| Release 1.0 last update on 2009-02-06 |
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This Internet database integrates information on sequence
and structure of PHA Depolymerases to facilitate protein engineering. We acknowledge your comments or contribution to this page: please send us information to be included in this database. |
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Q: How do you count sequences and proteins? A: All sequences with a sequence identity of more than 98% and the same organism are grouped into one protein. "Number of sequences" counts the number of non-identical sequences for each protein (check for 100% identity and identical length). "Number of structures" counts the number of structure entries (by separating different chains, thus chains A and B of a PDB entry will lead to two separate structure entries in the DED). This information is given for each protein by clicking on the protein name e.g. on http://www.ded.uni-stuttgart.de/cgi-bin/DEDTAX/index.pl?page=hfam&id=61 clicking the protein name polyhydroxyalkanoate depolymerase, intracellular leads to http://www.ded.uni-stuttgart.de/cgi-bin/DEDTAX/index.pl?page=prot&id=129 Example: "Sequences 1" means: the three entries given in the column "NCBI accession code" at http://www.ded.uni-stuttgart.de/cgi-bin/DEDTAX/index.pl?page=hfam&id=61 are identical. |
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This database is maintained by Jürgen Pleiss. Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany The database was developed by Michael Knoll, Thomas Hamm. The dynamic web interface was coded and constructed by Florian Wagner.
M.Fischer, Q.K.Thai, M.Grieb, J.Pleiss 2006. DWARF - a data warehouse system for analyzing protein families. BMC Bioinformatics 7: 495-495 M.Knoll, T.Hamm, F.Wagner, V.Martinez, J.Pleiss 2009. The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases BMC Bioinformatics 10: 89 |