The conserved domain database in 2023
Open accessAbstract
NLM's conserved domain database (CDD) is a collection of protein domain and protein family models constructed as multiple sequence alignments. Its main purpose is to provide annotation for protein and translated nucleotide sequences with the location of domain footprints and associated functional sites, and to define protein domain architecture as a basis for assigning gene product names and putative/predicted function. CDD has been available publicly for over 20 years and has grown substantially during that time. Maintaining an archive of pre-computed annotation continues to be a challenge and has slowed down the cadence of CDD releases. CDD curation staff builds hierarchical classifications of large protein domain families, adds models for novel domain families via surveillance of the protein 'dark matter' that currently lacks annotation, and now spends considerable effort on providing names and attribution for conserved domain architectures. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
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The dimerization (Zip) region of Rtg3 orthologs is generally conserved, and differences from the consensus cd14686 are apparent also in species such as S. cerevisiae and C. albicans.
“Importantly, the dimerization (Zip) region is also generally conserved, and differences from the consensus (cd14686) from the Conserved Domain Database (Wang et al. 2023) are apparent also in species such as S. cerevisiae and C. albicans.”
From Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts (2026) · cites this paper as Wang et al. 2023
Cites
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Gut microbiota drives structural variation of exogenous probiotics to enhance colonization
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“28 NLP P60 protein plays a widespread role in supporting the dynamics of the bacterial cell wall or bacterial growth.”
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ECOD: Classification of domains in AFDB Swiss-Prot structure predictions
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Łabędzka-Dmoch, K., Bui, T. H. D., Piątkowski, J., Dilling, M., Jagiełło, P., Kabza, W., & Golik, P. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag005 · Cited by 1 · see citing works
- Authors
- Wang, J., Chitsaz, F., Derbyshire, M. K., Gonzales, N. R., Gwadz, M., Lu, S., Marchler, G. H., Song, J. S., Thanki, N., Yamashita, R. A., Yang, M., Zhang, D., Zheng, C., Lanczycki, C. J., & Marchler-Bauer, A.
- Affiliations
- National Institutes of Health (US)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda , MD 20894 , USA
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-12-08
- Volume
- 51
- Issue
- D1
- Pages
- D384-D388
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC9825596
- OpenAlex
- W4310951880
- Cited by
- 1,277
- References
- 15
- Citations by year
- 2026: 392 · 2025: 546 · 2024: 309 · 2023: 28 · 2017: 1
- FWCI
- 73.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- protein domains, multiple sequence alignment, protein domain architecture, protein annotation
- MeSH terms
- Protein Domains, Amino Acid Sequence, Humans, Proteins, Conserved Sequence, Protein Structure, Tertiary, Databases, Protein
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