You can have many tools for annotation, and most of them they use FASTA files as input. As a starting point, which I presume it is, you have 2 straight-forward strategies:
Perform a blastx against a protein database, such us UniProt, letting you annotate your FASTA sequences using similarity.
Use the suite of programs HMMER, which allows you to predict functional domains/regions based on hidden-markov-models. You can access curated models at Pfam and/or TIGR databases.
There are other programs, that annotate using other strategies, but as a starting point, this should be enough. In case the you work either with bacteria, archea or viruses, I strongly recommend you to use Prokka (https://github.com/tseemann/prokka), a wrap-up program written by Dr Torsten Seeman, which combines several search strategies and outputs several standardised report formats, it works fast and doesn't require much resources.
You can also try eggnog-mapper in eggNOG database (http://eggnogdb.embl.de/). just upload your sequences and you will receive annotation of your sequences.