Downloading all Helix-turn-helix motif containing protein from bacteria

Question

[saadleeshehreen]

Hi,

I want to download all the bacterial protein containing helix-turn-helix domain. I did search in pfam database.

https://pfam.xfam.org/search/keyword?query=Hth

Here are 605 results. Each of the PF accession (eg PF01325) leads me different webpages and after clicking "Alignment" tab I found the following:

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

Is there any way to download all the protein sequences easily from pfam database? or is there any other database where I can get my required protein?

[Nitin Narwade]

There is one github repository which may help you. But it may need some or more programming and or the data processing.

Ex: You will get PFAM <=> UniProt id mapping along with subregions (i.e. domain region) information from the repository. You can download all the sequences using UniPort ids and then you have to fetch out subregions (sequences for domains only) from the complete downloaded UniPort sequences.

Answer 1

[Elisabeth Gasteiger]

You can download these proteins from UniProt (https://www.uniprot.org). For a given Pfam identifier, e.g. PF01325 use query

database:(type:pfam pf01325)

https://www.uniprot.org/uniprot/?query=database%3A%28type%3Apfam+PF01325%29&sort=score

And then click on "Download", selecting FASTA format.

You can also do this programmatically using the UniProt REST API, cf https://www.uniprot.org/help/api_queries