HNH and VSR endonuclease domains are found in terrestrial and marine nematode pPolB2s, respectively, but not in pPolB1. a) Aligned, nonaligned, and gap parts of pPolB1 and pPolB2 (middle panel) from sequence-free structural alignment are shown with pLDDT (predicted local distance difference test) score predicted at the single amino acid level by AlphaFold2. Overall aligned parts for both pPolB1 and pPolB2 showed high pLDDT score, suggesting confident prediction of the structures. b) The predicted structure of C. briggsae pPolB2 (green) with the HNH endonuclease domain (red). c to e) The predicted structure of pPolB2-specific HNH domain (c) and the crystal structure of P. alcaligenes PacI HNH endonuclease (d) (PDBid: 3M7K) (Shen et al. 2010) are superimposed e) (RMSD: 3.03, TM-score: 0.55) to show potentially conserved structural folds. f) Aligned and non-aligned parts of C. briggsae pPolB2 and T. latispiculum pPolB2 (middle panel) from sequence-free structural alignment are shown with pLDDT score. g) The predicted of T. latispiculum pPolB2 (cyan) with the VSR domain (yellow). h to j) The predicted structure of T. latispiculum pPolB2 VSR endonuclease domain (h) and the crystal structure of Escherichia coli VSR endonuclease (i) (PDBid: 1VSR) (Tsutakawa et al. 1999) are superimposed (j) (RMSD: 3.06, TM-score: 0.63) to show potentially conserved structural folds. Dark and light colors for both orange and blue (c to e and h to j) indicate aligned and nonaligned positions, respectively.