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A new framework for Subti Wiki, the database for the model organism Bacillus subtilis
Open accessPublished version of a preprint
Abstract
Bacillus subtilis is a Gram-positive model bacterium and one of the most-studied and best understood organisms. The complex information resulting from its investigation is compiled in the database SubtiWiki (https://subtiwiki.uni-goettingen.de/v5) in an integrated and intuitive manner. To enhance the utility of SubtiWiki, we have added novel features such as a viewer to interrogate conserved genomic organization, a widget that shows mutant fitness data for all non-essential genes, and a widget showing protein structures, structure predictions and complex structures. Moreover, we have integrated metabolites as new entities. The new framework also includes a documented API, enabling programmatic access to data for computational tasks. Here we present the recent developments of SubtiWiki and the current state of the data for this organism.
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Cites
Highly accurate protein structure prediction with AlphaFold
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ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391
Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850
UniProt: the Universal Protein Knowledgebase in 2023
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bye-A-Jee, H., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1052 · Cited by 7,210
Protein complex prediction with AlphaFold-Multimer
Evans, R., O’Neill, M., Pritzel, A., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., et al. (2021) · doi:10.1101/2021.10.04.463034 · Cited by 3,808
SynWiki: Functional annotation of the first artificial organism Mycoplasma mycoidesJCVI‐syn3A
Pedreira, T., Elfmann, C., Singh, N., & Stülke, J. (2022) · Protein Science · doi:10.1002/pro.4179 · Cited by 13
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Metadata
- Authors
- Elfmann, C., Dumann, V., van den Berg, T., & Stülke, J.
- Affiliations
- University of Göttingen (DE)
- Corresponding author
- Stülke, Jörg
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-10-23
- Volume
- 53
- Issue
- D1
- Pages
- D864-D870
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC11701700
- OpenAlex
- W4403684521
- Cited by
- 47
- References
- 6
- Citations by year
- 2026: 27 · 2025: 20
- FWCI
- 12.47
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (publishedVersion, other-oa)
- Funders
- Deutsche Forschungsgemeinschaft (469281184)
- Georg-August-Universität Göttingen
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- Bacillus subtilis, model organism databases, genome organization, mutant fitness, non-essential genes, protein structure, protein complex structure, metabolites, API, data integration
- MeSH terms
- Bacillus subtilis, Bacterial Proteins, Genes, Bacterial, Mutation, Software, Genome, Bacterial, Internet, Databases, Genetic, Genetic Fitness
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