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. 2014 Apr 5;11:66. doi: 10.1186/1743-422X-11-66

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Copyright © 2014 Silva et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Alignment of the common regions and the Rep proteins of ToSRV-[BR:PG1:Pep:03] and ToRMV-[BR:Ub1:96]. A. Common region alignment. The TATA box, G-box and the conserved nonanucleotide are indicated in light gray. Iterated direct and inverted repeats (iterons) are boxed. The arrows indicate the direction of the repeats. Asterisks indicate nucleotide positions which are conserved among all four aligned sequences. Arrowheads indicate differences in nucleotide sequence among the four CRs. B. Rep protein alignment. Dark gray boxes correspond to the domain associated with sequence-specific recognition of iterons (iteron-related domain, IRD), motif 1, motif 2 and specificity determinants (SPDs), which according to [15] and [37] are conserved in rolling-circle replication-initiator proteins, including geminivirus Rep proteins.