All metagenomic peptide sequences from CAMERA were downloaded and searched against PFAMs using hmmscan from the HMMER 3 beta 2 package.

Output looks like this:
#                                                   --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target             query                    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
#-------------------   -------------------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
PRK                  JCVI_PEP_1112677232318   2.9e-17   62.4   0.1   3.1e-17   62.3   0.1   1.0   1   0   0   1   1   1   1 -
FBPase               JCVI_PEP_1112677232314   6.2e-77  258.0   0.0   6.9e-77  257.8   0.0   1.0   1   0   0   1   1   1   1 -
ATP_bind_3           JCVI_PEP_1112677232286   1.5e-31  108.7   0.4   2.7e-31  107.9   0.2   1.4   1   0   0   1   1   1   1 -
CPSase_L_D2          JCVI_PEP_1112677232360   7.1e-55  185.3   0.0   9.2e-55  184.9   0.0   1.1   1   0   0   1   1   1   1 -
CPSase_L_chain       JCVI_PEP_1112677232360   1.2e-09   38.0   0.0   2.1e-09   37.3   0.0   1.3   1   0   0   1   1   1   1 -
ATP-grasp            JCVI_PEP_1112677232360   4.3e-06   26.5   0.0   5.7e-06   26.1   0.0   1.2   1   0   0   1   1   1   1 -
GARS_A               JCVI_PEP_1112677232360   8.1e-05   21.9   0.0   0.00013   21.2   0.0   1.4   1   0   0   1   1   1   1 -
...

Note: data can be decompressed faster by using pbzip2