NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes

Baltoumas, Fotis A.; Karatzas, Evangelos; Liu, Sirui; Ovchinnikov, Sergey; Sofianatos, Yorgos; Chen, I-Min; Kyrpides, Nikos C.; Pavlopoulos, Georgios A.

doi:10.1093/nar/gkad800

Title: NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes

Journal Article · 08 October 2023 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkad800 · OSTI ID:2008114

;

; Liu, Sirui; Ovchinnikov, Sergey; Sofianatos, Yorgos;

; Kyrpides, Nikos C.;

Abstract The Novel Metagenome Protein Families Database (NMPFamsDB) is a database of metagenome- and metatranscriptome-derived protein families, whose members have no hits to proteins of reference genomes or Pfam domains. Each protein family is accompanied by multiple sequence alignments, Hidden Markov Models, taxonomic information, ecosystem and geolocation metadata, sequence and structure predictions, as well as 3D structure models predicted with AlphaFold2. In its current version, NMPFamsDB hosts over 100 000 protein families, each with at least 100 members. The reported protein families significantly expand (more than double) the number of known protein sequence clusters from reference genomes and reveal new insights into their habitat distribution, origins, functions and taxonomy. We expect NMPFamsDB to be a valuable resource for microbial proteome-wide analyses and for further discovery and characterization of novel functions. NMPFamsDB is publicly available in http://www.nmpfamsdb.org/ or https://bib.fleming.gr/NMPFamsDB.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2008114

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 52; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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