BMC Genomics 2006, 7:282 http://www.biomedcentral.com/1471-2164/7/282 HMM for group II introns There were no hits identified in the P. falciparum organel- lar genomes (ORFs>50 amino acids) in PlasmoDB with E values less than 100 that demonstrated significant similar- ity to either of the two group II intron HMMs. Where sig- nificant similarity did arise, this was due to upstream exons being fused to the mitochondrial group II introns used in generating the HMM, e.g. PFB0795w is the Plasmo- dium gene orthologue of the ATP synthase gene and corre- sponds to a fused exon located upstream of several mitochondrial group II introns. Reverse transcriptase domain The WashU-BLASTP 2.0 search of PlasmoDB using the RT consensus sequence developed in this study, detected two P. y. yoelii (PY00479 and PY03683) and four P. falciparum (PF13_0080, PFC0960c, PFE1555c and PFC0165w) ORFs with similar E values (less than 10). Of the two P. y. yoelii genes, PY00479, which is annotated as a putative telomer- ase reverse transcriptase in PlasmoDB, was not detected by the InterPro TERT HMM. PY03683 is a hypothetical pro- tein of 48 amino acids, making it too short for any mean- ingful comparison, and was not investigated further. Of the four P. falciparum genes only PF13_0080 and PFE1555c appear to have significant non-random homol- ogy in the most conserved residues, despite the E values of all four being similar. PF13_0080 is annotated as a puta- tive telomerase reverse transcriptase in PlasmoDB and bioinformatic evidence for this has already been pub- lished [11,12]. PFE1555c is a hypothetical protein. An alignment of the RT consensus sequence generated in this study with these two genes is demonstrated in Figure 2. Some of the highly conserved residues, as well as some residues shown to be essential for RT activity, are present in both sequences. The RT consensus sequence was also used to probe the P. vivax genome available from TIGR [18]. A WashU-BLASTP (E value = 1, Blosum35 matrix) search revealed one hit that demonstrated significant similarity to the RT domain, including many of the highly conserved residues. This ORF (Pv122530) exhibits significant sequence similarity to the putative TERTs in P. falciparum and P. y. yoelii. Fig- ure 3 is an alignment of these two sequences with the putative P. vivax TERT (PvTERT) which is reported here for the first time. An orthologue of the PFE1555c gene, Pv079710, was identified by a simple BLASTP search of the P. vivax genome. MGE domains in the P. vivax genome Ten P. vivax ORFs were identified by a BLASTP homology search as orthologues of the P. y. yoelii and P. falciparum genes located in InterPro (without a corresponding match in Pfam). HMMER searches of the P. vivax genome using Pfam_fs HMMs identified 28 ORFs containing MGE domains. In total therefore, 40 P. vivax ORFs containing MGE domains were identified and these are listed in Table 2. Discussion We report here the presence of MGE signature domains in potential protein coding sequences of three Plasmodium species: six in P. falciparum, eight in P. y. yoelii and 40 in P. vivax. In each species there are three potential domesti- cated derivatives of MGEs. They are meiotic recombinase, DNA repair protein rad51 and TERT. Although these three proteins are common to all eukaryotes and are no longer active MGEs, they have clearly defined MGE domains and are included for completeness. Recently, identification of the putative TERT genes in P. falciparum and P. y. yoelii has been of interest and bioinformatic evidence of this has been published [11,12]. We have identified a candidate for the TERT orthologue (PvTERT) in P. vivax using the conserved RT sequence developed in this study (Figure 3). We cannot discount that other, as yet uncharacterized, domesticated derivatives may be among the ORFs detected. Of the remaining ORFs identified, only three are present in P. falciparum. One is homologous to the catalytic domain of a phage integrase, a second to an intron- encoded nuclease and a third to a reverse transcriptase. Although the latter does not contain all the highly con- served residues, there is significant homology to the RT consensus sequence used in this study and warrants fur- ther investigation (see Figure 2). The highly conserved "DD" motif, located in domain C, aligns with a "DE" res- idue pair in PFE1555c. While almost all RT sequences have been found to contain the "DD" motif, some non- LTR retrotransposons used in InterPro to generate the RT HMM (IPR000477) have a glutamic acid (E) substitution for aspartic acid (D). There were seven ORFs identified in P. y. yoelii with simi- larity to signature domains of MGEs: two transposases, two phage integrases, one intron-encoded nuclease and two domesticated derivatives. One of the ORFs with simi- larity to a phage integrase domain was a putative yir3 pro- tein (PY05943). The yir family in P. y. yoelii is analogous to the rif, stevor and var superfamilies in P. falciparum where recombination events play an important role in antigen switching. Analysis of the P. vivax genome yielded a relatively large number of RT domains, 23 in total. The reasons for this are not clear and require further investiga- tion. Page 4 of 10 (page number not for citation purposes)