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Insect Biochem Mol Biol. 2007 Aug;37(8):754-60. Epub 2007 Mar 19.

Drosophila cuticular proteins with the R&R Consensus: annotation and classification with a new tool for discriminating RR-1 and RR-2 sequences.

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  • 1Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 157 01, Greece.

Erratum in

  • Insect Biochem Mol Biol.2008 Jun;38(6):683.

Abstract

The majority of cuticular protein sequences identified to date from a diversity of arthropods have a conserved region known as the Rebers and Riddiford Consensus (R&R Consensus). This consensus region has been used to query the whole genome sequence of Drosophila melanogaster. One hundred one putative cuticular proteins have been annotated. Of these, 29 had been annotated previously, and for several their authenticity as cuticular proteins had been verified by protein sequence data from isolated cuticles or by localization of their transcripts in epidermis when cuticle synthesis was occurring. The original names have been retained, and the 72 newly annotated proteins have been given names beginning with Cpr followed by the chromosomal band in which the gene is located. Proteins with the R&R Consensus can be split into three groups RR-1, RR-2 and RR-3, with some correlation to the type or region of the cuticle in which they occur. Previous classification was manual and subjective. We now have developed a tool using profile hidden Markov models that allows more objective classification. We describe the development and verification of the validity of this tool that is available at the cuticleDB website http://bioinformatics2.biol.uoa.gr/cuticleDB/index.jsp.

PMID:
17628275
[PubMed - indexed for MEDLINE]

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