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We hypothesized that peptides of this group may contain two conserved structural motifs in K<jats:sup>+<\/jats:sup>and\/or Na<jats:sup>+<\/jats:sup>channels scorpion toxins, allowing these<jats:italic>birtoxin-like<\/jats:italic>peptides to be active on K<jats:sup>+<\/jats:sup>and\/or Na<jats:sup>+<\/jats:sup>channels.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Four multilevel motifs, overrepresented and specific to each group of K<jats:sup>+<\/jats:sup>and\/or Na<jats:sup>+<\/jats:sup>ion channel toxins have been identified, using GIBBS and MEME and based on a training dataset of 79 sequences judged as representative of K<jats:sup>+<\/jats:sup>and Na<jats:sup>+<\/jats:sup>toxins.<\/jats:p><jats:p>Unexpectedly<jats:italic>birtoxin<\/jats:italic>-like peptides appeared to present a new structural motif distinct from those present in K<jats:sup>+<\/jats:sup>and Na<jats:sup>+<\/jats:sup>channels Toxins. This result, supported by previous experimental data, suggests that<jats:italic>birtoxin<\/jats:italic>-like peptides may exert their activity on different sites than those targeted by classic K<jats:sup>+<\/jats:sup>or Na<jats:sup>+<\/jats:sup>toxins.<\/jats:p><jats:p>Searching, the<jats:italic>nr<\/jats:italic>database with these newly identified motifs using MAST, retrieved several sequences (116 with e-value &lt; 1) from various scorpion species (test dataset). The filtering process left 30 new and highly likely ion channel effectors.<\/jats:p><jats:p>Phylogenetic analysis was used to classify the newly found sequences. Alternatively, classification tree analysis, using CART algorithm adjusted with the training dataset, using the motifs and their 2D structure as explanatory variables, provided a model for prediction of the activity of the new sequences.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The phylogenetic results were in perfect agreement with those obtained by the CART algorithm.<\/jats:p><jats:p>Our results may be used as criteria for a new classification of scorpion toxins based on functional motifs.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2210-9-4","type":"journal-article","created":{"date-parts":[[2009,3,10]],"date-time":"2009-03-10T19:10:43Z","timestamp":1236712243000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["residues implicated in the formation K+ and Na+ ion channels effector toxins"],"prefix":"10.1186","volume":"9","author":[{"given":"Rima","family":"Soli","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Belhassen","family":"Kaabi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mourad","family":"Barhoumi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"El-Ayeb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Najet","family":"Srairi-Abid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2009,3,10]]},"reference":[{"issue":"2","key":"511_CR1","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.toxicon.2006.09.022","volume":"49","author":"WA Catterall","year":"2007","unstructured":"Catterall WA, Cest\u00e8le S, Yarov-Yarovoy V, Yu FH, Konoki K, Scheuer T: Voltage-gated ion channels and modifier toxins. 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