If you have a FASTA file for your proteins, this is a simple way to count proteins:

grep ">" your_file_name.fas | wc -l

To extract annotations and save them in annotations.txt:

grep ">" your_file_name.fas > annotations.txt

If you want to annotate your genome by metabolic or onthology criteria, KEGG will do the trick.It can give you an output that looks like this:

I solved this problem using program SnapGene. I put genebank sequences into the program. choosen chromosome -> features -> switch off "full descriptions" -> ctrl + a

You will have info about number of selected features. "(X - 1 - Y)/2" is number of your annotated ORFs. X - number of features Y - number of features that are not genes or CDS ( i. e regulatory regions) (to check if you have that type of features press "sort by gene" button

For smaller datasets you can just manually select all genes and program will count it for you, but it would be problematic with huge datasets.

I choose this pathway because I had my files in genebank format. For fasta files I would reccomend solution of Mr Dlakic, much quicker. Thank everyone for help