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cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution

Authors
Journal
Biology Direct
1745-6150
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Volume
3
Issue
1
Identifiers
DOI: 10.1186/1745-6150-3-21
Keywords
  • Discovery Notes
Disciplines
  • Biology

Abstract

ASCT: a new protein domain with patchy phylogenetic distribution shaped by horizontal gene transfer within and between prokary Supplementary Data to: cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution Marek Elias1* & Marian Novotny2 1Charles University in Prague, Faculty of Science, Department of Botany Benatska 2, 128 01 Prague 2, Czech Republic *Corresponding author 2Charles University in Prague, Faculty of Science, Department of Cell Biology Vinicna 7, 128 44 Prague 2, Czech Republic E-mail addresses: ME: [email protected] MN: [email protected] This file contains: Supplementary Methods Figure S1 Table S1 Corrected and newly assembled sequences of CPRas proteins 1. Supplementary Methods Sequences analysed in this study were identified by BLAST (Altschul et al., 1997) utilising sequence data from DDBJ/EMBL/GenBank (http://www.ncbi.nlm.nih.gov/), NCBI Trace Archive (http://www.ncbi.nlm.nih.gov/Traces/), Wellcome Trust Sanger Institute (http://www.sanger.ac.uk/), WUSTL Genome Sequencing Center (http://genome.wustl.edu/), DOE JGI (http://www.jgi.doe.gov/), and BCM HGSC (http://www.hgsc.bcm.tmc.edu/). Species with complete or high-coverage draft genome sequences that failed to reveal genes encoding a RAS-like circularly-permuted GTPase domain are listed in Table S1. Complete sequences of the CPRas proteins from Amphimedon queenslandica and Capsaspora owczarzaki were assembled from whole genome shotgun (WGS) reads available in Trace Archive (ftp://ftp.ncbi.nih.gov/pub/TraceDB/). The assemblies were generated with the aid of the CAP3 program (Huang and Madan, 1999; http://pbil.univ-lyon1.fr/cap3.php). Multiple alignments were constructed with the PROMALS web server (Pei et al., 2007; http://prodata.swmed.edu/promals/promals.php) and manually refined to account for the secondary structure of the closely related human HRAS structure (PDB accession number 1ZW6,

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