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. 2008 Apr 9;8:57. doi: 10.1186/1471-2180-8-57

Figure 3.

Figure 3

Tuber RhoGDI and RhoGDI proteins from other organisms. A. Multiple alignment of RhoGDI proteins from T. borchii and representative species. Sequences were aligned with ClustalX and the output file was subsequently edited manually. Dashes indicate gaps introduced for optimal alignment. Residues identical or similar in at least four sequences are boxed in black or grey, respectively. Secondary structure elements are indicated on top of the aligned sequences and are based on the structure of human LyGDI [61]. Residues involved in the formation of the isoprenyl-binding pocket, as determined for bovine RhoGDI [32], are indicated by open or blue circles under the aligned sequences. Blue circles indicate residues of the "hydrophobic triad" critical for binding of the distal isoprene unit. Cyan circles indicate residues involved in the formation of an acidic patch in the isoprenyl-binding pocket. Important residues involved in interactions with the Rho GTPase are indicated by green boxes and are compiled for bovine RhoGDI [32] and human LyGDI [61]. B. Phylogenetic tree showing the relationship of TbRhoGDI with RhoGDI proteins of selected species from several eukaryotic phyla. Sequences were aligned using the ClustalX program with a BLOSUM62 matrix and default settings, followed by manual edition. Only the GDI core, devoid of hypervariable amino-terminal sequences, was considered. Phylogenetic trees were constructed using the neighbor-joining algorithms of the ClustalX program. Construction of the tree was done with TreeView. The position of TbRhoGDI is highlighted. Note grouping of TbRhoGDI with other fungi, in particular ascomycetes. The scale bar indicates 10% divergence. Accession numbers of the sequences retrieved for the phylogenetic analysis are as follows. T. borchii, EU044761. S. cerevisiae, Z74183. S. pombe, Z98533. C. neoformans, EAL19587. U. maydis, EAK86096. K. lactis, CAG98029. P. guillermondi, EDK38281. C. albicans, EAL04316. A. niger, CAK43261. G. zeae, XP_385458. H. sapiens RhoGDI1, X69550; RhoGDI2 (LyGDI), L20688; RhoGDI-3, U82532. M. musculus RhoGDI1, AU080000; RhoGDI2, U73198; RhoGDI3, Q62160. B. taurus RhoGDI1, X52689; RhoGDI2, AF182001. C. elegans, U36431. E. histolytica, AF080396. D. melanogaster, AE003515. A. japonica, C24513. B. malayi, AW159949. S. japonicum, AAW27341. H. roretzi, AV383364. I. punctatus, BE468333. N. tabacum, CAB77025. A. thaliana RhoGDI1, AAF70843; RhoGDI2, AAC17610; RhoGDI3, AAF21198. For S. scrofa, G. gallus, D. rerio, X. laevis, B. mori, G. max, Z. mays, T. aestivum, L. esculentum, L. pennellii and G. arboreum sequences were reconstructed from diverse EST sequences.