Skip to main content
SpringerLink
Log in

Gene3D and Understanding Proteome Evolution

  • Chapter
Structural Approaches to Sequence Evolution

Part of the book series: Biological and Medical Physics, Biomedical Engineering ((BIOMEDICAL))

  • 900 Accesses

Gene3D is a database of protein sequence families. The families have been created through clustering the proteome sequences of over 200 species, including more than 15 eukaryotes, and totalling over 750,000 proteins (as derived from UniProt [1]). Each family is then further subclustered on the basis of sequence similarity. Using remote homologue detection methods, we have been able to assign structures – based on the CATH [2] and Pfam [3] databases – to a majority of these sequences. This allows a high resolution view of the functions and evolution of specific protein families, as well as the evolution of a species' gene content.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. R. Apweiler, A. Bairoch, C.H. Wu, W.C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, M.J. Martin, D.A. Natale, C. O'Donovan, N. Redaschi, L.S. Yeh, Nucleic Acid Res. 32, D115 (2004)

    Article  Google Scholar 

  2. F. Pearl, A. Todd, I. Sillitoe, M. Dibley, O. Redfern, T. Lewis, C. Bennett, R. Marsden, A. Grant, D. Lee, A. Akpor, M. Maibaum, A. Harrison, T. Dallman, G. Reeves, S. Diboun, S. Addou, S. Lise, C. Johnston, A. Sillero, J. Thornton, C. Orengo, Nucleic Acid Res. 33, D247 (2005)

    Article  Google Scholar 

  3. A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E.L.L. Sonnhammer, D.J. Studholme, C. Yeats, S.R. Eddy, Nucleic Acid Res. 32, D138 (2004)

    Article  Google Scholar 

  4. G.M. Edelman, W.E. Gall, Annu. Rev. Biochem. 38, 415 (1969)

    Article  Google Scholar 

  5. A.G. Rossman, A. Liljas, J. Mol. Biol. 85, 177 (1974)

    Article  Google Scholar 

  6. S.D. Bentley, M. Maiwald, L.D. Murphy, M.J. Pallen, C. Yeats, L.G. Dover, H.T. Norbertczak, G.S. Besra, M.A. Quail, D.E. Harris, A. von Herbay, A. Goble, S. Rutter, R. Squares, S. Squares, B.G. Barrell, J. Parkhill, D.A. Relman, Lancet 361, 637 (2003)

    Article  Google Scholar 

  7. B. Morgenstern, W.R. Atchley, Mol. Biol. Evol. 16, 1654 (1999)

    Google Scholar 

  8. S.A. Teichmann, J. Park, C. Chothia, Proc. Natl. Acad. Sci. USA 95, 14658 (1998)

    Article  ADS  Google Scholar 

  9. M. Gerstein, Prot. Struct. Func. Genet. 33, 518 (1998)

    Article  Google Scholar 

  10. D. Lee, A. Grant, R.L. Marsden, C. Orengo, Proteins 59, 603 (2005)

    Article  Google Scholar 

  11. A. Grant, D. Lee, C. Orengo, Genome Biol. 5, 107 (2004)

    Article  Google Scholar 

  12. A.E. Todd, R.L. Marsden, J.M. Thornton, C.A. Orengo, J. Mol. Biol. 348, 1235 (2005)

    Article  Google Scholar 

  13. T. Meinel, A. Krause, H. Luz, M. Vingron, E. Staub, Nucleic Acid Res. 33, D226 (2005)

    Article  Google Scholar 

  14. N. Kaplan, O. Sasson, U. Inbar, M. Friedlich, M. Fromer, H. Fleischer, E. Portugaly, N. Linial, M. Linial, Nucleic Acid Res. 33, D216 (2005)

    Article  Google Scholar 

  15. A. Heger, L.U. Holm, J. Mol. Biol. 328, 749 (2003)

    Article  Google Scholar 

  16. C. Bru, E. Courcelle, S. Carrére, Y. Beausse, S. Dalmar, D. Kahn, Nucleic Acid Res. 33, D212 (2005)

    Article  Google Scholar 

  17. T.F. Smith, M.S. Waterman, J. Mol. Biol. 147, 195 (1981)

    Article  Google Scholar 

  18. E. Hartuv, A. Schmitt, J. Lange, S. Meier-Ewert, H. Lehrach, R. Shamir, Proc. Recomb. 99, 188 (1999)

    Google Scholar 

  19. E.L.L. Sonnhammer, D. Kahn, Prot. Sci. 3, 482 (1994)

    Article  Google Scholar 

  20. J. Gouzy, F. Corpet, D. Kahn, Comput. Chem. 23, 333 (1999)

    Article  Google Scholar 

  21. A. Enright, S. van Dongen, C.A. Ouzounis, Nucleic Acid Res. 30, 1575 (2002)

    Article  Google Scholar 

  22. R.L. Tatusov, N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, E.V. Koonin, D.M. Krylov, R. Mazumder, S.L. Mekhedov, A.N. Nikolskaya, B.S. Rao, S. Smirnov, A.V. Sverdlov, S. Vasudevan, Y.I. Wolf, J.J. Yin, D.A. Natale, BMC Bioinform. 4, 41 (2003)

    Article  Google Scholar 

  23. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, G. Sherlock, Nat. Genet. 25, 25 (2000)

    Article  Google Scholar 

  24. M. Kanehisa, S. Goto, Nucleic Acid Res. 28, 27 (2000)

    Article  Google Scholar 

  25. A.P. Bird, Trends Genet. 11, 94 (1995)

    Article  Google Scholar 

  26. A. Mira, H. Ochman, N.A. Moran, Trends Genet. 17, 589 (2001)

    Article  Google Scholar 

  27. E.V. Koonin, Y.I. Wolf, G.P. Karev, Nature 420, 218 (2002)

    Article  ADS  Google Scholar 

  28. C. Chothia, J. Gough, C. Vogel, S.A. Teichmann, Science 300, 1701 (2003)

    Article  ADS  Google Scholar 

  29. H. Ochman, J.G. Lawrence, E.A. Groisman, Nature 405, 299 (2000)

    Article  ADS  Google Scholar 

  30. J.A. Ranea, A. Grant, J.M. Thornton, C.A. Orengo, Trends Genet. 21, 21 (2005)

    Article  Google Scholar 

  31. U. Dobrindt, J. Hacker, Curr. Opin. Microbiol. 4, 550 (2001)

    Article  Google Scholar 

  32. N.A. Moran, Cell 108, 583 (2002)

    Article  Google Scholar 

  33. M. Kendall, J.D. Gibbons, Rank Correlation Methods,5th edn.(Oxford University Press, New York, 1990), ISBN 0195208374

    MATH  Google Scholar 

  34. J.A. Ranea, D.W. Buchan, J.M. Thornton, C.A. Orengo, J. Mol. Biol. 336, 871 (2004)

    Article  Google Scholar 

  35. C. Chothia, Nature 357, 543 (1992)

    Article  ADS  Google Scholar 

  36. I. Cases, V. de Lorenzo, C.A. Ouzounis, Trends Microbiol. 11, 248 (2003)

    Article  Google Scholar 

  37. E. Nimwegen, Trends Genet. 19, 479 (2003)

    Article  Google Scholar 

  38. A.E. Todd, C.A. Orengo, J.M. Thornton, J. Mol. Biol. 307, 1113 (2001)

    Article  Google Scholar 

  39. N.G. Mankiw, Principles of Microeconomics, 2nd edn. (Dryden, Chicago, 1998), ISBN 0030776422

    Google Scholar 

  40. G. Frizelle, The Management of Complexity in Manufacturing, (Business Intel-ligence press, London, 1998), ISBN 1898085366

    Google Scholar 

  41. H.A. Orr, Evolution Int. J. Org. Evol. 54, 13 (2000)

    Google Scholar 

  42. A. Dufresne, L. Garczarek, F. Partensky, Genome Biol. 6, 1 (2005)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, University College London, Gower Street, WC1E 6BT, London, UK

    Juan Garcia Ranea

  2. Department of Biochemistry and Molecular Biology, University College London, Gower Street, WC1E 6BT, London, UK

    Corin Yeats

  3. Department of Biochemistry and Molecular Biology, University College London, Gower Street, WC1E 6BT, London, UK

    Russell Marsden

  4. Department of Biochemistry and Molecular Biology, University College London, Gower Street, WC1E 6BT, London, UK

    Christine Orengo

Authors
  1. Juan Garcia Ranea
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Corin Yeats
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Russell Marsden
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Christine Orengo
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Fac. de Ciencias, Universidad Autonoma Madrid, Cantoblanco, 28049, Madrid, Spain

    Ugo Bastolla

  2. Institut für Festkörperphysik, TU Darmstadt, Hochschulstr. 8, 64289, Darmstadt, Germany

    Markus Porto

  3. Dipartimento di Fisica, Universita di Milano-Bicocca, Piazza della Scienza 3, 29126, Milano, Italy

    H. Eduardo Roman

  4. Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK

    Michele Vendruscolo

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Ranea, J.G., Yeats, C., Marsden, R., Orengo, C. (2007). Gene3D and Understanding Proteome Evolution. In: Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M. (eds) Structural Approaches to Sequence Evolution. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-35306-5_2

Download citation

Publish with us

Policies and ethics

Search

Navigation