Fig. 4: Domain-level similarity search identifies conserved domain duplications.

A Domain-level similarities identified using a sliding window approach. The “SW Unique Hits” are the number of proteins that had a structurally similar query-target pair in the sliding window analysis that was absent from the full-length analysis. “Internal Duplications” are proteins where parts of the protein are similar to another part of itself. “Repetitive Acquisition” are proteins where a piece of a different protein matches the query protein multiple times at different positions. “Domain Addition” refers to proteins with multiple domains matching different proteins. Illustrative cartoons are shown above the corresponding bar. B HSV-1 UL15 is aligned to the known homolog HSV-2 UL15 and the structurally similar target HSV-1 UL9, which was only identified in the domain-level search. The part of HSV-1 UL15 that aligns with HSV-1 UL9 is colored blue. C The cluster of HCMV proteins that contain HCMV US22. The proteins that contain 2 domains, like the canonical US22, are shown in the HCMV color. The proteins with one domain are shown in light red, and the protein that has four domains is shown in dark red. D The tertiary structure of the core domain is similar between the proteins in this group. The top row is the full-length protein, the bottom row is a structural alignment of the core domain, and the RMSD against the 91 Cα of the core domain alignment is written below. HCMV US22 has two domains, shown in yellow and blue, which are aligned. HCMV UL29 has four domains and was aligned to US22. HCMV US22 was aligned to HCMV US23, which has two domains, and HCMV US23 was aligned to HCMV UL26, which has one domain. In the case of multiple domains, the best-fitting domain combination is shown. The corresponding UCSF ChimeraX sessions can be found at https://zenodo.org/records/13284140.