Fig. 2: Sequence analysis of BPSL1038, CRISPR-associated Cas2 proteins and VapD protein.

a Multiple sequence alignment of BPSL1038 with CRISPR-associated Cas2 proteins and VapD protein from archaea and bacteria that share high structural similarity but low sequence identity (10-15%). The D¹¹'(X20)SST motif of BPSL1038 is indicated with stars in red. The proteins are named using the format Organism abbreviation_Cas2-UniProtKB ID-PDB ID. Afu: Archaeoglobus fulgidus, Bha: Bacillus halodurans, Dvu: Desulfovibrio vulgaris, Eco: Escherichia coli, Hpy: Helicobacter pylori, Lin: Leptospira interrogans, Mth: Methanothermobacter thermautotrophicus, Pfu: Pyrococcus furiosus, Spy: Streptococcus pyogenes, Sso: Saccharolobus solfataricus, Tma: Thermotoga maritima, Ton: Thermococcus onnurineus, Tth: Thermus thermophilus, Xal: Xanthomonas albilineans. VapD is VapD protein. The multiple sequence alignment was performed using CLUSTAL W⁵⁹ and the secondary structure was incorporated with ESPript 3.0. b The multiple sequence alignment results were used to obtain the phylogenetic relationship of BPSL1038 with CRISPR-associated Cas2 proteins and VapD protein using Neighbor-Joining⁶⁰ within MEGA7⁶¹. The optimal tree with the sum of branch length 24.97425156 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches⁶². The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method⁶³ and are in the units of the number of amino acid substitutions per site. The analysis involved 15 amino acid sequences. All ambiguous positions were removed for each sequence pair. c Structure comparison of BPSL1038 and Cas2 homologs from four types of CRISPR-Cas systems. All the protomers are shown with cyan helices and magenta β-strands. All the homologs were superimposed on BPSL1038 and are shown in similar orientation. Helicobacter pylori 26695 VapD (PDB ID: 3IU3), Sso_Cas2: Saccharolobus solfataricus P2 Cas2 (PDB ID: 2I8E), Eco_Cas2: Escherichia coli K-12 Cas2 (PDB ID:5DQT), Bha_Cas2: Bacillus halodurans C-125 Cas2 (PDB ID: 4ES1), Spy_Cas2: Streptococcus pyogenes serotype M1 Cas2 (PDB ID: 4QR2), Xal_Cas2: Xanthomonas albilineans GPE PC73 Cas2 (PDB ID:5H1P), Dvu_Cas2: Desulfovibrio vulgaris str. Hildenborough Cas2 (PDB ID: 3OQ2), Efa_Cas2: Enterococcus faecalis TX0027 (PDB ID: 5XVN), Tth_Cas2: Thermus thermophilus (PDB id: 1ZPW), Pfu_Cas2: Pyrococcus furiosus DSM 3638 Cas2 (PDB Id: 4TNO) and Ton_Cas2: Thermococcus Onnurineus Cas2 (PDB ID: 5G4D).