PASS2
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Superfamily Details

Superfamily summary
Superfamily Name:  PLP-binding barrel
Class Name:  Alpha and beta proteins (a/b)
Fold Name:  TIM beta/alpha-barrel
Number of Members:  8
Average Size: 
Members
SCOP ID Name Source
d1bd0a2 Alanine racemase Bacillus stearothermophilus [TaxId: 1422]
d1rcqa2 Alanine racemase Pseudomonas aeruginosa [TaxId: 287]
d1vfsa2 Alanine racemase Streptomyces lavendulae [TaxId: 1914]
d7odca2 Eukaryotic ornithine decarboxylase Mouse (Mus musculus) [TaxId: 10090]
d1hkva2 Diaminopimelate decarboxylase LysA Mycobacterium tuberculosis [TaxId: 1773]
d1knwa2 Diaminopimelate decarboxylase LysA Escherichia coli [TaxId: 562]
d1twia2 Diaminopimelate decarboxylase LysA Archaeon Methanococcus jannaschii [TaxId: 2190]
d1ct5a- "Hypothetical" protein ybl036c Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Alignment Based On Similarities In Structural Features using Comparer

                             10        20        30        40        50  
d1bd0a2  (  12 )           vdldAIydNVenLrrlLpd-------dThIMAVVkanAyghgd
d1ct5a-  (   3 )    tgitydedrktqLiaqyesvrevVnaeak--nvkilLLVvSkl----k-p
d1hkva2  (  46 )            deddFrsrCreTaaaFg-----sGan--VhYaAka----flc
d1knwa2  (  32 )            daqiIrrqiaaLk-----------qFdvvRFaQka----csn
d1rcqa2  (   8 )           idlqALrhNYrLAreaT---------garALAVIkadAyghgA
d1twia2  (  50 )            seeqIkiNynrYieAFkrWeeetgkeFIVAYaYka----nan
d1vfsa2  (  13 )            dldAVraNVraLrarAp--------rSaLMAvVksnAyghga
d7odca2  (  44 )            dlgdIlkKhlrWlkALp--------rVtPFYaVkc----nds
                             aaaaaaaaaaaaaa            bbbbb          

                             60        70        80        90        100 
d1bd0a2  (  48 )    vqVArtAleAgAsrLAVafldeAlaLRekgIe------apILVlgas-rp
d1ct5a-  (  53 )    asDIqILydhgvreFGEnyVqeLiekaklLpd-----dIkWHFig-gLqt
d1hkva2  (  77 )    seVArwIseegL-cLDVctggeLavAlhasFp----per-ITLhgnnKsv
d1knwa2  (  59 )    ihiLrlMreqgV-kVDSvslgeIerAlaAgYnPqthpdd-IVFtadvIdq
d1rcqa2  (  42 )    vrCAeaLaa-eAdGFAVacieeGleLreagIr------qpILLleGFfea
d1twia2  (  88 )    laiTrlLAklgC-GADVvsggeLyiAklSnVp----skk-IVFngncKtk
d1vfsa2  (  47 )    vpCAraAqeAgAaWLGTatPeeAleLraagIq------grIMCwlWt-pg
d7odca2  (  74 )    raiVstLaaigT-GFdCaskteIqlVqglgVp----aer-VIYAnPcKqv
                    aaaaaaaaa    bbbb  aaaaaaaaa            bbb       

                             110       120       130       140       150 
d1bd0a2  (  91 )    adAalAAq-qrI-aLT-VfrsdwLeeAsaly-sGp---fpIhFHLKMdTg
d1ct5a-  (  97 )    nkCkdLAkvpnLySVEtIdslkkAkkLneSRakfqpdcnpIlCNVqInTS
d1hkva2  ( 121 )    seLtaAVk-agVghIV-VDsmtEIerLdaiAGeag---ivQdVLVrLtVG
d1knwa2  ( 107 )    aTlerVse-lqI-PVN-AGsvdMLdqLGqvsp-------gHrVWLrVNPg
d1rcqa2  (  85 )    seLelIVa-hdF-wCV-VhcawQLeaIera--sLa---rpLnVWL-MdSg
d1twia2  ( 132 )    eeIimGIe-anIrAFN-VDsiseLilIneTAkelg---etAnVaFrInPn
d1vfsa2  (  90 )    gpWreAIe-tdI-DVS-VsgmwALdeVraaAraAg---rtArIQL-AdTg
d7odca2  ( 118 )    sqIkyAas-ngVqmMT-FdseiELmkVarAHp-------kAkLVLrIat-
                      aaaaaa     bbb b  aaaaaaaaaa          bbbbb     

                             160       170       180       190       200 
d1bd0a2  ( 134 )    mg---------------------rlGVk-----deeeTkrIValIerhph
d1ct5a-  ( 147 )    he-------------------dqksGLnne-aeIfeVIdfFls--eeCky
d1hkva2  ( 166 )    VeAhthefista-------hedqkfGlsvasgaAmaAVrrVFa----tdh
d1knwa2  ( 147 )    fGhghs-------qktntGgenSkhGIwyt--dLpaAldViqr----hh-
d1rcqa2  ( 127 )    mh---------------------rvgffpe--dFraAHerLras----gk
d1twia2  ( 177 )    Vnpk-------thpkistglkknkfGLdvesgiAmkAIkmAle----mey
d1vfsa2  ( 134 )    lg---------------------rngcqpa--dWaeLVgaAvaAqae-gT
d7odca2  ( 169 )    -----------------------kfGatlk--tSrlLLerAke----ln-
                                                    aaaaaaaaaaa       

                             210       220       230       240       250 
d1bd0a2  ( 158 )    FvleGLYThFatAdevntdyfsyQytrFlhMlewLp---s-----rPplV
d1ct5a-  ( 175 )    IkLnGLTigsw----------nrdfatLvewkkkIdakfg------tsLk
d1hkva2  ( 205 )    LrLvGLHShIgsqIF-dvdGFelAAhrVIgLLrdVvgefgpekTaqIatV
d1knwa2  ( 183 )    LqLvGIHMhIgS-gv-dyahLeqVCgAMvrqVieF---gq-----dLqAI
d1rcqa2  ( 150 )    VakIvMmShFsrAdeldcprTeeQlaaFsaaSq-----gl-----eg-ei
d1twia2  ( 216 )    VnVvGVHChIgsqlt-dispFieETrkVMdFVveLkeegi-----eIeDV
d1vfsa2  ( 160 )    VqVTGVwshFacAdepghpsirlQldaFrdmLayAekegV-----dPevr
d7odca2  ( 189 )    IdViGVSFhVgsgct-dpdtFvqAVsdArcVFdmAteVgF-----sMhLL
                    bbbbbbb           aaaaaaaaaaaaaaaaa             bb

                             260       270       280       290       300 
d1bd0a2  ( 200 )    HCAn---------------SAASLrfp-------------drTfnMVRFg
d1ct5a-  ( 219 )    lSGsa----------------dFreAIrq---------g----TaeVrIg
d1hkva2  ( 254 )    DLGGgLGisylpsddpppiaeLAakLgtiVsdeS-tavglptPklVVEPg
d1knwa2  ( 223 )    SAGGgLsVpyqqgeeaVdTehYyglWnaAreqIa-rhlghp-VkLEIePg
d1rcqa2  ( 189 )    SLRn---------------SpAVLGwp-------------kVpSdwVRPG
d1twia2  ( 260 )    NLGggLGipyykdkqiptqkdLAdaIInTMlkyk-d--kVemPnLILEPg
d1vfsa2  ( 205 )    HIAn---------------SpATLtlp-------------eThfdLVRTG
d7odca2  ( 233 )    DIGGGFpGse--dtk-lkFeeITsvInpALdkyFpsdsg---VrIIAePg
                    b                  aaaaaa                    bb   

                             310       320  
d1bd0a2  ( 222 )    iAMYGlaPspgIkpllpyplkeA 
d1ct5a-  ( 242 )    tdIFg                   
d1hkva2  ( 303 )    raIAgpGt                
d1knwa2  ( 271 )    rfLVaqsg                
d1rcqa2  ( 211 )    iLLYGatpFerahplAd-rLrpVm
d1twia2  ( 307 )    rSLvatA                 
d1vfsa2  ( 227 )    lAVYGvspspeLgtpaqlgLrpA 
d7odca2  ( 277 )    rYYVasa                 
                                            

solvent inaccessible: UPPER CASE X
solvent accesible: lower case x
alpha helix: red x
beta strand: blue x
3 - 10 helix: maroon x
hydrogen bond to main chain amide: bold x
hydrogen bond to mainchain carbonyl: underline x
disulphide bond: cedilla ç
positive phi: italic x

Jmol view

Jmol Model View
Jmol Command prompt
Response Logs

Tree based on RMSD between structures

Matrices

1. Percentage Identity Matrix  [View | Download]
2. Distance Matrix  [View | Download]

PCA based on sequence identity

1. PCA  [View]
2. Plot file  [Download]

CUSP Results

CUSP Result   [View | Download]

Alistat - Alignment Statistics

Alignment Statistics  [Download]

SMotif - Conserved Structural Motifs

SMotif Result   [View | Download]

MeanRMS

MeanRMS  [Download]