Figure 3

Contrast alignments showing distinguishing sequence features of Arf/Arl GTPases. This is the mcBPPS program output file corresponding to the Arf1-related subgroup (second row in Fig. 2); the sequences shown correspond to the seed alignment, which consists of Arf1 GTPases from distinct phyla. (A) Conserved residues distinguishing the TRAFAC subclass of P-loop GTPases from non-GTPases (column 3 in Fig. 2). (B) Conserved residues distinguishing Ras-like from other TRAFAC GTPases (column 6). (C) Conserved residues distinguishing Arf/Arl/Sar GTPases from other P-loop GTPases (except for Gα subunits)(column 12). (D) Conserved residues distinguishing typical Arf/Arl GTPases (i.e., excluding Arl6 and Arl8) from Sar and Gα GTPases (column 13). In each alignment, the Arf1 seed sequences are shown explicitly, whereas directly below these only the most conserved residue patterns in the foreground (relative to the background) are shown. Directly below this the corresponding weighted residue frequencies are shown (denoted by 'wt_res_freqs'). Weighted frequencies are given in integer tenths, where an '8', for example, indicates that the corresponding residue occurs in 80%-90% of the (foreground) sequences. Below this the conserved patterns and their weighted frequencies for the background sequences are shown (in gray). The selective constraints imposed on the foreground (relative to the background) at pattern positions are indicated by the histograms above each alignment.