## 4 Results I: MIP and LacI families
### The MIP family  
Members of the MIP family assist the transport of both water and small neutral solutes through the cellular membrane. There are about six MIP subfamilies, the two major being the aquaporins (AQP) and the glycerol-uptake facilitators (GLP). Here, we ask SDPhound to identify SDPs responsible for the distinction between these two large subfamilies and then compare our results to those presented in the [PERSON] _et al._ paper. The alignment used as input for the different runs is the same as in references [2; 20], where all the necessary details on the nature of the set, containing 60 members of the family, can be found. In table 1 we compare the ranking of putative specificity determining positions obtained using SDPhound. Columns 1-4 report the outcome of successive runs performed using the different substitution matrices described in section 3.2.: BLOSUM45 (B45), BLOSUM62 (B62), the identity (Id), and the \"local\" \begin{table}
\begin{tabular}{l r r r r r r r r r} \hline  & B45 & S & B62 & S & Id & S & Bloc & S & SDPpred & S \\  & 21 & & 21 & & 22 & & 24 & & 24 & \\ \hline  
\hline \end{tabular}
\end{table} 
Table 1: SDPs inferred from 60 members of the MIP family. The Table shows the 24 best ranking SDPs responsible for the distinction between aquaporins and the glycerol-uptake facilitators within MIPs. (*) indicate a significant position according to the measure for functional significance used by [PERSON] _et al._[2] (see text for details). The corresponding positions are also colored in red to facilitate the table reading. Results from BLOSUM45 (B45), BLOSUM62 (B62), Identity (Id) and the local BLOSUM (Bloc) substitution matrices are also reported for comparison. Residue numbering refers to GlpF protein from _E. Coli._ In the second row the number of positions reckoned to be significant by the various runs are indicated. BLOSUM matrix (Bloc). The last column reports the results provided by the SDPpred web server. The asterisk in the column marked S in the table indicates a position identified as significant according to the criterion established in [2] to assess the performance of SDPpred, i.e. proximity to the glycerol molecules bound inside the pore channel in the crystal structure 1 FX8 (see reference for details). The second row of the table heading indicates the number of statistically significant positions in the ranking based on the Z-score criterion illustrated in section 3.5. (columns 1-4), and by the analogous indicator in the SDPpred scheme (column 5). As it can be seen from the table, both the identity matrix based run of SDPhound and SDPpred identify 8 significant positions. The performance of the SDPBound runs that use the alternative substitution matrices is very similar, and it is in fact difficult to assess if there is a difference given the limited statistics available. Table (2) presents the ranking produced by SDPbound when the mutual information used in the ranking is constructed using the probability defined in eq (13). The method points blindly - i.e. not guided by the researcher's insight into the problem - to a set of positions. Based on the ranking, an _a posteriori_ analysis can be performed to evaluate the characteristics of the isolated positions. Among the higher ranking positions, 48 is singled out. The relevance of this site on the functioning of the pore selectivity of the transported molecule has already been remarked experimentally [22, 23]. The residue at this position is part of the bottleneck of the transport channel. In GLPs, the pore cavity is almost exclusively constituted by hydrophobic and few positively charged residues, but in AQPs it is also constituted by some polar ones; in either case, the pore has a slightly different location through the protein. Pigeonholing suggests SDP 48 is important by way of its charge/polarity, while its dimension also has a minor influence.