Journal of Biosciences

, Volume 26, Issue 2, pp 277–284

Application of InterPro for the functional classification of the proteins of fish origin in SWISS-PROT and TrEMBL

Article

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is an integrated documentation resource for protein families, domains and sites, developed initially as a means of rationalizing the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. It is a useful resource that aids the functional classification of proteins. Almost 90% of theactinopterygii protein sequences from SWISS-PROT and TrEMBL can be classified using InterPro. Over 30% of theactinopterygii protein sequences currently in SWISS-PROT and TrEMBL are of mitochondrial origin, the majority of which belong to the cytochrome b/b6 family. InterPro also gives insights into the domain composition of the classified proteins and has applications in the functional classification of newly determined sequences lacking biochemical characterization, and in comparative genome analysis. A comparison of theactinopterygii protein sequences against the sequences of other eukaryotes confirms the high representation of eukaryotic protein kinase in the organisms studied. The comparisons also show that, based on InterPro families, thetrans-species evolution of MHC class I and II molecules in mammals and teleost fish can be recognized.

Keywords

Actinopterygii (ray-finned fish) fish proteins functional classification InterPro SWISS-PROT TrEMBL 

Abbreviations used

GPCRs

G-coupled protein receptors

PKD

polycystic kidney disease

MHC

major histocompatibility complex

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References

  1. Apweiler R, Attwood T K, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning M D R, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder N J, Oinn T M, Pagni M, Servant F, Sigrist C J A and Zdobnov E M 2001 The InterPro database, an integrated documentation resource for protein families, domains and functional sites;Nucleic Acids Res. 29 37–40PubMedCrossRefGoogle Scholar
  2. Attwood T K, Croning M D R, Flower D R, Lewis A P, Mabey J E, Scordis P, Selley J N and Wright W 2000 PRINTS-S: the database formerly known as PRINTS;Nucleic Acids Res. 28 225–227PubMedCrossRefGoogle Scholar
  3. Bairoch A and Apweiler R 2000 The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000;Nucleic Acids Res. 28 45–48PubMedCrossRefGoogle Scholar
  4. Bateman A, Birney E, Durbin R, Eddy S R, Howe K L and Sonnhammer ELL 2000 The Pfam Protein Families Database;Nucleic Acids Res. 28 263–266PubMedCrossRefGoogle Scholar
  5. Berman H M, Westbrook J, Feng Z, Gilliland G, Bhat T N, Weissig H, Shindyalov I N and Bourne P E 2000 The Protein Data Bank;Nucleic Acids Res. 28 235–242PubMedCrossRefGoogle Scholar
  6. Brenner S, Elgar G, Sandford R, Macrae A, Venkatesh B and Aparicio S 1993 Characterisation of the pufferfish (Fugu) genome as a compact model vertebrate genome;Nature (London) 366 265–268CrossRefGoogle Scholar
  7. Corpet F, Servant F, Gouzy J and Kahn D 2000 ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons;Nucleic Acids Res. 28 267–269PubMedCrossRefGoogle Scholar
  8. Etzold T, Ulyanov A and Argos P 1996 SRS: information retrieval system for molecular biology data banks;Methods Enzymol. 266 114–28PubMedCrossRefGoogle Scholar
  9. Graether S P, Deluca C I, Baardsnes J, Hill G A, Davies P L and Jia Z 1999 Quantitative and qualitative analysis of type III antifreeze protein structure and function;J. Biol. Chem. 274 11842–11847PubMedCrossRefGoogle Scholar
  10. Hofmann K, Bucher P, Falquet L and Bairoch A 1999 The PROSITE database, its status in 1999;Nucleic Acids Res. 27 215–219PubMedCrossRefGoogle Scholar
  11. Holm L and Sander C 1999 Protein folds and families: sequence and structure alignments;Nucleic Acids Res. 27 244–247PubMedCrossRefGoogle Scholar
  12. Lekven A C, Helde K A, Thorpe C J, Rooke R and Moon R T 2000 Reverse genetics in zebrafish;Physiol. Genomics 237–48Google Scholar
  13. Nonaka M, Yamada-Namikawa C, Flajnik M F and Du Pasquier L 2000 Trans-species polymorphism of the major histocompatibility complex-encoded proteasome subunit LMP7 in an amphibian genus, Xenopus;Immunogenetics 51 186–192PubMedCrossRefGoogle Scholar
  14. Rubin G M, Yandell M D, Wortman J R, Gabor Miklos G L, Nelson C R, Hariharan I K, Fortini M E, Li P W, Apweiler R, Fleischmann Wet al 2000 Comparative genomics of the eukaryote;Science 287 2204–2215PubMedCrossRefGoogle Scholar
  15. Wang J P, Hsu K C and Chiang T Y 2000 Mitochondrial DNA phylogeography ofAcrossocheilus paradoxus (Cyprinidae) in Taiwan;Mol Ecol. 9 1483–1494PubMedCrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2001

Authors and Affiliations

  1. 1.EMBL OutstationThe European Bioinformatics InstituteHinxtonUK

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