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Protein summary

Example page

One Ensembl protein is shown as a purple bar, with alternating shades of light and dark purple reflecting alternating exons. Below that, domains and motifs from multiple projects are mapped along the protein. Click on any motif to find the corresponding amino acid positions on the Ensembl protein, along with domain IDs in the respective databases. Sequence variations are displayed if they are found in the coding sequence.

For a table of protein motifs and domains, go to the domains and features page

Motifs and domains in Ensembl proteins are predicted using InterProScan, which includes annotation from:

Other motifs come from the following analyses and sources:

Coiled-coils - The Ensembl analysis and annotation pipeline uses the ncoils program implemented by R.B. Russell and A.N. Lupas for coiled-coil domain characterisation and annotation. Rob Russel's group at the EMBL Heidelberg provides a public service.

  • Lupas A, Van Dyke M and Stock J.

    Predicting coiled coils from protein sequences.

    Science. 1991 May 24;252(5010):1162-1164.

    PubMed

Low-complexity regions - Low complexity regions are annotated with the SEG program.

  • Wootton, J. C. and S. Federhen

    Statistics of local complexity in amino acid sequences and sequence databases.

    Computers in Chemistry 1993; 17:149-163.

    doi:10.1016/0097-8485(93)85006-X

  • Wootton, J. C. and S. Federhen.

    Analysis of compositionally biased regions in sequence databases.

    Methods in Enzymology 1996; 266: 554-571.

    doi:10.1016/S0076-6879(96)66035-2

Signal sequences - These regions are characterised with SignalP.

  • Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.

    Protein Eng. 1997 Jan;10(1):1-6.

    Abstract Full Text PDF

  • Nielsen H, Krogh A. Prediction of signal peptides and signal anchors by a hidden Markov model.

    In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 122-130, Menlo Park, CA, 1998.

    AAAI Press PubMed]

  • Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0.

    J Mol Biol. 2004 Jul 16;340(4):783-795.

    doi:10.1016/j.jmb.2004.05.028

Transmembrane regions - Ensembl uses TMHMM for the annotation of transmebrane helices.

  • A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer.

    Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes.

    Journal of Molecular Biology, 305(3):567-580, January 2001.

    doi:10.1006/jmbi.2000.4315

  • E. L.L. Sonnhammer, G. von Heijne, and A. Krogh.

    A hidden Markov model for predicting transmembrane helices in protein sequences. In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors

    Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology

    175-182, Menlo Park, CA, 1998.

    AAAI Press PubMed