SignalP V1.1 World Wide Web Prediction Server Center for Biological Sequence Analysis

Results: Characteristics of signal peptides

The common structure of signal peptides from various proteins is commonly described as a positively charged n-region, followed by a hydrophobic h-region and a neutral but polar c-region. The (-3,-1)-rule states that the residues at positions -3 and -1 (relative to the cleavage site) must be small and neutral for cleavage to occur correctly.

We have analyzed the characteristics of the new signal peptide data set and displayed them in the form of sequence logos. The differences between signal peptides from different organisms are apparent from the sequence logos:

	Eukaryotes	Prokaryotes
		Gram-negative	Gram-positive
Total length (average)	22.6 aa	25.1 aa	32.0 aa
n-regions	only slightly Arg-rich	Lys+Arg-rich
h-regions	short, very hydrophobic	slightly longer, less hydrophobic	very long, less hydrophobic
c-regions	short, no pattern	short, Ser+Ala-rich	longer, Pro+Thr-rich
-3,-1 positions	small and neutral residues	almost exclusively Ala
+1 to +5 region	no pattern	rich in Ala, Asp/Glu, and Ser/Thr