Figure 3.

Multidimensional scaling analysis and distance analysis of EamA-derived nucleotide sugar transporters, first and second domains. Figure 3A: Two-dimensional representation of the similarity relationships between the domains of the nucleotide sugar transporter DMT families with human members, as obtained by non-metric multidimensional scaling. First domains are represented by red circles, second domains by blue triangles. The MDS fit measures (s-stress = 0.08, RSQ = 0.97) indicate that the inter-domain distances in this configuration reflect well the original inter-domain similarity values. Figure 3B: HHsearch all-against-all clustering is done, using a 99.05% probability cutoff, because this was the highest cutoff we could use and still retain a connected graph. The results are organized as a pivot table in Open Office 3 and viewed as a graph in Cytoscape (v2.6.3). The graph is arranged manually to achieve maximum separation between first and second domains, and to achieve no overlapping edges (planarity). The HHsearch values quoted between two DMT domains may fluctuate slightly depending on which domain is used as query; if so, the number presented is the average result.

Västermark et al. BMC Evolutionary Biology 2011 11:123   doi:10.1186/1471-2148-11-123
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