Figure 3

Structural organization of the two identified full-length candidate surface proteins with cysteine rich segments. A: Domain organization of the putative protein encoded by Sp10orf2 (573 residues) [GenBank:DQ812527]. The diagram shows the position of the seven furin-like domains (SM00261 – orange boxes) relative the transmembrane domain (blue box) as determined by SMART4.0 [125]. Several variations were inferred by SMART including some where furin-like domains corresponded to the related EGF-like domain (SM00181 – green boxes, see below). Due to the overlap between these inferences only the furin-like domains are shown for simplicity. The orientation of the protein in the membrane is N-terminus outside and C-terminus inside as inferred by TMHMM2.0 [126]. This is consistent with the hypothesis that cysteine-rich domains are facing the extracellular milieu where they could interact with other proteins. The alignment of the seven inferred furin-like domains as inferred by T-COFFEE [127] is shown below the diagram, with the positions of the first and last residue of each domain indicated on the left. Cysteines are highlighted in red and bold. No putative signal peptide was found with SignalP3.0 [128]. B: Domain organization of the putative protein encoded by Sp1orf4 (453 residues) [GenBank:DQ812518]. This protein has a similar structural organization as the one shown in A with three EGF-like domains inferred to face the external milieu. The three EGF-like domains were aligned manually. In addition, this sequence may have a signal peptide (indicated by a red box) since the S-score is positive in SignalP3.0 [128]. C: Domain organization of G. lamblia VSP417-6 protein (704 residues) [GenBank:AAF02907] [129] is shown for comparison. Four furin-like and two EGF-like domains identified by SMART4.0 [125] were aligned with T-COFFEE [127]. The G. lamblia sequence possesses a signal peptide according to SignalP3.0 [128]. All diagrams are drawn to scale.