I have 22 amino acid sequences known to be from proteins that are plasma membrane localized in yeast. I want to try and identify if they have an amino acid signal sequence that is localizing them to the plasma membrane. I've aligned them with Mafft as recommended by another BioStar user. Below are the results that I get but I'm unsure how to interpret them. The dark alignment itself does not seem to be particularly good, as there are many gaps present. Therefore even if I did see a strong signal somewhere, I wouldn't have that much faith in it, due to the large gaps in the alignments. However, I do see about 10 places in the alignment where amino acids of similar type are found. These are indicated by the dark grey vertical lines. These are not necessarily identical amino acids, as a Blosum 62 matrix was used with threshold of 1. From this initial analysis, I do not think that there is a peptide localization signal in these data. Do you have any other suggestions for looking for one? Thanks.
What leads you to believe that a motif is responsible for localization to the membrane? In many cases, membrane proteins are defined by the presence of hydrophobic alpha-helices, rather than by specific motifs.
Thanks @Neilfws, I was expecting to find a signal recognition particle or something similar that would be responsible for membrane localization. I know that membrane proteins are characterized by hydrophobic alpha-helices, but I thought this was just what embedded it in the membrane, rather than what got it to the membrane in the first place? I will keep searching.
Did you try SignalP or possibly TMHMM?