I would like to know how can I search for example for such proteins or find them?
Lets say, I find one, then how can I search family members (those which are similar or have similar functions), should I simply use blast or is there a better way to find them?
I am looking to find the easiest way and if you have any idea, please do not hesitate to let me know
I think there are many approaches you can follow. This also depends from the dataset you are working with.
The first thing would be to take a reference protein sequence and use it as query for a blast search against your dataset/genome.
You can then take the hits and use them as query for a second round fo blast search in you dataset. However, this second step might led to a high number of false positive so you may want to check the hits manually.
A second approach is to take a representative number of sequences for the protein you are interested in for public db. You align them, create a Hidden Markov model and use this model to scan your dataset.
I would recommend you to always double check manually your hits.
@dago thanks but is there any example? paper? or something like this already published?