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. 2016 Jan 4;44(D1):D279-85.
doi: 10.1093/nar/gkv1344. Epub 2015 Dec 15.

The Pfam protein families database: towards a more sustainable future

Robert D Finn  1 , Penelope Coggill  2 , Ruth Y Eberhardt  3 , Sean R Eddy  4 , Jaina Mistry  2 , Alex L Mitchell  2 , Simon C Potter  2 , Marco Punta  5 , Matloob Qureshi  2 , Amaia Sangrador-Vegas  2 , Gustavo A Salazar  2 , John Tate  3 , Alex Bateman  2
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The Pfam protein families database: towards a more sustainable future

Robert D Finn et al. Nucleic Acids Res. .

Abstract

In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.

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Figures

Figure 1.
Figure 1.
Example of the improved representation of relationships graph, indicating the similarity between the Pfam entries within a clan. This particular entry shows the relationship between the entries in the Glutaminase I clan (accession:CL0014). Each entry in the clan is a node in the graph and is represented as circle, with the diameter of the circle being proportional to the number of sequences in the full alignment. Nodes are connected (edges) based on the HHsearch results between the clan members, with the width of edges proportional to the E-value of the HHsearch similarity (E-values ≤ 0.01 are deemed significant). The clanviewer component has been included in the BioJS registry (http://biojs.io/d/clanviewer) and its code is freely available in github (https://github.com/ProteinsWebTeam/clanviewer). In this particular clan, there are three entries (ThuA (PF06283), GATaseI_like (PF07090) and Glyco_hydro_42M (PF08532)) that from a disconnected sub-cluster. DUF4159 (PF13709) is also unconnected to any other entry. However, these entries are included as part of this clan based on the structural similarities to other entries in the clan.
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