Fig 1.
Statistics of ECOD assignments and distributions of sequence and structural similarity scores of well-assigned DPAM domains.
A. The distribution of ECOD architectures for well-assigned DPAM domains. B. The most frequently occurring X-groups in each ECOD architecture. Only X-groups with 15 or more occurrences are shown. C. The distribution of Best_Seq_Rel scores of well-assigned DPAM domains. Each bar consists of cases where the DALI score is less than 10 (blue) and cases where the DALI score is 10 or above (orange). D. The distribution of Dali scores of well-assigned domains. Each bar consists of cases where the Best_Seq_Rel score is less than 0.95 (blue) and cases where the Best_Seq_Rel score is 0.95 or above (orange).
Fig 2.
Comparison of overlap fractions of well-assigned DPAM domains and corresponding TED CNF domains.
432 domains are consistently defined domains with both DPAM overlap fraction and TED overlap fraction greater than 0.8 (bounded by red dashed lines). 888 domains have DPAM overlap fraction less than 0.6 and TED overlap fraction greater than 0.8 (bounded by magenta dashed lines), suggesting that TED CNF domains are embedded mainly in the ECOD domains. 202 domains have TED overlap fraction less than 0.6 and DPAM overlap fraction greater than 0.8 (bounded by orange dashed lines), suggesting that ECOD domains are primarily embedded in the TED CNF domains. The remaining 968 domains fall into intermediate cases where neither definition is largely embedded in the other, indicating partial overlaps or more complex boundary relationships between TED and DPAM.
Fig 3.
DPAM overlap fractions and TED overlap fractions for ECOD architectures that show predominance of TED CNF domains embedded in DPAM domains.
The names of the architectures are shown as the titles of the plots with the number of domains in parentheses. Consistently defined domains are those with DPAM overlap fraction and TED overlap fraction greater than 0.8 (top right corner bounded by red dashed lines, with the number of domains shown in red). TED CNF domains largely embedded in DPAM domains have a DPAM overlap fraction less than 0.6 and a TED overlap fraction greater than 0.8 (bottom right corner bounded by magenta dashed lines, with the number of domains shown in magenta). DPAM domains largely embedded in TED CNF domains have TED overlap fraction less than 0.6 and DPAM overlap fraction greater than 0.8 (top left corner bounded by orange dashed lines, with the number of domains shown in orange). The numbers of domains not in the color-bounded regions are shown in black.
Fig 4.
Examples of TED CNF domains largely embedded in DPAM domains.
In each example, the right structure depicts the TED CNF domain in rainbow colors, with the remaining regions shown in gray. Note that these gray regions in the right structures may include TED domains that are not classified as CNF domains. The left structure shows the DPAM domain (overlapping with the TED CNF domain) in rainbow colors, with non-DPAM regions shown in gray. The UniProt accession number, the ECOD X-group and the ECOD architecture are shown for each domain. Details on the residue ranges of DPAM domains and TED CNF domains, along with the ECOD assignments and best-matching templates, are available at: http://conglab.swmed.edu/ted_web/dpam90.html.
Fig 5.
DPAM overlap fractions and TED overlap fractions for ECOD architectures that have a relatively large fraction of consistently assigned domains.
The names of the architectures are shown as the titles of the plots with the number of domains in parentheses. Consistently defined domains are those with DPAM overlap fraction and TED overlap fraction greater than 0.8 (top right corner bounded by red dashed lines, with the number of domains shown in red). TED CNF domains largely embedded in DPAM domains have a DPAM overlap fraction less than 0.6 and a TED overlap fraction greater than 0.8 (bottom right corner bounded by magenta dashed lines, with the number of domains shown in magenta). DPAM domains largely embedded in TED CNF domains have TED overlap fraction less than 0.6 and DPAM overlap fraction greater than 0.8 (top left corner bounded by orange dashed lines, with the number of domains shown in orange). The numbers of domains not in the color-bounded regions are shown in black.
Fig 6.
Examples of consistently assigned TED and DPAM domains.
In each instance, the left structure is the ECOD domain template with the best DPAM probability score (with ECOD ID shown below), the middle structure shows DPAM domain-defined regions colored in rainbow; the right structure shows the TED CNF domain colored in rainbow. Regions not defined by DPAM or TED are colored gray. The UniProt accession number, the ECOD X-group and the ECOD architecture are shown for each domain.
Fig 7.
Examples of DPAM domains largely embedded in TED CNF domains.
In each example, the left structure is the ECOD domain template with the best DPAM probability score, with ECOD id shown below the structure. The middle structure shows two DPAM domains colored orange and blue. The ECOD assignment is for the orange DPAM domain. For panels A and B, the blue DPAM domain has the same X-group assignment as the orange DPAM domain. For panel C, the blue DPAM domain is unassigned (DPAM confidence score less than 0.9). The right structure shows the TED CNF domain colored in rainbow. Regions not defined by DPAM or TED are colored gray. The UniProt accession number, the assigned ECOD X-group and the ECOD architecture are shown for each orange DPAM domain.