Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues [1,2].

The crystal structure of the S13 protein has been solved as part of the small ribosomal subunit (see <PDB:1J5E; M>) [3]. It consists of two separated domains, an approximately 60-residue N-terminal domain which forms a small helical domain consisting of two-turn helices and two α-turn structure, and a C-terminal long straight α helix followed by a region devoid of secondary structure. The N-terminal domain makes several base specific interactions with the 16S RNA. Several lysine residues in the C-terminal helix also contact RNA.

Proteins known to belong to this family are listed below.

• Eubacterial S13.
• Plant chloroplast S13 (nuclear encoded).
• Red algal chloroplast S13.
• Cyanelle S13.
• Archaebacterial S13.
• Plant mitochondrial S13.
• Mammalian and plant S18.

As a signature pattern, we selected the best conserved regions located at the C-terminal end of the long straight α helix. We also developed a profile which covers the N-terminal domain and the long straight α helix.