Do you have UniProt identifiers?
In that case, you could use the "Retrieve" tab on the UniProt web site, http://www.uniprot.org
If the domains you are looking for are annotated in UniProtKB/Swiss-Prot, you might find the instructions given in this FAQ useful:
If you have any questions concerning the use of the UniProt web site, please do not hesitate to contact firstname.lastname@example.org
Batch CD-Search serves as both a web application and a script
interface for a conserved domain search on multiple protein sequences,
accepting up to 4,000 proteins in a single job. It enables you to view
a graphical display of the concise or full search result for any
individual protein from your input list, or to download the results
for the complete set of proteins. The Batch CD-Search Help provides
additional details. (https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml)
Enter a list of sequence identifiers, separated by newlines. Use
standard Swiss-Prot or Ensembl style IDs or ACCs. You can also paste a
set of sequences in FASTA format. There is a limit of 10000 sequences
per access. You will only get results for sequences that have a match
in SMART database, ie. only precomputed results will be displayed.