Figure 3

Transmembrane topology of some selected CIR proteins. To examine the predicted transmembrane topology of selected CIR Proteins two different analyses tools were used. With the Protscale analysis, hydrophobicity plots were created according Kyte & Doolite [45]. With the TMHMMM 2.0 server [47], probabilities of predicted transmembrane topologies were calculated. For three different CIR proteins (A-C) the results of the Protscale and TMHMM 2.0 were here compiled in one graph. On the x-axis the amino acid positions are given whereas on the left y-axis the hydrophobicity scores and on the right y-axes the probabilities for extracellular, intracellular and transmembrane localization are shown, respectively. The CIR proteins PCHAS_060060 of subfamily 1 (A) and PCHAS_000320 of subfamily 2 (B) were analysed as well as one of the unassigned CIR protein (PCHAS_010040) (C). For the first two proteins, only one transmembrane helix was predicted with more than 99% probability immediately close to the COOH-terminus of the CIR-BIR-YIR conserved domain, whereas the long NH₂-termininal part was assumed to be located outside. For the longer unassigned CIR protein, an additional second helix was located behind the CIR-BIR-YIR conserved domain close to the COOH-terminus in this CIR. The large NH₂-terminus as well as less than 10 amino acids of the COOH-terminus were predicted to be outside. The individual curves were highlighted by different colours (see graphic legend). Additionally, schematic presentations of the transmembrane topologies of subfamily 1 and 2 CIR proteins are schematically shown in (D) while topology of a CIR protein with two predicted transmembrane helices is given in (E).