I'm working on my first sequencing related project and I'm trying to find proteins with a specific PFAM ID (PF11999). The project is called "MMETSP", I searched the annotations for that ID, identified signal peptides using SignalP and their target locations with a tool called MultiLoc2 (I was looking for extracellular targets only).
Out of the very few sequences that where left after all this filtering, none of the DNA-bits started with the basepair-code "ATG", for Methionine. How can this be?
I used the shell to calculate that only 1,83% of all the sequences start with ATG.
Any ideas on this?