The signal recognition particle (SRP) is an oligomeric complex that mediates targeting and insertion of the signal sequence of exported proteins into the membrane of the endoplasmic reticulum. SRP consists of a 7S RNA and six protein subunits. One of these subunits, the 54 Kd protein (SRP54), is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. The N-terminal 300 residues of SRP54 include the GTP-binding site (G-domain) and are evolutionary related to similar domains in other proteins which are listed below [1].

• Escherichia coli and Bacillus subtilis ffh protein (P48), a protein which seems to be the prokaryotic counterpart of SRP54. Ffh is associated with a 4.5S RNA in the prokaryotic SRP complex.
• Signal recognition particle receptor α subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane. The G-domain is located at the C-terminal extremity of the protein.
• Bacterial ftsY protein, a protein which is believed to play a similar role to that of the docking protein in eukaryotes. The G-domain is located at the C-terminal extremity of the protein.
• The pilA protein from Neisseria gonorrhoeae which seems to be the homolog of ftsY.
• A protein from the archaebacteria Sulfolobus solfataricus. This protein is also believed to be a docking protein. The G-domain is also at the C- terminus.
• Bacterial flagellar biosynthesis protein flhF.

The best conserved regions in those domains are the sequence motifs that are part of the GTP-binding site, but as those regions are not specific to these proteins, we did not use them as a signature pattern. Instead, we selected a conserved region located at the C-terminal end of the domain.