Additional file 11: Figure S7. of Sequence-based prediction of permissive stretches for internal protein tagging and knockdown

PSS-identified permissive stretches are enriched to be surface accessible. Each plot summarizes the predicted surface accessibility and the predicted secondary structure of each residue for all test proteins (upper panel within each plot) as well as relative surface accessibility and secondary structure calculated from available crystal structures by the DSSP algorithm (lower panel within each plot). (a) Adk, (b) Bla, (c) TpiA, (f) AtpA, (g) AtpD, and (h) GpsA. PSs are highlighted in grey. The RSA of a site is defined as the geometric mean of the RSAs of its flanking residues, while the RSA of a predicted stretch is defined as the maximum site RSA in the stretch. RSAs of stretches derived from predictions and crystal structures are summarised in Additional file 10: Table S4. For illustration, identified permissive stretches were mapped onto the surface representation of the crystal structures of TEM1 β-lactamase (PDB 1AXB) (d), TpiA (shown as dimer, PDB 1TRE) (e), and the F1 part of ATP synthase (PDB 3OAA) (i). α-subunits (AtpA) are shown in light green, β-subunits are shown in dark green, and the γ-subunit is shown in yellow. PSs are marked in grey. For permissive site numbering refer to Additional file 3: Figure S1; Additional file 4: Figure S2, and Additional file 9: Figure S6. For TpiA and Bla, two different orientations are displayed to capture all PSs. Note that PSVIII within TpiA is not surface exposed and therefore not visible. PSI and PSVII within AtpA are not resolved in the crystal structure and therefore not given. (ZIP 13 kb)