Sequence alignment of the RepBRA3 and homologous replication initiation proteins. Conserved residues in replication initiation proteins from RA3 (ABD64829), Rms149 (YP_245484), pRSB105 (ABI20460), pAb5S9 (YP_001220601), pMATVIM-7 (YP_001427363), pKBB4037 (CAI47016), and Plasmid2 (YP_743798) (GenBank/EMBL database protein accession numbers are given in parentheses) are shown by a black background. Residues identical or functionally similar in five polypeptides are marked with a dark grey background, and residues conserved in four representatives are shown with a light grey background. The predicted HTH motif in the RepB polypeptide of RA3 is indicated.