To provide a schematic graphical overview of DEAD-box sequence motif conservation, we performed a multiple sequence alignment for each motif and then used the WebLogo software to obtain a precise description of sequence similarity [37, 38] (Figure 1 – inset). Analysis of regions separating each pair

of consecutive motifs was consistent with the reported low sequence but high length conservation (Figure 1) [33, 34]. The DEAD-box family has an N-terminal length ranging from 2 to 233 amino acids and a C-terminal length from 29 to 507 amino acids, but lack any additional domain described in other DEAD-box proteins (Figure 1) [39]. In agreement with the analyses of Banroques [40], we found that almost 55% of Giardia AZD0530 putative DEAD-box helicases have an N-terminal length of 2-45 residues and a C-terminal length of 29-95 residues, whereas the size of the HCD containing the conserved motifs ranges between 331 and 403 residues in almost 70% of

this family sequences. Figure 1 Schematic diagram of the DEAD-box RNA helicase family in G. lamblia . Each motif is represented by a different color. The distances between the motifs, and the size of the N- and C- terminal extensions for each ORF, are indicated (number of aa). The AZD2281 mw red bars within the N- or C-terminal extensions represent the regions amplified with specific primers for the qPCR. The representation is to scale. Inset: sequence LOGO view of the consensus amino acids. The height of each amino acid represents the degree of conservation. Colors mark properties of the amino acids as follows: green (polar), blue (basic), red

(acidic) and black (hydrophobic). The DEAH-box family The 6 putative RNA helicases belonging to the DEAH-box family were analyzed by multiple sequence alignment and subsequent manual scanning, in search of conserved motifs characteristic of this family. As shown in Additional file 6: Figure S3, the 5 helicases present the eight characteristic motifs, with the exception of Clomifene GL50803_13200, which was incomplete in its N-terminal region, missing Motif I. As with the missing motif of DEAD-box helicase GL50803_34684, a new database search showed a homologous gene, GL50581_4549 from the isolate GS, with the complete N-terminal region that was used to search the isolate WB for the entire ORF. Surprisingly, this new putative 5´ DNA genomic region does not have a traditional ATG start codon; instead, there are two putative alternative initiation codons already described in rare cases for the fungus Candida albicans[41] or in mammalian NAT1 [42]. Studies in progress are analyzing this finding. The consensus sequence was obtained and was in agreement with the DEAH-box motifs published by Linder and Owttrim [43] (Figure 2 – inset).