Welcome to the BioCatNet database system
The BioCatNet database system is a repository of sequence, structure and biocatalytic data on protein families to facilitate protein engineering.
The BioCatNet concept
Proteins are assigned to homologous families by their sequence similarity. Homologous families are then grouped hierarchically to superfamilies (similar to the DWARF system by Fischer et al. 2006).
On the sequence level, annotations may include functionally relevant positions and domain boundaries. Given sufficient structural information, a standard numbering scheme is provided for a protein family which allows for the unambiguous identification of functionally and structurally relevant residues, to communicate results on mutations and to systematically analyze sequence-function relationships in protein families (Vogel et al. 2012).
Currently, we extend the BioCatNet data model to store biocatalytic data and to analyze experimental data by selected kinetic models (Buchholz et al. 2018).
The BioCatNet Excel template for the exchange of biocatalytic data or time-course data is described in the wiki.
Available databases
The BioCatNet infrastructure currently contains the following family-specific protein databases:
| Abbreviation | Database | No. of sequences | No. of structures |
|---|---|---|---|
| CYPED | CYtochrome P450 Engineering Database | 52674 | 595 |
| ExED | Expansin Engineering Database | 15089 | 21 |
| GH19ED | Glycoside Hydrolase 19 Engineering Database | 22461 | 27 |
| HYED | Hydratase Engineering Database | 2046 | 3 |
| IRED | Imine Reductase Engineering Database | 1409 | 8 |
| LCCED | LaCCase and multicopper oxidase Engineering Database | 51058 | 229 |
| LED | Lipase Engineering Database | 283672 | 1590 |
| oTAED | ω-Transaminase Engineering Database | 114655 | 234 |
| SDRED | Short-chain Dehydrogenase / Reductase Engineering Database | 168212 | 688 |
| TEED | Thiamine diphosphate-dependent Enzymes Engineering Database | 119567 | 308 |
| TEMLACED | TEM LACtamase Engineering Database | 483 | 65 |
| TTCED | TriTerpene Cyclase Engineering Database | 2794 | 18 |
Contact
BioCatNet is maintained by the Bioinformatics group at the Department of Technical Biochemistry at University of Stuttgart, Germany.
We acknowledge your comments to this page. Please contact Jürgen Pleiss for contributions or collaborations.
For technical questions, please use our bug tracking page.
References
- Fischer, M., Thai, Q. K., Grieb, M., & Pleiss, J. (2006). DWARF–a data warehouse system for analyzing protein families. BMC Bioinformatics, 7:495.
- Vogel, C., Widmann, M., Pohl, M., & Pleiss, J. (2012). A standard numbering scheme for thiamine diphosphate-dependent decarboxylases. BMC Biochemistry, 13:24.
- Pleiss, J. (2014). Systematic analysis of large enzyme families: identification of specificity- and selectivity-determining hotspots. ChemCatChem, 6:944.
- Buchholz, P.C.F., Vogel, C., Reusch, W., Pohl, M., Rother, D., Spieß, A. & Pleiss, J. (2016). BioCatNet: a database system for the integration of enzyme sequences and biocatalytic experiments. ChemBioChem, 17:2093.
- Buchholz, P.C.F., Ohs, R., Spieß, A. & Pleiss, J. (2018). Progress curve analysis within BioCatNet: comparing kinetic models for enzyme-catalyzed self-ligation. Biotechnology Journal, Jul 12:e1800183.