The Pfam protein families database

Abstract

Pfam is a widely used database of protein families, currently containing more than 13 000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80%. Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages. We continue to improve the Pfam website and add new visualizations, such as the ‘sunburst’ representation of taxonomic distribution of families. In this work we additionally address two topics that will be of particular interest to the Pfam community. First, we explain the definition and use of family-specific, manually curated gathering thresholds. Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam.

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

“…R-gene classification. All genes from the G. max and G. soja samples were annotated using the HMM model against the Pfam-A database 62 . Genes with the Pfam domain of PF00931 were defined as R-genes, classified by different Pfam domains with E-value of 0.001.…”

“…Finally, we checked gene models that were split into small fragments due to the discontinuity of scaffolds and revised our prediction of genes in each of the seven G. soja genomes. Putative biological functions of individual genes were assigned according to the best BLAST 57 hits in the Arabidopsis thaliana proteome, and by searching publicly available databases including Pfam 62 , PRINTS, PROSITE, ProDom and SMART with InterProScan 63 . Gene Ontology (GO) 64 terms for individual genes were retrieved from the corresponding InterPro descriptions.…”

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

“…The domain composition of VIR was examined using S mart (Letunic et al ., 2012) and P fam (Punta et al ., 2012) databases. For creating the multiple sequence alignments, the protein sequences were aligned using the C lustal O mega algorithm (Sievers et al ., 2011) and graphically visualized by J al V iew v.2.8.0b1 using default C lustal X colour code (Waterhouse et al ., 2009).…”

Deciphering the tRNA-dependent lipid aminoacylation systems in bacteria: Novel components and structural advances

“…These observations were recently confirmed by the crystal structures of aaPGSs from Bacillus licheniformis and Pseudomonas aeruginosa . 30 In the Protein Family database (Pfam 41 ), the GNAT fold is found in 39 families of transferases which altogether constitute the N-acyltransferases clan (CL0257). This clan includes many acyl-CoA and aa-tRNA transferases.…”