Extended Data Fig. 2: Vms1 is the founding member of the VLRF1 clade. | Nature

Extended Data Fig. 2: Vms1 is the founding member of the VLRF1 clade.

From: Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes

Extended Data Fig. 2

a, Extended sequence alignment of aeRF1 superfamily with representatives from all families and clades (compared to the limited subset shown in Fig. 2a). b, Phylogenetic tree depicting relationships within the aeRF1 superfamily; colouring matches clade labels in Fig. 2a. In the classical aeRF1 clade, two branches contain eukaryotic orthologues (eRF1) and archaeal orthologues (aRF1), respectively. Of the bacterial (baeRF1) versions, certain members are misannotated as ‘Host_attach’ in the Pfam database while most cannot be detected by existing profiles. The total number of prokaryotic representatives of the VLRF1 clade in the non-redundant database (NCBI, as of 1 December 2017) is 1,044. Of these, the archaeal VLRF1 family (aVLRF1) has 279 members, actino-chloroflexi VLRF1 family (acVLRF1) has 669 and the bacteroidetes VLRF1 family (bVLRF1) has 96. Notable domain architectures and conserved gene neighbourhoods are shown to the right of tree. A gene encoding a ribosome hibernation factor (HPF-like or YfiA-like) that facilitates inactive ribosome aggregation frequently co-occurs and is predicted to function with the baeRF1 domains. The labels below the architecture diagrams list the well-characterized clade representatives, PDB structure accessions and phyletic distributions. The dashed outline indicates domains that are not universally present.