Web document 6.2. Example of a benchmark database for multiple sequence alignment: the HOMSTRAD entry for lipocalins. Note that the highly conserved GXW motif found in almost all lipocalins occurs at the beginning of the first conserved beta strand.

 

This entry is available at:

http://www-cryst.bioc.cam.ac.uk/cgi-bin/homstrad/showpage.cgi?family=lipocalin&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  
1i4ua  (   1 )    dkipdfvvpgkÇasVdrnklwaeqt-pnrnsYagvWyQfAlTnNp-----
1bbpa  (   2 )        nvyhdgaçpeVk---pvdnF---dwsnYhgkWwEvAkYpNs-----
1exsa  (   1 )                     vevtpimteldtqkvagtwhTVamAVSdvslld
1beba  (   5 )                         qtmkgLdiqkVagtWySLAMAASdislLd
2a2ua  (   1 )               eeASstrg------nLdvakLngdWfSIVVASnkrekIe
1jv4a  (   1 )               eeasStgr------nFnvekIngeWhTIILASdkrekIe
1ew3a  (  23 )               vair----------nFdiskIsgeWySIFLASdvkekIe
1bj7   (   7 )                              idpskIpgeWrIIyAAAdnkdkIv
1e5pa  (   3 )                                faeLqgkWyTIvIAAdnlekIe
1hn2a  (1001 )                       aqeeeaeqnlselsgpWrTVyIGStnpekIq
1dzka  (  10 )                                 felsgkWiTSyIGSsdlekIg
1iiua  (   2 )                 mdçrvssfkvkenFdknrYsgtWyAmaKkdPe-----
1aqb   (   1 )                erdçrVssFrvkenFdkarFsgtWyAmaKkdPe-----
1epaa  (   3 )                           vkdFdiskFlgfWyEIAfAsk------
1qqsa  (   4 )            tsdlipApplskVplqqnFqdnqFqgkWyVVGLAGNai--lr
                                                   bb bbbbbb        
 
                           60        70        80        90        100 
1i4ua  (  45 )    ----yQlIekÇVrNeYsfdg--kqFvIeSTGiay----dgnllkrnGkLy
1bbpa  (  37 )    ----vEkyGkÇGwAeYtpeg--ksVkVsNyHVi-----hGkeyfiegtAy
1exsa  (  34 )    akssPlkA---YVegLkptp-egdLeIlLqkren-----dkçaqevllAk
1beba  (  34 )    aqsApLrV---yVeeLkPtp-egdLeilLqkwen-----geçaqkkiiAe
2a2ua  (  34 )    -engsMrv---FMqhIdvle--nSLGfkFriken-----geçrelylvAy
1jv4a  (  34 )    -dngnFrL---FLeqIhvle--ksLvLkFHtvrd-----eeçselsmvAd
1ew3a  (  52 )    -engsMrV---FVDvIrald-nssLyAeYQtkvn-----geÇtefpmvFd
1bj7   (  31 )    -egGpLRn---YYrrIeÇindçesLsItFylkdq-----gtçllltevAk
1e5pa  (  25 )    -eggplrf---YFRhIdçyknÇs-eeitFyvitn-----nqçskttviGy
1hn2a  (1032 )    -engpfrt---yfreLvFddekgtVdfyFsVkrd-----gkwknvhvkAt
1dzka  (  31 )    -enapFQV---FMrsIeFddkeskVyLnFfSken-----giçeefsliGt
1iiua  (  34 )    ----glFLqdNVvAqFtVde-ngqMsAtAkGrVrlfnnwdvçAdMiGsFt
1aqb   (  34 )    ----glFLqdnIvAeFsvde-nghMsAtAkGrVrllnnwdvçAdMvGtFt
1epaa  (  33 )    ----eekM---GAmvVelke--nllalttTyyse-----dhçvlekvtAt
1qqsa  (  44 )    edkdpqkM---yATiYeeke-dasYNVTSvlfrk-----kkçdyairtFv
                             bbbbbbb      bbbbbbbbb       bbbbbbbbbb
 
                           110       120       130       140       150 
1i4ua  (  85 )    pnpf-gepHLsIdYe------nsfaapLVILeTdysnYAÇLYSÇidyn-f
1bbpa  (  76 )    PvgdskiGkIyHkLtygg---vtkenvFnVLsTdnknYIIGYyÇkydedk
1exsa  (  75 )    ktdi--pavfkIn------aLd--EnqLflldtdydshLLLÇMensaspe
1beba  (  75 )    ktki--pAvFkId------aln--EnkvlVldTdykkyLLfÇMensaepe
2a2ua  (  73 )    ktpe--dgeyfve------ydg--gNtftIlkTDydrYVMFhliNfk--n
1jv4a  (  73 )    ktek--ageYsvt------ydg--fNtFtIpkTdydnFLMAhLiNek--d
1ew3a  (  92 )    ktee--dgvYsLn------ydg--yNvFrIseFendehIILyLvNfd--k
1bj7   (  72 )    rqe---gyvYvle------fyg--tNtLeVIhVs-enMLVTyveNy--dg
1e5pa  (  66 )    lkg---ngtYetq------feg--nnifqPlyit-sdKIFFtnkNd--ra
1hn2a  (1073 )    kqd---dgtYvad------yeg--qnvfkivsls-rthLVahniNvd-kh
1dzka  (  72 )    kq-e--gntYdVn------yag--nNkFvvsyas-etALIIsNiNvd-ee
1iiua  (  79 )    dted--pAkFkMkYwGvasfLqkgnddHwVVdTdydtyALHYSÇrelned
1aqb   (  79 )    dted--pAkFkMkYwGvasfLqkgnddHwIIdTdYdtYAVQYSÇrlqnld
1epaa  (  69 )    egdg--pAkfqVtr--l-----sgkkevvVeaTdyltyaIiditslv--a
1qqsa  (  85 )    pgcq--pGeFtLgn--iksypgLtsYlVrVVsTnynqhAmVFFkkvs--q
                  b        bbbb           bbbbbbbbb    bbbbbbbbb    
 
                           160       170       180       190       200 
1i4ua  ( 127 )    g-yhSDFSFIFSrsa-nLadqyvkkÇeaaFknin-Vdttr--fvkTvQgs
1bbpa  ( 126 )    k-ghqDFVWVLSrsk-vltgeaktaVenyligSpvVdsqk--Lvysdfse
1exsa  ( 115 )    ---hsLQSLartl-evddqirekFedaLktls-vp---MrIlpaqlee
1beba  ( 115 )    q---slQCLVrtp-evddeAlekFdkaLkalp-mh----irlsfnptq
2a2ua  ( 111 )    ge-tfqLMvLYGrtk-dLssdikekFaklCeahg-Itrdn--iidLTktd
1jv4a  ( 111 )    ge-tFqLMGLYGrep-dLssdikerFaqlCeehg-Ilren--iidLsnan
1ew3a  ( 130 )    dr-pFqLFeFYArep-dvspeikeeFvkiVqkrg-Ivken--iidLTkid
1bj7   ( 108 )    er-iTkMTEGLAkgt-sFtpeelekYqqlNserg-Vpnen--ienLiktd
1e5pa  ( 103 )    gq-eTn-IVVAGkgn-aLtpeeneiLvqfAhekk-Ipven--ilnIlatd
1hn2a  (1110 )    gq-tTeLTeLfvkl--nvedeDlekFwklTedkg-Idkkn--VvnFlene
1dzka  ( 109 )    gd-kTiMTGLLgkgt-diedqDlekFkevTreng-Ipeen--ivnIierd
1iiua  ( 127 )    gtçadSYSFVFSrdpkglppeaqkivrqrqidLç-ldr---kYrvIvhng
1aqb   ( 127 )    gtçadSYSFVFArdphgfspevqkivrqrqeeLç-lar---qYriIthng
1epaa  ( 108 )    ga-vhrtMkLYSrsl-ddngeAlynFrkiTsdhg-Fsetd--LyiLkhdl
1qqsa  ( 129 )    nr-eyFkITLYgrtk-eltselknnFirfSksLg-Lpenh--IvfPvpid
                      bbbbbbbb       aaaaaaaaaaaaa     333  bbb     
 
                           210 
1i4ua  ( 172 )    sÇpydtQktl
1bbpa  ( 173 )    aaçkvn    
1exsa  ( 157 )    qÇrv      
1beba  ( 156 )    Leeqç     
2a2ua  ( 156 )    rÇl       
1jv4a  ( 156 )    rç        
1ew3a  ( 175 )    rÇfqlrg   
1bj7   ( 153 )    nÇpp      
1e5pa  ( 148 )    tÇpe      
1hn2a  (2154 )    n---hph   
1dzka  ( 154 )    dÇpa      
1iiua  ( 173 )    fÇs       
1aqb   ( 173 )    yÇd       
1epaa  ( 153 )    tÇVkvLqsaa
1qqsa  ( 174 )    qçId