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Identification and analysis of novel tandem repeats in the cell surface proteins of archaeal and bacterial genomes using computational tools.

ABSTRACT: 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.

SUBMITTER: Adindla S

PROVIDER: S-EPMC2447325 | biostudies-other | 2004

REPOSITORIES: biostudies-other

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Identification and analysis of novel tandem repeats in the cell surface proteins of archaeal and bacterial genomes using computational tools.

Adindla S S Inampudi K K KK Guruprasad K K Guruprasad L L

Comparative and functional genomics 20040101 1

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 L ...[more]

PMID: 18629042

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