Supplementary sequence alignments
Sequence analysis of two plasmids from the phytoplasma beet leafhopper-transmitted virescence agent, by L. W. Liefting, M. E. Shaw and B. C. Kirkpatrick
Microbiology vol. 150, part 6, pp. 1809 - 1817
Multiple alignments of the deduced amino acid sequences of ORFs 1 and 5, ORFs 2, 6 and 7, and ORFs 3 and 8 (Fig. S1), ORF4 and ORF11 with homologous rep genes (Fig. S2), and ORF4 and ORF11 with homologous rep genes (Fig. S3). Gaps (-) were used to maximize the alignment, and shading indicates identical (black) or similar amino acids (grey).
Fig. S1. Alignment of the deduced amino acid sequences of (a) ORFs 1 and 5, (b) ORFs 2, 6 and 7, and (c) ORFs 3 and 8 from pBLTVA-1.
Fig. S2. Multiple alignment of the deduced amino acid sequences of ORF4 and ORF11 of pBLTVA-1 with homologous rep genes. The sequences included in the alignment were: TbLCYNV, tobacco leaf curl Yunnan virus (accession no. CAD54833); WmCSV, watermelon chlorotic stunt virus (accession no. CAB65506); pPNWB, plasmid from peanut witches'-broom phytoplasma (accession no. AAP44293); EcOYW1, plasmid from onion yellows phytoplasma (accession no. BAA36391). Motifs 1, 2 and 3 denote the conserved Rep protein motifs and the asterisk denotes the active Tyr residue identified by Ilyina & Koonin (1992).
Fig. S3. Multiple alignment of the deduced amino acid sequence of ORF9 of pBLTVA-1 with homologous dnaG genes. The sequences included in the alignment were: pPNWB, plasmid from peanut witches'-broom phytoplasma (accession no. AAP44294); Sa, Staphylococcus aureus (accession no. NP_646331); Hp, Helicobacter pylori (accession no. NP_222732). The Zn-finger (ZnF_CHCC) and topoisomerase/primase (TOPRIM) domains are indicated. The asterisks denote the Cys and His residues probably involved in Zn-finger formation (Ilyina et al., 1992). The conserved active site residues of the TOPRIM domain (Aravind et al. , 1998) are indicated by arrowheads.
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