Fig. 3

Comparison of T. pallidum primary and tertiary structure annotations. Predicted functions of 605 T. pallidum proteins derived from tertiary structure models with high confidence were compared with functional annotations from genome sequencing. a Distribution of T. pallidum proteins modeled by Phyre2 (≥ 90% confidence, ≥10% alignment coverage) predicted to have the same, related (same PDB functional group classification and/or related PDB molecule/template function), or different functions (including unknown functions) compared to the published T. pallidum (Nichols) genome annotations. This analysis only used the top-ranking tertiary structure model protein template function. b Distribution of T. pallidum proteins as outlined above after genome annotated functions were compared to all confident (≥90% confidence, ≥10% coverage alignment) top 20-ranking templates used to model each protein. A functional match was assigned when the genome annotated function matched at least one protein tertiary structure model template function. c Distribution of T. pallidum proteins as outlined above according to their PDB functional classification using the top-ranking template only, or (d) using all confident tertiary structure model top 20-ranking templates for each protein function comparison. It should be noted that in (c) and (d), protein templates used to model a small number of T. pallidum proteins in the current study were categorized as “unknown function” by the PDB classification system. However, these proteins were ascribed functions in the current study based on their PDB molecule function annotation and/or PDB structure title which allowed for comparisons with their genomic protein annotations