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Monday, March 5th 2001 : Geno3D (automatic modeling of proteins 3D structure) is now available (see news)
Job CLUSTALW (ID: 8372970) is running on NPS@ server (started on Mon Jul 16 12:57:14 CEST 2001).
Results will be shown below. Please wait and don't go back.

CLUSTALW multiple alignment

AbstractThompson, J.D., Higgins, D.G. and Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. (1994) Nucleic Acids Research, 22, 4673-4680 [HELP]
alignment with width : 
residues.
Conservation level of % (works with "using conservation level of" option in list above).

with percentage of secondary structure.

DSC (King and Sternberg, 1996) (Do it alone) [HELP]
DPM (Deleage and Roux, 1987) [HELP]
GOR I (Garnier et al.,1978) Choose parameters [HELP]
GOR III (Gibrat et al.,1987) [HELP]
GOR IV (Garnier et al., 1996) [HELP]
HNN (Guermeur, 1997) [HELP]
SIMPA96 (Levin et al., 1996) [HELP]
PHD (Rost et al., 1994) (Do it alone) [HELP]
PREDATOR (Argos et al., 1996) Choose parameters [HELP]
SOPM (Geourjon and Deleage, 1994) (Do it alone) [Choose parameters] [HELP]
A prediction method with the Do it alone sentence must be the only newly selected one between two clicks on SHOW button. The other methods can be kept if they have been computed or can be added after. All methods can be displayed at the same time in the alignement.

View CLUSTALW in: [MPSA (Mac, UNIX) , About...] [AnTheProt (PC) , Download...] [HELP] 

                     10        20        30        40        50        60
                      |         |         |         |         |         |
p140mDia     YKPEVQLRRPNWSKFVAED--LSQDCFWTKVKEDRFEN--NELFAKLTLAFSAQTKTSKA
Diaphanous   WDVKNPMKRANWKAIVPAK--MSDKAFWVKCQEDKLAQ--DDFLAELAVKFSSKP----V
Fuguxx2      IKTKFRLPVFNWTALKPNQ--INGTVFN-EIDDERELE--LERFEELFKTRAQGP-----
Cappuccino   --------------PPTAP--PATKEIWTEIEETPLDN--IDEFTELFSRQAIAP-----
Bni1xx4      PRPHKKLKQLHWEKLDCTDNSIWGTGKAEKFADDLYEKGVLADLEKAFAAREIKSLASKR
                                          :  :    :     : :        .     
Prim.cons.   4KPK44LKR4NW42LVPADNSISG25FWTKI5EDRLENGVL25F2ELF5A22IKP22SK3

                     70        80        90       100       110       120
                      |         |         |         |         |         |
p140mDia     KK-DQEGGEEKKSVQKKKVKELKVLDSKTAQNLSIFLG-SF-R-MPYQEIKNVILEVNEA
Diaphanous   KK-EQKDAVDKPTTLTKKNVDLRVLDSKTAQNLAIMLGGSL-KHLSYEQIKICLLRCDTD
Fuguxx2      ---IMDLSCTKSKVAQKAVNKVTILDANRSKNLAITLR---------KANK--TFDLK--
Cappuccino   -------VSKPKELKVKRAKSIKVLDPERSRNVGIIWR--S-LHVPSSEIEHAIYHIDTS
Bni1xx4      KEDLQKITFLSRDISQQFGINLHMYSSLSVADLVKKILNCDRDFLQTPSVVEFLSKSEII
                             :   .: : ..    ::                        .  
Prim.cons.   KKD4QK4555KK5V5QKKVK5LKVLDSK22QNLAI5L22S4R4HLPY5EIK442L55DT4

                    130       140       150       160       170       180
                      |         |         |         |         |         |
p140mDia     VLTESMIQNLIKQMPEPEQLKMLSELKEEY---DDLAESEQFGVVMGT--VPRLRPRLNA
Diaphanous   ILSSNILQQLIQYLPPPEQLKRLQEIKAKG---EPLPPIEQFAATIGE--IKRLSPRLHN
Fuguxx2      TLPVDFVECLMRFLPTEMEVKALRQYERERRPLDQLAEEDRFMLLFSK--IERLTQRMNI
Cappuccino   VVSLEALQHMSNIQATEDELQRIKEAAGGD---IPLDHPEQFLLDISL--ISMASERISC
Bni1xx4      EVSVNLARNYAPYSTDWEGVRNLEDAKPPEKDPNDLQRADQIYLQLMVNLESYWGSRMRA
              :. .  .      .    :: : :          *   :::   :          *:  
Prim.cons.   VLSVN5LQNLI5YLPT2E2LKRL5EAK5E5222D2LAE5EQF5L5I25NLISRLSPR2NA

                    190       200       210       220       230       240
                      |         |         |         |         |         |
p140mDia     ILFKLQFSEQVENIKPEIVSVTAACEELRKSENFSSLLELTLLVGNYMNAG-SRNAGAFG
Diaphanous   LNFKLTYADMVQDIKPDIVAGTAACEEIRNSKKFSKILELILLLGNYMNSG-SKNEAAFG
Fuguxx2      ITFIGNFSDNVAMLTPQLNAIIAASASVKSSPKLKRMLEIILALGNYMNS--SKRGCVYG
Cappuccino   IVFQAEFEESVTLLFRKLETVSQLSQQLIESEDLKLVFSIILTLGNYMNGGNRQRGQADG
Bni1xx4      LTVVTSYEREYNELLAKLRKVDKAVSALQESDNLRNVFNVILAVGNFMND---TSKQAQG
             : .   :      :  .:         : .* .:  ::.: * :**:**        . *
Prim.cons.   ITFKL5F225V55LKPKLVAVTAA2EELRESE2L25VLE2IL2LGNYMNSGNSK2GQAFG

                    250       260       270       280       290       300
                      |         |         |         |         |         |
p140mDia     FNISFLCKLRDTKSADQKMTLLHFLAELCENDHP-------EVLKFPDELAHVEKASRVS
Diaphanous   FEISYLTKLSNTKDADNKQTLLHYLADLVEKKFP-------DALNFYDDLSHVNKASRVN
Fuguxx2      FKLQSLDLLLDTKSTDRKMTLLHYIALIVKEKYP-------ELANFYNELHFVDKAAAVS
Cappuccino   FNLDILGKLKDVKSKESHTTLLHFIVRTYIAQRRKEGVHPLEIRLPIPEPADVERAAQMD
Bni1xx4      FKLSTLQRLTFIKDTTNSMTFLNYVEKIVRLNYP-------SFNDFLSELEPVLDVVKVS
             *::. *  *   *.     *:*:::      .         .      :   *  .  :.
Prim.cons.   F2LS5L5KL5DTKS2DNKMTLLHY2A52VE5KYPKEGVHPLE5LNFYDELAHVEKA2RVS

                    310       320       330       340       350       360
                      |         |         |         |         |         |
p140mDia     AENLQKSLDQMKKQIADVERDVQNFPAATDE--K--DKFVEKMTSFVKDAQEQYNKLRMM
Diaphanous   MDAIQKAMRQMNSAVKNLETDLQNNKVPQCD--D--DKFSEVMGKFAEECRQQVDVLGKM
Fuguxx2      LENVLLDVRELGKGMDLIRRECSLHDHS-------------VLKGFLQASDTQLDKVQRD
Cappuccino   FEEVQQQIFDLNKKFLGCKRTTAKVLAASRPEIM--EPFKSKMEEFVEGADKSMAKLHQS
Bni1xx4      IEQLVNDCKDFSQSIVNVERSVEIGNLSDSSKFHPLDKVLIKTLPVLPEARKKGDLLEDE
              : :     :: . .   .        .                 .   .  .   :   
Prim.cons.   5EN2QKD5R22NK5I5NVERDVQN55A2444224PLDKF4EKM55F2EEA2KQ5DKL55M

                    370       380       390       400       410       420
                      |         |         |         |         |         |
p140mDia     HSNMETLYKELGDYFVFDP-KKLSVEEFFMDLHNFRNMFLQAVKENQKRRETEEKMRRAK
Diaphanous   QLQMEKLYKDLSEYYAFDP-SKYTMEEFFADIKTFKDAFQAAHNDNVRVREELEKKRRLQ
Fuguxx2      AKTAEEAFNNVVNYFGESA-KTAPPSVFFPVFVRFLKAYKDAVEENELRKKQEQAMREKL
Cappuccino   LDECRDLFLETMRFYHFSP-KACTLTLAQCTPDQFFEYWTNFTNDFKDIWKKEITSLLNE
Bni1xx4      VKLTIMEFESLMHTYGEDSGDKFAKISFFKKFADFINEYKKAQAQNLAAEEEERLYIKHK
                    : .    :  .. .  .          * . :     :     :         
Prim.cons.   5K5ME5LFKELM5YYGFDPGKK5T5EEFF5DF55F5NA2K5AVN2N55RREEEEKMRR5K

                    430       440       450       460       470       480
                      |         |         |         |         |         |
p140mDia     LAKEKAEKE-RLEKQQKREQLIDMNAEGDETGVMDSLLEALQSGAAF-------RRKR--
Diaphanous   EAREQSARE-QQERQQRKKAVVDMDAPQTQEGVMDSLLEALQTGSAFGQRNRQARRQRPA
Fuguxx2      LAEEAKQQDPKVQAQKKRQQQHELIAELRKRQAKDHRPVYEGKDGTIEDIITVLK-----
Cappuccino   LMKKSKQAQ-----IESRRNVSTKVEKSGRISLKERMLMRRSKN----------------
Bni1xx4      KIVEEQQKRAQEKEKQKENSNSPSSEGNEEDEAEDRRAVMDKLLEQLKNA----------
                :           : ..          .    :                         
Prim.cons.   LAKE5KQKE2Q4E4QQKR5QVSDM5AE55E5G22D22L2ALQKG4AF3332222RR2RPA

                    490       500       510
                      |         |         |
p140mDia     ------------------------------------
Diaphanous   GAERRAQLSRSRSRTRVTNGQLMTREMILNEVLGSA
Fuguxx2      ------------------------------------
Cappuccino   ------------------------------------
Bni1xx4      ------------------------------------
                                                                         
Prim.cons.   GAERRAQLSRSRSRTRVTNGQLMTREMILNEVLGSA                        
Alignment data :
Alignment length : 516
Identity (*) : 17 is 3.29 %
Strongly similar (:) : 52 is 10.08 %
Weakly similar (.) : 37 is 7.17 %
Different : 410 is 79.46 %
Sequence 0001 : p140mDia ( 444 residues).
Sequence 0002 : Diaphanous ( 487 residues).
Sequence 0003 : Fuguxx2 ( 424 residues).
Sequence 0004 : Cappuccino ( 418 residues).
Sequence 0005 : Bni1xx4 ( 460 residues).
CLUSTALW options used :
endgaps=1
gapdist=8
gapext=0.2
gapopen=10.0
hgapresidues=GPSNDQERK
ktuple=1
matrix=gonnet
maxdiv=30
outorder=aligned
pairgap=3
score=percent
topdiags=5
type=PROTEIN
window=5
Result files (text) :
CLUSTALW
Garnier parameters

Auto calculated
Decision constants HelixSheetTurnCoil
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PREDATOR parameters

Secondary structure data
Return
 

SOPM parameters

Number of conformational states
Similarity threshold : Window width : 
Return

SOPMA parameters

Number of conformational states
Similarity threshold : Window width : 
Return

User : public@134.219.40.186. Last modification time : Mon Jul 16 12:57:24 2001. Current time : Mon Jul 16 12:57:24 2001This service is supported by MESR (ACC-SV13), CNRS (IMABIO, COMI, GENOME) and Région Rhône-Alpes (Programme EMERGENCE) . Comments.