Depending on your species, you can have a look at this one as well : Trapid
Alternatively you can do interproscan searches (somewhat in line with Mehmet's answer) and especially have a look at the superfamily and Panther output (they specifically denote 'gene families' )
These will still only get you info on a gene by gene basis, so you still will have to extrapolate that to the gene fams you have.
Omicstools is a good source for suggestions. If you have the amino acid sequences, interproscan does a great job in annotation. If you are looking into TMM or signal peptides in particular, signalP or TMHMM are useful. Trinotate is another annotation pipeline setup for de novo stuff.