Comparison of the HCA plots of TFIIA large subunit (TOA1/TFIIA α/β panel A) and small subunit (TOA2/TFIIA γ panel B) subunits from different species, highlighting the conservation of the hydrophobic core of the domains constituting the two proteins in the hypothetical proteins from Plasmodium falciparum. The sequences are shown on a duplicated α-helical net, in which strong hydrophobic amino acids (VILFMYW) are circled. These form clusters, which mainly correspond to the internal faces of regular secondary structures (α-helices and β-strands). The way to read the sequence and special symbols is indicated in the inset. The regions initially detected by PSI-BLAST (either with significant (TOA1/TFIIA α) or marginal E-value (TOA2/TFIIA γ) are indicated with a dotted line. Cluster similarities are shaded in grey, identities are shown in white on a black background. Despite low level of sequence identity, hydrophobic clusters are well conserved, supporting the presence of a common fold. The deduced 1D alignment is shown at the bottom and at right. The positions of regular secondary structures, as observed from experimental data (pdb 1nh2) are shown up to the HCA plot. Two hypothetical proteins from Plasmodium falciparum share significant similarities with the small subunit of TFIIA (bottom panel) and are thus PfTFIIA small subunit candidates. The similarity with PFI1630c was revealed using its homolog sequence in Plasmodium yoelii (see text). This sequence was missed during our first PSI-BLAST search because of an error in the intron prediction. This novel ortholog has been found through HCA sequence comparison of the translated DNA sequences (the boxed and underlined sequences in the HCA plot and 1D alignment, respectively, correspond to the sequence which was first included in an intron, as predicted automatically from genome data).