Analysis of protein domain families in Caenorhabditis elegans

Genomics
Erik L L Sonnhammer, R Durbin

Abstract

The Caenorhabditis elegans genome sequencing project has completed over half of this nematode's 100-Mb genome. Proteins predicted in the finished sequence have been compiled and released in the data-base Wormpep. Presented here is a comprehensive analysis of protein domain families in Wormpep 11, which comprises 7299 proteins. The relative abundance of common protein domain families was counted by comparing all Wormpep proteins to the Pfam collection of protein families, which is based on recognition by hidden Markov models. This analysis also identified a number of previously unannotated domains. To investigate new apparently nematode-specific protein families, Wormpep was clustered into domain families on the basis of sequence similarity using the Domainer program. The largest clusters that lacked clear homology to proteins outside Nematoda were analyzed in further detail, after which some could be assigned a putative function. We compared all proteins in Wormpep 11 to proteins in the human, Saccharomyces cerevisiae, and Haemophilus influenzae genomes. Among the results are the estimation that over two-thirds of the currently known human proteins are likely to have a homologue in the whole C. elegans genome and that a signifi...Continue Reading

References

Dec 11, 1991·Nucleic Acids Research·S Henikoff, J G Henikoff
May 24, 1991·Science·A LupasJ Stock
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jul 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·M GribskovD Eisenberg
Oct 20, 1995·Science·J HodgkinR H Waterston
Jun 1, 1994·Computer Applications in the Biosciences : CABIOS·E L Sonnhammer, R Durbin
Feb 25, 1993·Nucleic Acids Research·D K Braithwaite, J Ito
Apr 1, 1996·Current Opinion in Structural Biology·D T Jones, J M Thornton
Jul 1, 1996·Trends in Genetics : TIG·G CasariR Schneider
Aug 1, 1996·Current Opinion in Biotechnology·J Moult
Jan 1, 1997·Nucleic Acids Research·A Bairoch, R Apweiler
Jan 1, 1997·Nucleic Acids Research·B L MaidakC R Woese
Jan 1, 1997·Nucleic Acids Research·A BairochK Hofmann

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Citations

Mar 10, 2000·Nucleic Acids Research·E R ZabarovskyC Wahlestedt
Dec 26, 2001·Nucleic Acids Research·Takeshi KawabataKen Nishikawa
Jul 24, 2002·Nucleic Acids Research·Alexey S KutsenkoEugene R Zabarovsky
Oct 6, 1999·Genome Research·L X LiuC D Johnson
Mar 19, 2011·Pharmacological Reviews·Udai Bhan Pandey, Charles D Nichols
Mar 1, 2008·BMC Evolutionary Biology·Vladimir M MilenkovicBernhard H F Weber
May 10, 2005·BMC Genomics·Ivica TamasAna Vaz Gomes
Jul 4, 2008·PLoS Neglected Tropical Diseases·James WasmuthMark Blaxter
Jun 8, 2011·PloS One·Daniel D Shaye, Iva Greenwald
Jul 29, 2008·FEBS Letters·Sofia Duque SantosMaria João Saraiva
Apr 13, 2010·Phytomedicine : International Journal of Phytotherapy and Phytopharmacology·S Abbas, M Wink
Jun 29, 2006·Annals of the New York Academy of Sciences·Anders OlsenGordon J Lithgow
Oct 20, 2009·Molecular and Biochemical Parasitology·You-Jin HaoNelson Simões
Jul 23, 2016·Journal of Applied Toxicology : JAT·Piper Reid Hunt
Dec 18, 2013·Advanced Drug Delivery Reviews·Linda P O'ReillyStephen C Pak
Aug 5, 2016·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Muniesh Muthaiyan Shanmugam, Tuhin Subhra Santra
Jun 27, 2002·Journal of Molecular Biology·Paul M Harrison, Mark Gerstein
Dec 7, 2013·Revista brasileira de psiquiatria : orgão oficial da Associação Brasileira de Psiquiatria, Asociación Psiquiátrica de la América Latina·Fabíola Mara RibeiroAntonio Lucio Teixeira
May 29, 2002·European Journal of Human Genetics : EJHG·Heidi StöhrBernhard H F Weber
Sep 12, 2018·Current Protocols in Molecular Biology·Sakthimala Jagadeesan, Abdul Hakkim
Aug 14, 2003·Current Neurology and Neuroscience Reports·Leslie Michels Thompson, J Lawrence Marsh
Mar 1, 2003·Nature Reviews. Genetics·Monica Driscoll, Beate Gerstbrein
May 5, 2006·Nature Reviews. Drug Discovery·Titus Kaletta, Michael O Hengartner
Feb 13, 1999·Nature Genetics·M MarraR Waterston
Mar 3, 2012·Cellular and Molecular Life Sciences : CMLS·Márcio S BaptistaPatrícia Maciel
Aug 31, 2018·The Journal of Pharmacology and Experimental Therapeutics·Luisa L ScottJonathan T Pierce

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