Figure 4

Structure based sequence alignment of SH3-fold and OB-fold proteins. The alignment was generated by COMPARER [30] server (http://www-cryst.bioc.cam.ac.uk/~robert/cpgs/COMPARER/comparer.html). The proteins were shown with their PDB code. Single letter code for amino acids was used. The proteins aligned for SH3-fold were 1shg: SH3 domain of chicken brain spectrin; 1ihv: the DNA-binding domain of HIV-intergrase; 1d0z: myosin S1 motor domain fragment; 1bia: BirA-biotin operon repressor protein; 1vie: dihydrofolate reductase; 1dj7: ferridoxin-thioredoxin reductase; 1psf: photosystem I protein PsaE; 1whi: ribosomal protein L14. The proteins aligned for OB-fold were 1csp: cold shock protein; 1bov: verotoxin-1; 1ltt: enterotoxin; 1cuk: ruvA protein; 1fjf: ribosomal protein S17; 1asy: aspartyl tRNA-synthetase; 1a0i: T7 DNA-ligase; 1ey0: staphylococcal nuclease. The β-strand regions were marked as 'bbbbb' and the 3₁₀-turn as '333'. The 3₁₀-turn was conserved in many of the SH3-fold proteins. Highly conserved hydrophobic regions in the strands were marked with ^* or # depending on the extent of conservation, ^* being all hydrophobic and # being majority hydrophobic. It is significant that out of 22 residues forming the strands, there were 15 residues have homology.