There are at least two ways of doing this. The easier one is to go to Pfam directly and download aligned hits for the domain of interest. Let's say that you want hits for
Alignments on the left-hand side, and select the database in the
Format an alignment section. Let's say you want all UniProt members (~165K sequences) so click on a button that corresponds to it, select the alignment type and click on
Generate to download. This works if you are OK with the database choices they have.
If you want to search a custom database, click on
Curation & model and download a raw HMM for your domain - in this case
PF00001.hmm. Now, do the
HMMer installation required):
hmmsearch -E 0.001 --cpu 4 -A out_alignment.stk PF00001.hmm /path/to/your_database.fasta
In this case
out_alignment.stk will contain a Stockholm alignment of all the hits, which
esl-reformat can convert to other formats as needed. You may want to adjust the
E-value threshold and the number of CPUs.