(A) Alpha-helical protein model, (B) beta-sheet protein model, and (C) alpha-helical/beta-sheet protein model. The x-axis is the P_MCM; the y-axis the number of matches that are incorrect (black) and correct (red). The blue line is the ratio (correct/incorrect).

Red line represents the superfamily distribution for the predicted structures, P(SF|D); blue line, the superfamily distribution based on GO annotations, P(SF|GO). Black line represents the Bayesian combination (P(SF|D,GO); Equation 2). Only superfamilies with a probability over 0.001 in either category are displayed. The names of the proteins and the GO annotations for which the black line is derived are (A) 1KMDA (Vam7p Px Domain)/Golgi to vacuole transport (process), (B) 1IOUA (v-SNARE)/vesicle fusion (process), (C) 1F32 (Ascaris pepsin inhibitor-3)/endopeptidase inhibitor activity (function), and (D) 1DUJA (Spindle Assembly Checkpoint protein Human Mad2)/Chromosome (component).

(A) Alpha-helical proteins, (B) beta-sheet proteins, and (C) alpha-helical/beta-sheet proteins. The x-axis is P(SF|D,GO); the y-axis the number of matches with that score that are incorrect (black) and correct (red). The blue line is the ratio (correct/incorrect).

The predicted structure is shown in panel 1 (left), and the native structure or the structure of the homolog is shown in panel 2 (middle). The section matching the domain in the solved structure is colored red in panel 3 (right).
(A) TRS20/YBR254C is involved in the endoplasmic reticulum (ER) to Golgi transport and was predicted to belong to the SNARE-like (d.110.4) SCOP superfamily with a P(SF|D,GO) = 0.98 (P_MCM = 0.69). The Z-score between the predicted structure and the structure of a homolog with 33% sequence identity was 7.76.
(B) ECM15/YBL001C is involved in cell wall organization and biogenesis, and was predicted to belong to the MTH1187/YkoF-like (d.58.48) superfamily with P(SF|D,GO) = 0.87 (P_MCM = 0.82; MAMMOTH Z-score to native structure was 8.18).
(C) KAP104/YBR017C is involved in nuclear localization sequence binding and was predicted to belong to the ARM repeat (a.118.1) superfamily with P(SF|D,GO) = 0.99 (P_MCM = 0.8; MAMMOTH Z-score to homologous structure [31% sequence identity] was 4.41).
(D) FIS1/YIL065C was predicted to belong to the SCOP superfamily TPR-like (a.118.8) with a P_MCM of 0.98. The Mammoth Z-score between the predicted structure and the experimental structure was 13.34.

The predicted structure with the highest P(SF|D,GO) (left) is shown for (A) ROX3, (B) MED4, (C) GAL11, (D) TIF35, (E) MRPL37, (F) MRPL44, and (G) INH1 displayed next to the matching SCOP representative (right).