BMC Genomics 2006, 7:282 http://www.biomedcentral.com/1471-2164/7/282 1 #RT_domains ---------- ---------- ---------- ---------- ---------- ---------- ---------- ------EXVX #PF13_0080 NNNNINNNNN NNNNNNINNN NNNKCKLSNS KRYNIRNNNN NKKAKNNEKN NIDDSNLEKK KKKIYIYKIK NIIEKRNFML #PFE1555c IQDNISRENN ISWKEEEYFD DKEELHHKEQ TTYSEKNQKS CLNSDNEEML SHINQNNITY KNNLELYNKK YTNDKKNKKD : 1 2 #RT_domains XXXXXQKFAP GKLRL--IPK KNXTFRPIMT FX-------- ---------- ---------- --------RK DKXQXKLXXX #PF13_0080 KLNSINHFIS KKLRINWIPK KK-GLRPLIN LSTLNVPEIV KQRIFEILKS KKSSEFYFHN ILNNLEREKK DKNIK.RKKY #PFE1555c IKKIVSYIRI KHVKNHNIIK EFNYLSIKIN KYNLFKHLDI KEERLNYITS IYHSFDYYNK RIKKKDQEKI NKINDLVYQY . : ::: : : :. : : 2 A #RT_domains X--------- --LXNXXLQX EX-------- ---------- ---------- --PKLYFVKX ---------- ---------- #PF13_0080 NKKNFNPVSL NNICNFSLKC LGNMRHNNNS LFKNTLTKTG EIELKLKKWL HYLKNWFYKK KRMKKYIKNK LKNNKKIYAY #PFE1555c SNETKN---K TNIDNYKKKF EENLLNIINY NRQQEEHEQN EEEYNLYSCE SNTNINNNEF IGKNKKYNNS NNNSNNNNRN : : : : A #RT_domains ----DVKKCY DSXX------ ---------- ------QXEL LRXLKXXXX- ---------- ---XKQYXQK X--------- #PF13_0080 ICIGDFSNCY EHIN------ ---------- ------HNYL FKILKNFFDN INNFEFIYLF KRSFRLYNKN LNNSFLSYYP #PFE1555c SSIPKYHRCS NNIKDNMQNE LSGDKSYNVN SENSQKENIL LSNENDKEKY VEEDLSYNDK DKFVNIKDDI KNIIPYNDYN . . : . : : . . B’ #RT_domains ---------- ---------- ---------- ---------- ---------- ------GIPQ GXXLSSILCS FYYXDLEEXX #PF13_0080 ……260 amino acids………. IIKYHKTIDT DNSKNHTYFK NKFLNFLDKK IISNIYGLPQ GFSLSNILCS LYYAYLDKNE #PFE1555c ……260 amino acids…….. HYEKKDPIKP HFVKDQNEYM INNKNLNNNQ NIYNFEKIHE INNISNQESI IHTSEKSQVQ .: : : . . :: .: C D #RT_domains ---------- ---------- -------LQF LLXRXVDDXL XIXTSXNNAX XFIELLXXXS LX-------- ---------- #PF13_0080 EFQNLLYSEK QINNKYFLAN GTCNYFNLNS LILRFIDDFL FITLNKKNIK IFKNLLLKKK IWGSNINSSK TKIFKIPLIY #PFE1555c NTNELMEHQS DHMRKQKWSI YCKEMFSLFF EFNSSFDEHF KDNYEMHIDN IINNIKNIKD MIPMSFINFI IHYNSLYQIN : . : : . : : :: . : FMiuglutirpele2sequence alignment of conserved RT domains and two potential RT-encoding genes in P. falciparum Multiple sequence alignment of conserved RT domains and two potential RT-encoding genes in P. falciparum. #RT_domains is the RT consensus sequence developed in this study. It includes the fingers (1 and 2) and palm (A, B', C and D) domains. #PF13_0080 is the putative PfTERT identified by Figueiredo et al, 2005 [12]. #PFE1555c is a hypothetical protein with similarity to the RT consensus sequence developed in this study. The alignment was performed using ClustalW with default parameters. Residues shaded in yellow have been demonstrated to be in contact with nucleic acid [29]; residues shaded in red are critical for RT activity [30]. * residues common to all threesequences. : conserved residues. . semi-conserved residues Whole genome analytical methods The InterPro entries for TERT failed to detect the two TERT orthologues in P. falciparum and P. y. yoelii, probably due to the stringency of the HMM search. This highlights the pitfalls of using generic bioinformatic programmes for studying a genome as exceptional as that of Plasmodium. The problems associated with using bioinformatic meth- ods to compare divergent sequences have been discussed before [19]. It must be stressed therefore that the findings presented here cannot be extrapolated further than the limits of the methods used. In particular, MGE detection in compositionally biased genomes may be affected by the lack of sensitivity of the scanning techniques employed. It is also possible that not all MGEs have been described to date and therefore not detected in this com- parative study. We did, however, refine the genome min- ing process in two ways. Firstly, we employed biological data (crystal structure and point mutation data for RT sequences) to generate a consensus RT sequence to expand the scanning process. This increased the sensitivity and detected the P. y. yoelii and P. falciparum TERTs and the PFE1555c ORF discussed above. Secondly, less strin- gent statistics were used in the scanning process. While it is more common to use E values of 10-5, we used values of Page 5 of 10 (page number not for citation purposes)