Error propagation

While annotating an orotidine 5′-phosphate decarboxylase from Thermotoga maritima (PDB id: 1vqt), I was surprised to come across an apparent paralog (PDB id: 2yyu) as Pfam showed a single gene for this enzyme in T. maritima. On closer inspection, it turned out the protein was actually an ortholog from Geobacillus kaustophilus but wrongly annotated in the PDB and propagated onto the relevant TOPSAN page. I checked to see how far the error had reached. A quick search showed it to be present in the PDB, PDBsum, PSI-KB, Proteopedia, SSM, PISA and NCBI. All programs relying on a sequence analysis (BLAST, STRING, COGnitor) correctly identified G. kaustophilus as the species.

Error propagation in the automatic annotation of proteins has been previously described (Valencia 2005). I have notified the PDB of the problem. It will be interesting to see the time it takes to correct the error and whether or not the correction back-propagates.

One Response to Error propagation

  1. Andreas says:

    Looks like the PDB file for 2yyu got updated on february 3rd.


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