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© Arne Elofsson

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1. Summary


Given the amino acid sequence of a putative alpha-helical membrane protein, SCAMPI predicts the topology of the protein, i.e. a specification of the membrane spanning segments and their IN/OUT orientation relative to the membrane. The prediction is based on an experimentally determined scale of free energy contributions from each amino acid to helix insertion efficiency. See the SCAMPI2 paper for a detailed description of the method. Note that the server does not predict cleavable signal peptides, which are easily confused with TM segments. If signal peptides are likely to be present in the input data, please use TOPCONS, which predict also the signal peptide.

SCAMPI2 is supported by the EGI FedCloud with the VO VO.NBIS.SE for computational resource.



2. Usage


This server is appropriate for topology predictions of large protein datasets. Input to the server is amino acid sequences in FASTA format. Using the text window, the maximum number of characters to be pasted is 100,000, or using the file upload option, the maximum number of sequences per query is 100,000 (i.e. enough for all bacterial and even most eukaryotic proteomes). If you only have one or a few sequences, use the TOPCONS server instead.

Example input:
>sp|O93740|BACR_HALS4 Bacteriorhodopsin Halobacterium sp.
MCCAALAPPMAATVGPESIWLWIGTIGMTLGTLYFVGRGRGVRDRKMQEFYIITIFITTI
AAAMYFAMATGFGVTEVMVGDEALTIYWARYADWLFTTPLLLLDLSLLAGANRNTIATLI
GLDVFMIGTGAIAALSSTPGTRIAWWAISTGALLALLYVLVGTLSENARNRAPEVASLFG
RLRNLVIALWFLYPVVWILGTEGTFGILPLYWETAAFMVLDLSAKVGFGVILLQSRSVLE
RVATPTAAPT
>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha Homo sapiens
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP
AVHASLDKFLASVSTVLTSKYR
>sp|P47865|AQP1_BOVIN Aquaporin-1 Bos taurus
MASEFKKKLFWRAVVAEFLAMILFIFISIGSALGFHYPIKSNQTTGAVQDNVKVSLAFGL
SIATLAQSVGHISGAHLNPAVTLGLLLSCQISVLRAIMYIIAQCVGAIVATAILSGITSS
LPDNSLGLNALAPGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSGPLAIGFSVAL
GHLLAIDYTGCGINPARSFGSSVITHNFQDHWIFWVGPFIGAALAVLIYDFILAPRSSDL
TDRVKVWTSGQVEEYDLDADDINSRVEMKPK
>sp|P62737|ACTA_MOUSE Actin, aortic smooth muscle Mus musculus
MCEEEDSTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHSFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
LSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIS
KQEYDEAGPSIVHRKCF
>sp|P00803|LEP_ECOLI Signal peptidase I Escherichia coli
MANMFALILVIATLVTGILWCVDKFFFAPKRRERQAAAQAAAGDSLDKATLKKVAPKPGW
LETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTL
IETGHPKRGDIVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENA
LPVTYSNVEPSDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILT
VPIAQDQVGMYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRYWGFVPEANLVGRATAI
WMSFDKQEGEWPTGLRLSRIGGIH



3. Output


The server outputs prediction results in three text files:

  • Predicted topologies: Text file containing the predicted topologies for all proteins in a FASTA-like format, where i=inside (cytoplasmic side), M=membrane and o=outside (extra-cytoplasmic side).
  • List of predicted TM proteins: A list containing the names of all proteins with at least one predicted TM region.
  • List of predicted non-TM proteins: A list containing the names of all proteins with no predicted TM regions.



4. References


SCAMPI2:
Improved topology predictions using the first and last hydrophobic helix rule. Christoph Peters, Konstantinos D. Tsirigos, Nanjiang Shu, Arne Elofsson [Submitted]
SCAMPI: Prediction of membrane-protein topology from first principles.
Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G and Elofsson A (2008) Proc. Natl. Acad. Sci. USA. 105, 7177-7181. [Pubmed]


5. Contact


Arne Elofsson group

Department for Biochemistry and Biophysics
The Arrhenius Laboratories for Natural Sciences
Stockholm University
SE-106 91 Stockholm, Sweden

Science for Life Laboratory
Box 1031, 17121 Solna, Sweden

E-mail:   arne@bioinfo.se
Phone:   (+46)-8-16 4672
Fax:   (+46)-8-15 3679