Prediction of secreted proteins

Complementing the signal peptide based prediction of Type III secreted proteins we have integrated a novel method for class 1B chaperone prediction. Those chaperones facilitate the correct selection and unfolding of type III dependent effector proteins. A commonly shared sequence within the region of the 70 N-terminal residues of type III secreted proteins was shown to serve as binding site of the chaperones. This 'conserved chaperone-binding domain' (CCBD) follows the explicit pattern (LMIF)1XXX(IV)5XX(IV)8X(N)10 according to Costa et al, 2012.

We implemented EffectiveCCBD, allowing to compare any given collection of protein sequences against this motif by using Biopython. The output informs the user whether the pattern was found within the expected region (26-70 amino acids from the N-terminus) or in the surrounding regions (1-25 and 71-150 amino acids from the N-terminus).