An important FAQ: why should I go look for my own collection of sequences? After all, there are plenty of websites that will provide prêt-à-porter sets for me.
Use those collections, by any means, but with the grain of salt. They were all constructed automatically, and all automated algorithms or pipelines tend to fail now and then.
In all likelihood, you are currently the world's premier expert for the protein you are working on. You are the most qualified person to decide which sequences belong to your analysis.
Take a look at your sequences (read here about viewing sequences):