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Superfamily Details

Superfamily summary
Superfamily Name:  Nucleotide-binding domain
Class Name:  Alpha and beta proteins (a/b)
Fold Name:  Nucleotide-binding domain
Number of Members:  9
Average Size: 
Members
SCOP ID Name Source
d1djqa3 Trimethylamine dehydrogenase, middle domain Methylophilus methylotrophus, w3a1 [TaxId: 17]
d1ps9a3 2,4-dienoyl-CoA reductase, middle domain Escherichia coli [TaxId: 562]
d1cjca2 Adrenodoxin reductase of mitochondrial p450 systems Cow (Bos taurus) [TaxId: 9913]
d1lqta2 Ferredoxin:NADP reductase FprA Mycobacterium tuberculosis [TaxId: 1773]
d1gtea4 Dihydropyrimidine dehydrogenase, domain 2 Pig (Sus scrofa) [TaxId: 9823]
d1kifa1 D-aminoacid oxidase, N-terminal domain Pig (Sus scrofa) [TaxId: 9823]
d1c0pa1 D-aminoacid oxidase, N-terminal domain Rhodotorula gracilis [TaxId: 5286]
d1i8ta1 UDP-galactopyranose mutase, N-terminal domain Escherichia coli [TaxId: 562]
d2bi7a1 UDP-galactopyranose mutase, N-terminal domain Klebsiella pneumoniae [TaxId: 573]

Alignment Based On Similarities In Structural Features using Comparer

                             10        20        30        40        50  
d1c0pa1  ( 999 )                                                lmmhsq
d1cjca2  (   6 )                                                     t
d1djqa3  ( 341 )    dirvcIgcnv-cisrweiggppmicTQnATagEeyrrgWhpekFrqtknk
d1gtea4  ( 184 )                                                  eays
d1i8ta1  (   1 )                                                     m
d1kifa1  (   1 )                                                      
d1lqta2  (   2 )                                                    rp
d1ps9a3  ( 331 )     intcIgcnqAcldqifv-gkvtscLVnprachetkmp-----ilpavqk
d2bi7a1  (   2 )                                                    ks
                                                                      

                             60        70        80        90        100 
d1c0pa1  (1005 )    krVVVLgSgViGLSSALiLArkg-------YsVhILard-lpedvss--q
d1cjca2  (   7 )    pqICVVgSgpaGFYTAqhLlkhhs-----rAhVDIYekqlVPFglVrfgv
d1djqa3  ( 390 )    dsVLIvgAgPsGSEAARVLMesg-------YtVhLtdtaekIGghLnqva
d1gtea4  ( 188 )    AkIALLgAgpASisCAsfLArlgYs------dITIfekqeyvGglstsei
d1i8ta1  (   2 )    ydYIIvgSglFGAVCANeLkkln-------kkVlVIekrnhiGgnAy--T
d1kifa1  (   1 )    mrVVVIgAgViGLSTALCIheryhsvlqp-LdVkVyadr-ftp-------
d1lqta2  (   4 )    yyiAivgSgpsAFfAAasllkaAdttedldMavDMlemlPtPwglvrsgv
d1ps9a3  ( 374 )    knLAVvgAgpaGLAFAinAAaRg-------HqVtLFdahseIGgqfniak
d2bi7a1  (   4 )    kkILIvgAgFsGAVIGrqLAekg-------HqVhIIdqrdhiGgnsy--D
                     bbbbb   aaaaaaaaaaa           bbbbb              

                             110       120       130       140       150 
d1c0pa1  (1045 )    --------tfasPwagAnWtPfmtltdGprqakWEesTFkkWvelvpt--
d1cjca2  (  52 )    -ap-----------------------------------------------
d1djqa3  ( 433 )    alp-----------------------------------------------
d1gtea4  ( 232 )    -pq-----------------------------------------------
d1i8ta1  (  43 )    edce--giqih-kygahiFhTn------------dkyIwdyVndlveFnr
d1kifa1  (  42 )    --------ftttDvaaGlWqPytsepsnpqEanwNqqTFnyLlshigspn
d1lqta2  (  54 )    -ap-----------------------------------------------
d1ps9a3  ( 417 )    qip-----------------------------------------------
d2bi7a1  (  45 )    ardsetnvmvh-vygphiFhTd------------netVwnyVnkhaeMmp
                                                                      

                             160       170       180       190       200 
d1c0pa1  (1085 )    ---ghAmwlkgtrrfaqnedgLlghwYkdiTpnYrpLpsseC--pp----
d1cjca2  (  54 )    --------------------------------------------------
d1djqa3  ( 436 )    --------------------------------------------------
d1gtea4  ( 234 )    --------------------------------------------------
d1i8ta1  (  78 )    ftnsplaiykdklFnl-----PfNMnTFhqmwgVk-dpqeAqniInaqkk
d1kifa1  (  84 )    aanMGLtpvs-gynlfre--avpdPyWkdmVlgfrkLtpreldmfp----
d1lqta2  (  56 )    --------------------------------------------------
d1ps9a3  ( 420 )    --------------------------------------------------
d2bi7a1  (  82 )    yvnrvkatvngqvFsl-----pINLhTInqffsktCspdeAralIaekGd
                                                                      

                             210       220       230       240       250 
d1c0pa1  (1126 )    --------------------------------------------------
d1cjca2  (  54 )    --------------------------------------------------
d1djqa3  ( 436 )    --------------------------------------------------
d1gtea4  ( 234 )    --------------------------------------------------
d1i8ta1  ( 122 )    kygdkvpenLeeqaislVGedLYqaLikgyTekqwgrsAkeLpafIikri
d1kifa1  ( 127 )    --------------------------------------------------
d1lqta2  (  56 )    --------------------------------------------------
d1ps9a3  ( 420 )    --------------------------------------------------
d2bi7a1  ( 127 )    stia-dPqtFeeeAlrfIGkeLYeAFfkgytikqwgmqPseLpasilkrl
                                                                      

                             260       270       280       290       300 
d1c0pa1  (1126 )    -----ga-iGVTYdTLsVh----ApkYCqyLareLqkl-----gAtfer-
d1cjca2  (  54 )    -------------------dhpevknvintFtqtArs-----drCaFyGn
d1djqa3  ( 436 )    -------------------glgewsyHrdyRetQItkLlkknkeSqlalg
d1gtea4  ( 234 )    -------------------frlpydvVnfeIelMkdl------gVkIicg
d1i8ta1  ( 172 )    pvrftfdnnyfsdryqGiP----vgGYtkLIekMLeg-------Vdvklg
d1kifa1  ( 127 )    -----dyryGWfNtsLiLe----GrkYLqwLterLter-----gVkffl-
d1lqta2  (  56 )    -------------------dhpkiksiskqFektaed-----prFrFFGn
d1ps9a3  ( 420 )    -------------------gkeefyeTLryYrrmIevtg-----Vtlkln
d2bi7a1  ( 176 )    pVrfnyddnyfnhkfqGmP----kcgYtqMIksILnhe-----nIkvdlq
                                              aaaaaaaaa          bbb  

                             310       320       330       340       350 
d1c0pa1  (1160 )    rtVt----SLeqAFd-gadLVVNAtg-------lgAksiAGIddqarggp
d1cjca2  (  80 )    VeVG-rdVtVqeLqdA-YhAVVLSygAedkSr-----piDpsVpfdpklG
d1djqa3  ( 467 )    qkp----mtAddVLqygAdkVIIAtga---sectlwneLkaresewaen-
d1gtea4  ( 259 )    ksLseneitLntLkeegykAAFIGiglpevLrdpkvkeALspIkfnr-wd
d1i8ta1  ( 211 )    idFlk---dkdslas-kAhrIIYtg---------pIdqYFdyrf------
d1kifa1  ( 162 )    rkVe----sFeeVArggAdVIINCtg-------vwAgvLq--pdpl--qV
d1lqta2  (  82 )    vvvG-ehvqPgelser-YDAviYAvgAqsrGv-----ptp-glpfddqsG
d1ps9a3  ( 446 )    h-t----vtadq--lqafdetILAsgi---pnralaqpLids--------
d2bi7a1  ( 217 )    refi------veert-hydHVFYsg---------pLdaFygyqy------
                                       bbbb                           

                             360       370       380       390       400 
d1c0pa1  (1293 )    rVeaerIvLpLdrtkSplSlgrgsaraakekeVTLVHAy----gFssagY
d1cjca2  ( 348 )    vVpnm--------------------eGrVvdvpgLYCS-GwVKrgptgvi
d1djqa3  ( 665 )    ------------------------------dIkgIylI-GdAea--prli
d1gtea4  ( 461 )    lPeVd-------------------petMqTsepwVFAG-GdIvg-mantt
d1i8ta1  ( 242 )    --gaLnd----nknmelfkkYrelAsred----kViFGg-rlAeykyydm
d1kifa1  ( 290 )    rLereqlrfg-------------------ssnTEVIHNy----gHggygl
d1lqta2  ( 340 )    tipnv--------------------gGringspneYvv-Gwikrgptgvi
d1ps9a3  ( 640 )    ------------------------------gk-tVhlI-GgCdvameLda
d2bi7a1  ( 245 )    --grLrq----mgemalLekYLslAenet----nITFvg-rlGTyryldm
                                                      bbb            a

                             410       420       430       440       450 
d1c0pa1  (1339 )    QQSwGAAedVAqlVdeAfqryhg                           
d1cjca2  ( 377 )    tttmtdSflTGqiLlqDlkag----hLpsgprpGsafIkalLdsrgvwPV
d1djqa3  ( 682 )    AdATftGHrVArEIeea-----nPqiaipykretiawgtphmp-------
d1gtea4  ( 490 )    vesvndGkqASwyIhkyIQaqyg-asvsa----------------kpelp
d1i8ta1  ( 350 )    hqvIsaAlyqVknimstd                                
d1kifa1  ( 317 )    TIHwGCAleVAklFgkVLeernl                           
d1lqta2  ( 369 )    gtnkkdAqdtvdtliknlgnakegaecks--fdhadqvadwlaarqpklv
d1ps9a3  ( 658 )    rraIaqGTrlALei                                    
d2bi7a1  ( 353 )    dvtIaeAlkTAevYlnSltenqpMpvftvsVr                  
                    aaaaaaaaaaaaaaa                                   

                             460       470       480      
d1c0pa1                                                   
d1cjca2  ( 423 )    sFsdWekLdaeEvsrGqasgkprekLldpqemlrlLgh
d1djqa3  ( 720 )    ---------------------ggnfkieykv       
d1gtea4  ( 523 )    lfytpvdlvd                            
d1i8ta1                                                   
d1kifa1                                                   
d1lqta2  ( 419 )    tsahWqvidafEraaGephgrprvklaslaellriGlg
d1ps9a3                                                   
d2bi7a1                                                   
                                                          

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]