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Figure 6 | BMC Evolutionary Biology

Figure 6

From: Phylogeny and evolution of Rab7 and Rab9 proteins

Figure 6

Alignment of consensus sequences for Rab9 and different subgroups of Rab7 proteins. Cap/Mon denotes Capsaspora/Monosiga. Highly conserved residues (with p ≥ 0.5) are shown in upper case and others are presented in lower case. Particular residues are shaded according to their levels of conservation in the alignment. Secondary structure consensuses for Rab7 and Rab9 proteins are shown below the alignment. Particular secondary structure elements are denoted by: H (α-helix), G (310-helix), E (extended β-sheet), B (β-bridge), S (bend), T (turn), – (nonregular states and loops). The symbols of secondary structure elements are shown in different typefaces according to their frequency in the compared structures and α-helices and β-strands are marked with colored boxes. Different motifs, sequence elements and structural features related to Rab proteins are highlighted: G1 to G3 (conserved motifs involved in guanine nucleotide binding); PM1 to PM3 (conserved motifs responsible for binding and coordination Mg2+ with phosphates groups); RabF1 to RabF5 (Rab family specific motifs); RabSF1 to RabSF4 (regions specific for particular subfamilies of Rab GTPases); switch I and II (flexible domains that substantially change their conformation upon exchange between GDP and GTP); hypervariable domain (HVD, unstructured region showing the highest level of sequence divergence among Rab proteins); PR (C-terminal prenylation motif); CDRI to CDRIII (complementary-determining regions); I to VII (seven regions showing substantial conformational variation among structures superimposed with Rab9 [53]). Some sites involved in interaction with regulators and effectors are pointed out above the alignment. Two key hydrophobic residues in the HVD region that make important contacts of Ypt1 with GDI [125] and Rab7 with REP1 [116] are marked with arrows. Other sites of Rab7 interacting with REP1 [116] are marked with *. Sites involved in the interaction of Rab7 with RILP are marked with # and # if their role was additionally confirmed by site-directed mutagenesis [119]. Another important site revealed by Harrison et al. [41] is marked with:.

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