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Protein Clusters

Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP

URL: http://www.ncbi.nlm.nih.gov/proteinclusters

Resource ID: nif-0000-03354     Resource Type: Resource     Version: Latest Version


bacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standard


Access: open
Reuse: open
Start date: NA
Type: governmental/disciplinary
Deposit: NA
(info provided by re3data.org)

Listed By







Protein Clusters Database, Entrez Protein Clusters, NCBI Protein Clusters

Parent Organization

Funding Information

NIH, Intramural Research Program, NLM,

Additional Resource Types



archaea, bacteria, plant, fungus, protozoa

Original Submitter


Version Status


Submitted On

12:00am September 21, 2010

Originated From


Changes from Previous Version

  • Description was changed
  • Funding Information was changed
  • Additional Resource Types was changed

Version 2

Created 2 months ago by Christie Wang

Version 1

Created 5 years ago by Anonymous

The National Center for Biotechnology Information's Protein Clusters Database.

  • Klimke W
  • Nucleic Acids Res.
  • 2009 16

Rapid increases in DNA sequencing capabilities have led to a vast increase in the data generated from prokaryotic genomic studies, which has been a boon to scientists studying micro-organism evolution and to those who wish to understand the biological underpinnings of microbial systems. The NCBI Protein Clusters Database (ProtClustDB) has been created to efficiently maintain and keep the deluge of data up to date. ProtClustDB contains both curated and uncurated clusters of proteins grouped by sequence similarity. The May 2008 release contains a total of 285 386 clusters derived from over 1.7 million proteins encoded by 3806 nt sequences from the RefSeq collection of complete chromosomes and plasmids from four major groups: prokaryotes, bacteriophages and the mitochondrial and chloroplast organelles. There are 7180 clusters containing 376 513 proteins with curated gene and protein functional annotation. PubMed identifiers and external cross references are collected for all clusters and provide additional information resources. A suite of web tools is available to explore more detailed information, such as multiple alignments, phylogenetic trees and genomic neighborhoods. ProtClustDB provides an efficient method to aggregate gene and protein annotation for researchers and is available at http://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters.