Entering edit mode
5.2 years ago
marlenejensen
▴
20
Hey, can you recommend a good protein secretion predictor? I am running SignalP, TatP,SecretomeP, Phobia and PrediSi but the results differ a lot. Do you have some experience with that?
Thanks a lot in advance!
There are a lot of secretion pathways (I assume you're talking about bacteria). SignalP would probably give you the best results for the SRP, although you should be aware of secretion signals without cleavage signals, they might be functional and not have a good score overall. Do you know which pathways are available in your bacteria? (type III, IV, VI etc.)
Yes, right....I forgot that. I have bacteria sequences and want to look at pathway IV..
Take a look at the schema in KEGG: https://www.genome.jp/kegg-bin/show_pathway?ko03070 Substrates don't need to pass through the SRP although they might. Take a look at this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5942808/ it's recent and cites all the relevant predictors.I personally think that methods like comparative genomics would have some use here.
The best predictor is a lab experiment. All of these sorts of tools rely on different, and flawed, models. To my knowledge there is no 'best', though SignalP is perhaps the most widely used that I'm aware of.