Where can I download ALL pfam flat-file annotations?

Question

[O.rka]

I tried downloading the following: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/mappings/pdb_pfam_mapping.txt

but it's missing a huge number of PFAM ids. For example, PF13276 isn't in there. Is there another place where I can get these flatfiles?

[lieven.sterck]

perhaps from the PFAM website ? on their ftp site look in to the 'current_release' folder.

[O.rka]

I only found one file with annotations ^^^. Do you know if there is another file on the ftp site?

[lieven.sterck]

Not without looking into them, but these notes might be informative?

What do you mean with "annotations" btw?

[O.rka]

I essentially want to get the name and description given a pfam identifier. For example, 'PF01565': {'NAME': 'FAD_binding_4', 'DESCRIPTION': 'FAD binding domain'}

Answer 1

[mwylerCH]

The Pfam-A.hmm.dat.gz file contains the required informations. Each entry looks like:

# STOCKHOLM 1.0
#=GF ID   ZZ
#=GF AC   PF00569.20
#=GF DE   Zinc finger, ZZ type
#=GF GA   21.4; 21.4;
#=GF TP   Domain
#=GF ML   45
#=GF CL   CL0006

alternatively a shorter version is available in the Pfam-A.clans.tsv.gz file

PF00569 CL0006  C1  ZZ  Zinc finger, ZZ type