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Monday, February 17th 2003 : NPS@ release 3.0 is now running on a Linux cluster
HMMER (hmmbuild and hmmsearch) is now available (see news)
Job CLUSTALW (ID: 2484) is running on NPS@ server (started on Mon Aug 4 02:10:49 CEST 2003).
Results will be shown below. Please wait and don't go back.
In your publication cite :
NPS@: Network Protein Sequence Analysis
TIBS 2000 March Vol. 25, No 3 [291]:147-150
Combet C., Blanchet C., Geourjon C. and Deléage G.

CLUSTALW multiple alignment

Abstract Thompson, 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
                      |         |         |         |         |         |
18044190     -----PLLFGPSFERKVVPVTDEVV-AAVAMLSVAARSGPFAPVLSATSRGVAGALRPLL
2842219      -----PLLFGPSFERKVVPVTDEVV-AAVAMLSVAARSGPFAPVLSATSRGVAGALRPLL
13385167     ------ALFGPSFERKVVPVTDEVV-AAVAMLSVAARSGPFAPVLSATSRGVAGALRPLL
12852344     ------ALFGPSFERKVVPVTDEVV-AAVAMLSVAARSGPFAPVLSATSRGVAGALRPLL
12848765     ------------------------V-AAVAMLSVAARSGPFAPVLSATSRGVAGALRPLL
16343x6      ----------------G---------AAVAMLSVAARSRHSRPSYRPRPAGWR-ALRPWY
Mature       ------------------------------------------------------------
5174742      VVTRPAPPRACTVVGRSSPVTGWAVGAAVAMLSVAARSGPFAPVLSATSRGVAGALRPLV
                                                                         
Prim.cons.   VVTRPP2LFGPSFERKVVPVTDEVVGAAVAMLSVAARSGPFAPVLSATSRGVAGALRPLL

                     70        80        90       100       110       120
                      |         |         |         |         |         |
18044190     QGAVPAASEPPVLDVKRPFLCRESLSGQAAARPLVATVGLNVPASVRFSHTDVKVPDFSD
2842219      QGAVPAASEPPVLDVKRPFLCRESLSGQAAARPLVATVGLNVPASVRFSHTDVKVPDFSD
13385167     QGAVPAASEPPVLDVKRPFLCRESLSGQAAARPLVATVGLNVPASVRFSHTDVKVPDFSD
12852344     QGAVPAASEPPVLDVKRPFLCRESLSGQAAARPLVATVGLNVPASVRFSHTDVKVPDFSD
12848765     QGAVPAASEPPVLDVKRPFLCRESLSGQAAARPLVATVGLNVPASVRFSHTDVKVPDFSD
16343x6      S---RSSKESPVLDLKRSVLCRESLRGQAAA-ALVASVSLNVPASVRYSHTDIKVPDFSD
Mature       ------------------------------------------------VHNDVTVPDFSA
5174742      QATVPATPEQPVLDLKRPFLSRESLSGQAVRRPLVASVGLNVPASVCYSHTDIKVPDFSE
                                                              *.*:.***** 
Prim.cons.   QGAVPAASEPPVLDVKRPFLCRESLSGQAAARPLVATVGLNVPASVRFSHTDVKVPDFSD

                    130       140       150       160       170       180
                      |         |         |         |         |         |
18044190     YRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMS
2842219      YRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMS
13385167     YRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMS
12852344     YRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMS
12848765     YRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMS
16343x6      YRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMS
Mature       YRREDVMDATTSSQTSSEDRKGFSYLVTATACVATAYAAKNVVTQFISSLSASADVL---
5174742      YRRLEVLDSTKSSRESSEARKGFSYLVTGVTTVGVAYAAKNAVTQFVSSMSASADVLALA
             *** :*:*:*.**: *** *********..: *..******.*:**:**:*******   
Prim.cons.   YRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMS

                    190       200       210       220       230       240
                      |         |         |         |         |         |
18044190     KIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLDRVKKPEW
2842219      KIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLDRVKKPEW
13385167     KIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLDRVKKPEW
12852344     KIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLDRVKKPEW
12848765     KIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLDRVKKPEW
16343x6      KIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERVKKPEW
Mature       -IEIKLSDIPEGKNVAFKWRGKPLFVRHRTQAEINQEAEVDVSKLRDPQHDLDRVKKPEW
5174742      KIEIKLSDIPEGKNMAFKWRGKPLFVRHRTQKEIEQEAAVELSQLRDPQHDLDRVKKPEW
              *************:***************: **:*** *::*:********:*******
Prim.cons.   KIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLDRVKKPEW

                    250       260       270       280       290       300
                      |         |         |         |         |         |
18044190     VILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPAYEFTSDDV
2842219      VILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPAYEFTSDDV
13385167     VILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPAYEFTSDDV
12852344     VILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPAYEFTSDDV
12848765     VILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPAYEFTSDDV
16343x6      VILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPSYEFTSDDM
Mature       VILVGVCTHLGCVPIANSGDFGGYYCPCHGSHYDASGRIRKGPAPYNLEVPTYQFVGDDL
5174742      VILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRLGPAPLNLEVPTYEFTSDDM
             ***:*************:********************** **** *****:*:*..**:
Prim.cons.   VILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPAYEFTSDDV

                    310       320       330       340       350       360
                      |         |         |         |         |         |
18044190     VVVGTRGLRAVSVGLQVPSEEWR-VSLVYVVGFKIF--KNCCIG--KHCEVIEFTVKYYQ
2842219      VVVGTRGLRAVSVGLQVPSEEWR-VSLVYVVGFKIF--KNCCIG--KHCEVIEFTVKYYQ
13385167     VVVGTRGLRAVSVGLQVPSEEWR-VSLVYVVGFKIF--KNCCIG--KHCEVIEFTVKYYQ
12852344     VVVGTRGLRAVSVGLQVPSEEWR-VSLVYVVGFKIF--KNCCIG--KHCEVIEFTVKYYQ
12848765     VVVGTRGLRAVSVGLQVPSEEWR-VSLVYVVGFKIF--KNCCIG--KHCEVIEFTVKYYQ
16343x6      VIVG-RDLDSSYRLLSSSCHLRR-VTRTSLLCFELVDLKYLRIANNVFANMIEFNVEYFQ
Mature       VVVG--------------------------------------------------------
5174742      VIVG-ETWTQVIGFFQSLCHLRRLIEEAFCTSFEIC--KNCICK-----HC-EINICILS
             *:**                                                        
Prim.cons.   VVVGTRGLRAVSVGLQVPSEEWRLVSLVYVVGFKIFDLKNCCIGNNKHCEVIEFTVKYYQ

                    370       380       390       400       410       420
                      |         |         |         |         |         |
18044190     ALANHCTSLDSVIDLKGAMSLIANSNKTLQIVVKKKK-----------------------
2842219      ALANHCTSLDSVIDLKGAMSLIANSNKTLQIVVKKKK-----------------------
13385167     ALANHCTSLDSVIDLKGAMSLIANSNKTLQIVVLVFSSKFLFVSTEKVGTLFFISKWMGK
12852344     ALANHCTSLDSVIDLKGAMSLIANSNKTLQIVVLVFSSKFLFVSTEKVGTLFFISKWMGK
12848765     ALANHCT-----------------------------------------------------
16343x6      AFT-KSPPLN-IVMLKG-CSVFDSFLKIVDECIKYLNL----------------------
Mature       ------------------------------------------------------------
5174742      GIHLIKTLLS-TVMLSHTRERYNVFLILIKNYRLVYKILV--------------------
                                                                         
Prim.cons.   ALANHCTSLDSVIDLKGAMSLIANSNKTLQIVV2V2KSKFLFVSTEKVGTLFFISKWMGK

                    430
                      |
18044190     ----------------
2842219      ----------------
13385167     SFYLIFFCFDIKPFTV
12852344     SFYLIFFCFDIKPFTV
12848765     ----------------
16343x6      ----------------
Mature       ----------------
5174742      ----------------
                                                                         
Prim.cons.   SFYLIFFCFDIKPFTV
Alignment data :
Alignment length : 436
Identity (*) : 150 is 34.40 %
Strongly similar (:) : 22 is 5.05 %
Weakly similar (.) : 10 is 2.29 %
Different : 254 is 58.26 %
Sequence 0001 : 18044190 ( 386 residues).
Sequence 0002 : 2842219 ( 386 residues).
Sequence 0003 : 13385167 ( 424 residues).
Sequence 0004 : 12852344 ( 424 residues).
Sequence 0005 : 12848765 ( 337 residues).
Sequence 0006 : 16343x6 ( 363 residues).
Sequence 0007 : Mature ( 192 residues).
Sequence 0008 : 5174742 ( 390 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
Return


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@131.243.195.148. Last modification time : Mon Aug 4 02:10:53 2003. Current time : Mon Aug 4 02:10:53 2003 This service is supported by Ministere de la recherche (ACC-SV13), CNRS (IMABIO, COMI, GENOME) and Région Rhône-Alpes (Programme EMERGENCE) . Comments.