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Comparative and Functional Genomics
Volume 5, Issue 1, Pages 2-16
Primary research paper

Identification and Analysis of Novel Tandem Repeats in the Cell Surface Proteins of Archaeal and Bacterial Genomes Using Computational Tools

1School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
2Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India

Received 30 May 2003; Revised 21 October 2003; Accepted 23 October 2003

Copyright © 2004 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


We have identified four novel repeats and two domains in cell surface proteins encoded by the Methanosarcina acetivorans genome and in some archaeal and bacterial genomes. The repeats correspond to a certain number of amino acid residues present in tandem in a protein sequence and each repeat is characterized by conserved sequence motifs. These correspond to: (a) a 42 amino acid (aa) residue RIVW repeat; (b) a 45 aa residue LGxL repeat; (c) a 42 aa residue LVIVD repeat; and (d) a 54 aa residue LGFP repeat. The domains correspond to a certain number of aa residues in a protein sequence that do not comprise internal repeats. These correspond to: (a) a 200 aa residue DNRLRE domain; and (b) a 70 aa residue PEGA domain. We discuss the occurrence of these repeats and domains in the different proteins and genomes analysed in this work.