Pfam: The Protein Families Database in 2021

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2020 Oct 30

PMID 33125078

Citations 2336

Authors

Jaina Mistry

Sara Chuguransky

Lowri Williams

Matloob Qureshi

Gustavo A Salazar

Erik L L Sonnhammer

Silvio C E Tosatto

Lisanna Paladin

Shriya Raj

Lorna J Richardson

Robert D Finn

Alex Bateman

Affiliations

Soon will be listed here.

Abstract

The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this journal, over 350 new families have been added in Pfam 33.1 and numerous improvements have been made to existing entries. To facilitate research on COVID-19, we have revised the Pfam entries that cover the SARS-CoV-2 proteome, and built new entries for regions that were not covered by Pfam. We have reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family. The new Pfam-B is based on a clustering by the MMseqs2 software. We have compared all of the regions in the RepeatsDB to those in Pfam and have started to use the results to build and refine Pfam repeat families. Pfam is freely available for browsing and download at http://pfam.xfam.org/.

Citing Articles

Sporophyte-directed gametogenesis in Arabidopsis.

Sivakumar P, Pandey S, Ramesha A, Davda J, Singh A, Kumar C Nat Plants. 2025; .

PMID: 40087543 DOI: 10.1038/s41477-025-01932-y.

Genome mining the black-yeast Aureobasidium pullulans NRRL 62031 for biotechnological traits.

Xiao D, Driller M, Stein K, Blank L, Tiso T BMC Genomics. 2025; 26(1):244.

PMID: 40082747 PMC: 11905612. DOI: 10.1186/s12864-025-11395-2.

Genome-Wide Identification and Expression Analysis of the Gene Family in Banana () Under Various Nitrogen Conditions.

Zhang B, Wang W, Wang C, Cai B, Feng J, Zhou D Int J Mol Sci. 2025; 26(5).

PMID: 40076789 PMC: 11900138. DOI: 10.3390/ijms26052168.

Genome-Wide Exploration and Characterization of the Gene Family's Expression Patterns in Response to Abiotic Stresses in Siberian Wildrye ( L.).

Liu T, Peng J, Dong Z, Liu Y, Wu J, Xiong Y Int J Mol Sci. 2025; 26(5).

PMID: 40076552 PMC: 11900556. DOI: 10.3390/ijms26051925.

An acyl-homoserine lactone acylase found in Stenotrophomonas maltophilia exhibits both quorum quenching activity and the ability to degrade penicillin antibiotics.

Bravo M, Conchillo-Sole O, Coves X, Garcia-Navarro A, Gomez A, Marquez-Martinez M Sci Rep. 2025; 15(1):8557.

PMID: 40074792 PMC: 11903891. DOI: 10.1038/s41598-025-92749-4.

References

Chen C, Natale D, Finn R, Huang H, Zhang J, Wu C . Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One. 2011; 6(4):e18910. PMC: 3083393. DOI: 10.1371/journal.pone.0018910. View

Cong Y, Ulasli M, Schepers H, Mauthe M, Vkovski P, Kriegenburg F . Nucleocapsid Protein Recruitment to Replication-Transcription Complexes Plays a Crucial Role in Coronaviral Life Cycle. J Virol. 2019; 94(4). PMC: 6997762. DOI: 10.1128/JVI.01925-19. View

Mitchell A, Attwood T, Babbitt P, Blum M, Bork P, Bridge A . InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2018; 47(D1):D351-D360. PMC: 6323941. DOI: 10.1093/nar/gky1100. View

Berman H, Henrick K, Nakamura H, Markley J . The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2006; 35(Database issue):D301-3. PMC: 1669775. DOI: 10.1093/nar/gkl971. View

Hauser M, Steinegger M, Soding J . MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinformatics. 2016; 32(9):1323-30. DOI: 10.1093/bioinformatics/btw006. View

Heger A, Wilton C, Sivakumar A, Holm L . ADDA: a domain database with global coverage of the protein universe. Nucleic Acids Res. 2004; 33(Database issue):D188-91. PMC: 540050. DOI: 10.1093/nar/gki096. View

Kim Y, Jedrzejczak R, Maltseva N, Wilamowski M, Endres M, Godzik A . Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2. Protein Sci. 2020; 29(7):1596-1605. PMC: 7264519. DOI: 10.1002/pro.3873. View

El-Gebali S, Mistry J, Bateman A, Eddy S, Luciani A, Potter S . The Pfam protein families database in 2019. Nucleic Acids Res. 2018; 47(D1):D427-D432. PMC: 6324024. DOI: 10.1093/nar/gky995. View

Soding J . Protein homology detection by HMM-HMM comparison. Bioinformatics. 2004; 21(7):951-60. DOI: 10.1093/bioinformatics/bti125. View

10.

Lupas A, Van Dyke M, Stock J . Predicting coiled coils from protein sequences. Science. 1991; 252(5009):1162-4. DOI: 10.1126/science.252.5009.1162. View

11.

Berman H, Henrick K, Nakamura H . Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003; 10(12):980. DOI: 10.1038/nsb1203-980. View

12.

Mitchell A, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G . MGnify: the microbiome analysis resource in 2020. Nucleic Acids Res. 2019; 48(D1):D570-D578. PMC: 7145632. DOI: 10.1093/nar/gkz1035. View

13.

Paladin L, Hirsh L, Piovesan D, Andrade-Navarro M, Kajava A, Tosatto S . RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. Nucleic Acids Res. 2016; 45(D1):D308-D312. PMC: 5210593. DOI: 10.1093/nar/gkw1136. View

14.

Sonnhammer E, Eddy S, Durbin R . Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 1997; 28(3):405-20. DOI: 10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l. View

15.

Bursteinas B, Britto R, Bely B, Auchincloss A, Rivoire C, Redaschi N . Minimizing proteome redundancy in the UniProt Knowledgebase. Database (Oxford). 2016; 2016. PMC: 5199198. DOI: 10.1093/database/baw139. View

16.

Kirchdoerfer R, Ward A . Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nat Commun. 2019; 10(1):2342. PMC: 6538669. DOI: 10.1038/s41467-019-10280-3. View

17.

. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2018; 47(D1):D506-D515. PMC: 6323992. DOI: 10.1093/nar/gky1049. View

18.

Kopec K, Lupas A . β-Propeller blades as ancestral peptides in protein evolution. PLoS One. 2013; 8(10):e77074. PMC: 3797127. DOI: 10.1371/journal.pone.0077074. View

19.

Finn R, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T . Pfam: clans, web tools and services. Nucleic Acids Res. 2005; 34(Database issue):D247-51. PMC: 1347511. DOI: 10.1093/nar/gkj149. View

20.

Finn R, Coggill P, Eberhardt R, Eddy S, Mistry J, Mitchell A . The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2015; 44(D1):D279-85. PMC: 4702930. DOI: 10.1093/nar/gkv1344. View