Bioinformatic Approaches to Identifying and Classifying Rab Proteins
The bioinformatic annotation of Rab GTPases is important, for example, to understand the evolution of the endomembrane system. However, Rabs are particularly challenging for standard annotation pipelines because they are similar to other small GTPases and form a large family with many paralogous subfamilies. Here, we describe a bioinformatic annotation pipeline specifically tailored to Rab GTPases. It proceeds in two steps: first, Rabs are distinguished from other proteins based on GTPase-specific motifs, overall sequence similarity to other Rabs, and the occurrence of Rab-specific motifs. Second, Rabs are classified taking either a more accurate but slower phylogenetic approach or a slightly less accurate but much faster bioinformatic approach. All necessary steps can either be performed locally or using the referenced online tools. An implementation of a slightly more involved version of the pipeline presented here is available at RabDB.org.
Key wordsBioinformatics RabF motifs RabSF regions Subfamily classification RabDB.org Evolution
We thank Mark Gouw for including the links to the sequence and motif files on the Rabifier website. This work was supported by a grant from Fundação para a Ciência e Tecnologia (PTDC/EBB-BIO/119006/2010)