Figure 5.

Breadth-first clustering of first domain of 19 DMTs using HHsearch HMMs. This figure was prepared using HHsearch all-against-all comparison of first domain of DMTs, to establish closest neighbor of each DMT. The arrows indicate in relation to which family the neighbor is closest, and the HHsearch score is printed in red next to the arrow (giving the uni-directional HHsearch score when the query family is used). Bi-directional arrows indicate cases where there is a reciprocal nearest neighbor relationship; in such cases the HHsearch score represents the average of the two measurements. The gingerbread man icons indicate which families are present in H. sapiens. No arrows are drawn from Cation and Zip, because their nearest neighbors (DUF1632 and DUF486) are very distant: only 3.2 and 5.4% HHsearch probability. Using the Phobius (v1.04) prediction [30], the prevalent membrane orientation is indicated in the figure as the cytosol being in the upper direction of the figure, and the lower direction representing Golgi/endoplasmatic reticuluum/extracellular space. Three clusters are defined: EamA (purple; based on nearest neighbor principle), DUF1632 (green; based on membrane orientation), and metal transporters (turquoise; based on TM and substrate profile). The schematic figure of example structures were drawn using TMRPres2D [36] and InkScape vector graphics editor (v0.47): SLC35B3 (UAA); C1ORF91 (UPF0546); [WormBase:ZC250.3] (NST); SLC35C2 (TPT); SLC35C1 (EamA); SLC35F1 (DUF914); NIPAL1 (DUF803); BOTT52 (DUF486); [UniProt:Q13PK0] (UPF0060); [UniProt:Q7B1Y7] (MDR); [UniProt:Q55C66] (CRT-like); [UniProt:A4A8W4] (FAE 3-kCoA syn1); [UniProt:Q99VZ6] (DUF606); [UniProt:Q9CDF7] (Sugar tranport); [UniProt:Q93P85] (RhaT); TMEM144 (DUF1632); [UniProt:A3IRG4] (CRCB); SLC39A2 (ZIP); SLC30A1 (Cation efflux).

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