Searching Pfam¶
There are multiple ways to look for information in Pfam by using the IntePro website.
Searching a specific Pfam entry¶
Users can navigate to specific Pfam entry page by entering the Pfam identifier or accession number or a keyword that form part of its name Users can navigate to specific Pfam entry page by entering the Pfam identifier or accession number or a keyword that form part of its name via three different Search boxes:
1. When selecting the Browse + By member database option, the search box is located in the header of the results table. The results can be filtered by Member Database Entry Type and InterPro state, and can be ordered by accession in ascending or descending order by clicking on the arrow at the right side of the column name Accession.

Example of browsing the Pfam database. A paginated list of all available Pfam entries is displayed. A Search box is available in the table header, next to the Download button. A Search box is available in the table header, next to the Download button.¶
2. After selecting Search + By text, a text box is displayed. 2. After selecting Search + By text, a text box is displayed.

Example of searching specific Pfam entry pages by entering the Pfam identifier or accession number or a keyword.¶
In the top right corner of any InterPro page, next to the magnifying glass.

On the InterPro website header, a search box appears when hovering the mouse next to the magnifying glass on the right; it can be used to search for Pfam information.¶
This text box allows you to go quickly to the relevant page in the InterPro site, by using:
Searching a protein sequence against Pfam¶
Searching a protein sequence against the Pfam library of HMMs will enable you to find out the domain architecture of the protein, and thus what its potential function might be. If your protein is present UniProt version used to make the current release of InterPro, we have already calculated its domain architecture. You can access this by entering the Uniprot sequence identifier in any of the Search boxes mentioned above (see Searching a specific Pfam entry).
Using the InterPro online sequence search¶
If your sequence is not in the InterPro database, you could perform a single or multiple sequence search against the Pfam database on the InterPro website. This search uses the InterProScan tool, which allows you to search up to 100 nucleotide (DNA/RNA) or protein sequences at a time with a maximum length of 40,000 characters. To run any online search you can follow these steps: If your sequence is not in the InterPro database, you could perform a single or multiple sequence search against the Pfam database on the InterPro website. This search uses the InterProScan tool, which allows you to search up to 100 nucleotide (DNA/RNA) or protein sequences at a time with a maximum length of 40,000 characters. To run any online search you can follow these steps:
Click the Search + By Sequence in the InterPro website menu. This opens the InterPro sequence search page.

Selecting Search + By Sequence in the InterPro website menu.¶
2. Provide the FASTA formatted nucleotide or protein sequence(s) of interest by pasting them into the text box or import them by uploading a file. 2. Provide the FASTA formatted nucleotide or protein sequence(s) of interest by pasting them into the text box or import them by uploading a file.

Example of protein sequence in FASTA format in the text box.¶
3. Expand the Advanced options, select the appropriate sequence type (protein -amino acids-, or RNA/DNA -nucleotides-), click on Unselect all protein sequence applications and select Pfam. 3. Expand the Advanced options, select the appropriate sequence type (protein -amino acids-, or RNA/DNA -nucleotides-), click on Unselect all protein sequence applications and select Pfam.

Select only Pfam to search your sequence(s) against this database.¶
Click on the Search button.
While the sequence search is running, you can continue to navigate through the website, other browser tabs or applications and will get a pop-up notification when the job has been completed (this requires the browser notifications to be enabled).
The results of the submitted job are accessible by selecting Results + Your InterProScan Searches in the InterPro website menu. This page displays the sequence searches that have been performed in the last seven days, with the most recent one being displayed at the top. The Status column gives an indication of whether or not the search has completed (green tick symbol / searching), if the search has been saved locally (the results will still be available even after the seven days limit set up on InterPro servers), or if the results have been imported (file symbol). Searches can be deleted or saved locally by clicking on the bin or file icon in the Action column, respectively.

The results of the submitted job are accessible by selecting Results + Your InterProScan Searches in the InterPro website menu. This page displays the sequence searches that have been performed in the last seven days, with the most recent one being displayed at the top. The Status column gives an indication of whether or not the search has completed (green tick symbol / searching), if the search has been saved locally (the results will still be available even after the seven days limit set up on InterPro servers), or if the results have been imported (file symbol). Searches can be deleted or saved locally by clicking on the bin or file icon in the Action column, respectively.

Select Results + Your InterProScan Searches in the InterPro website menu.¶
Clicking on the job ID or on the text in the Results column opens a page summarising the search, including the sequence type, number of sequences, status and expiry date (see figure below). When a search has been run using a previous version of InterProScan, it can be re-run using the latest version of the software by clicking on the Resubmit All button. If the search has been run in the last seven days, the results can be saved in the browser to be able to access them once the seven days limit has been reached by clicking on the Save results in Browser button. The results can be downloaded by clicking on the Download button. If the search has been run in the last seven days the results can be downloaded in TSV, JSON, XML and GFF formats, thereafter, if the search has been saved locally, the results are only available in JSON format.
All the submitted sequences are listed in a table. Clicking on the name in the Sequence column allows to access the results summarised in a protein sequence viewer (see the protein viewer section below).

List of sequences for a search, select one sequence to view the Pfam matches.¶
Clicking on the job ID or on the text in the Results column opens a page summarising the search, including the sequence type, number of sequences, status and expiry date (see figure below). When a search has been run using a previous version of InterProScan, it can be re-run using the latest version of the software by clicking on the Resubmit All button. If the search has been run in the last seven days, the results can be saved in the browser to be able to access them once the seven days limit has been reached by clicking on the Save results in Browser button. The results can be downloaded by clicking on the Download button. If the search has been run in the last seven days the results can be downloaded in TSV, JSON, XML and GFF formats, thereafter, if the search has been saved locally, the results are only available in JSON format.
All the submitted sequences are listed in a table. Clicking on the name in the Sequence column allows to access the results summarised in a protein sequence viewer (see the protein viewer section below).

List of sequences for a search, select one sequence to view the Pfam matches.¶
Interpreting the protein viewer¶
All Pfam entries are displayed in the protein sequence viewer. They are grouped by entry types (family, domain, repeat, site). The coloured bars indicate the location of entry matches on the protein sequence. The first line of the Domains category contains a summary of the domains found in the protein. On the right-hand side, the Pfam accession and short name and, when the Pfam is integrated, the InterPro entry information is displayed above the Pfam information. The Pfam entries that remain unintegrated in InterPro entries are displayed separately in the Unintegrated category. All Pfam entries are displayed in the protein sequence viewer. They are grouped by entry types (family, domain, repeat, site). The coloured bars indicate the location of entry matches on the protein sequence. The first line of the Domains category contains a summary of the domains found in the protein. On the right-hand side, the Pfam accession and short name and, when the Pfam is integrated, the InterPro entry information is displayed above the Pfam information. The Pfam entries that remain unintegrated in InterPro entries are displayed separately in the Unintegrated category.
On top of the protein sequence viewer, different icons allow to display the viewer on full screen and zoom in and out of the protein sequence. The Options button offers the possibility to personalise the display by changing the colour code of the entries, the labels (accession number, short name and/or description can be displayed on the right-hand side of the viewer). The tooltip should be kept active to see a pop-up box with the accession number, description and amino acid coordinates of the match of a Pfam and the InterPro entry accession when hovering the mouse over it. Snapshots of the results can be taken in PNG format. Results can be downloaded in multiple formats by clicking on the Download button.
(accession number, short name and/or description can be displayed on the right-hand side of the viewer). The tooltip should be kept active to see a pop-up box with the accession number, description and amino acid coordinates of the match of a Pfam and the InterPro entry accession when hovering the mouse over it. Snapshots of the results can be taken in PNG format. Results can be downloaded in multiple formats by clicking on the Download button.


Results of a protein sequence search. The integrated and unintegrated Pfam entries matching this protein sequence are shown in the protein viewer. The colour of the matches is customised as Colour By + Member Database for all Pfam entries to be Results of a protein sequence search. The integrated and unintegrated Pfam entries matching this protein sequence are shown in the protein viewer. The colour of the matches is customised as Colour By + Member Database for all Pfam entries to be highlighted in blue.¶
Local protein search¶
Alternatively, if you have a very large number of protein searches to perform, or you do not wish to share your sequence, it may be more convenient to install and run InterProScan.
Finding proteins with a specific set of domain combinations (Domain architectures)¶
Users can search protein sequences that contain specific Pfam entries in a particular arrangement by selecting Search + By Domain architecture Users can search protein sequences that contain specific Pfam entries in a particular arrangement by selecting Search + By Domain architecture in the InterPro website menu. Pfam entries that the proteins should or should not contain can be included or excluded from the domain architecture. The Order of domain matters option offers the possibility to arrange the domains in a particular order. The Exact match option fine tunes the search to find only proteins containing the selected domains (no extra domain in the proteins). Domains can be selected by entering a domain name, Pfam accession or InterPro accession.

Select Search + By Domain architecture in the InterPro menu, enter the desired Pfam entries and select/unselect the relevant options.¶