk-eFtpevqa
1hbra  (  77 )    sqaMaelSnlHAynl--rVdpvnFklLsqCIqvVLavhmgk-dytpeVha
1a6m   (  83 )    eaeLkplAqsHAtkh--kIpikyLefISeAIihvLhsrhpg-dFgadAqg
1cg5a  (  78 )    hlhLedlArkHGenl--lVdphNFhlFadCIvvTLavnlq--aftpvthc
1cg5b  (  78 )    einFqnlSgkHqei---gVdtqnFklLgqTFMveLalhykk-tFrpkeha
                  aaa aaaaaaaa         aaaaaaaaaaaaaaaaa       aaaaa
 
                           160       170  
1bina  ( 128 )    AWevAYdeLaaaIkka        
1lh1   ( 133 )    AWtiAYdeLaivIkkeMddaa   
1hlm   ( 140 )    AwaktfaivqGvliTkhas     
1hlb   ( 140 )    AWakAfsvvqavllvkhg      
2mm1   ( 130 )    AMnkALelFrkdMasnYkelgfqg
1pmba  ( 130 )    AMskALelFrndMaakYkelgfqg
1ymb   ( 130 )    AMtkALelFrndIaakYkelgfqg
1mbs   ( 130 )    AMkkAlelFrndIaakYkelgfhg
1emy   ( 130 )    AMkkALelFrndIaakYkelgfqg
1lht   ( 130 )    AMkkALelFrndMaskYkefgfqg
1myt   ( 130 )    aLrnVMgiIiadLeanYkelgfsg
2pghb  ( 129 )    AFqkVVagVanALahkyh      
2hhbb  ( 129 )    AYqkVVagVAnALahkyh      
1hdab  ( 129 )    DFqkVVagVAnALahryh      
2mhbb  ( 129 )    SYqkVVagVanALahkyh      
1hdsb  ( 128 )    lFqkvVagvanALahkyh      
1fdhg  ( 129 )    SWqkMVtgVAsALssryh      
1spgb  ( 130 )    aWqkFLavVvsaLgrqyh      
1hbhb  ( 129 )    AFqkFLavVvsALgkqyh      
1outb  ( 129 )    tWqkFMkvVvaAMgsryf      
1spga  ( 126 )    SVdkFLacLAlALsekyr      
1pbxa  ( 125 )    SldkFLsgValALaeryr      
1hdaa  ( 124 )    SLdkFLanVstvLtskyr      
2hhba  ( 124 )    SLdkFLasVstvLtskyr      
2mhba  ( 124 )    SLdkFLssVstvLTskyr      
2pgha  ( 124 )    SLdkFLanVstvLtskyr      
1hdsa  ( 124 )    nLnkFLanDstvLtskyr      
1outa  ( 125 )    AvdkFLaaVsaALadkyr      
2lhb   ( 133 )    GFekLMSmICilLrsay       
2hbg   ( 129 )    AWaaAyadIsgALisGlqs     
3sdha  ( 134 )    AWakLVaVVqaal           
1mba   ( 129 )    AWtkLFglIIdaLkaaga      
1itha  ( 128 )    AWgdAAgvLvaaMk          
1ecd   ( 120 )    AWgaTLdtFFgmIfskm       
1a4fa  ( 124 )    SLdkFLcaVgtvLTakyr      
1a4fb  ( 129 )    AWqkLVrvVahaLarkyh      
1a9we  ( 129 )    AWqkLVsAVAiaLahky       
1hbra  ( 124 )    AFdkFLsaVSaVLaekyr      
1a6m   ( 130 )    AMnkALelFrkdIaakYkelgy  
1cg5a  ( 124 )    AVdkFLelVayeLsscyr      
1cg5b  ( 124 )    AAykFFrlVaeALssnyh      
                  aaaaaaaaaaaaa