PDB Structures Track Settings
 
Protein Data Bank (PDB) Sequence Matches   (All Genes and Gene Predictions tracks)

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Data last updated: 2020-10-03 06:37:38

Description

This track shows alignments of sequences with known protein structures in the Protein Data Bank (PDB). The PDB protein sequence has to match the genome over at least 80% of its length, so somewhat similar sequences, e.g. from the SARS 2003 outbreak, are also shown.

Display Conventions and Configuration

Genomic locations of PDB matches are labeled with the accession number. A click on them shows a standard feature detail page with the PDB page integrated into it. The protein structure is shown on the PDB page.

Methods

PDB sequences were downloaded from the PDB website and aligned with BLAT. Only alignments with a minimum identity of 80% that span at least 80% of the query sequence were kept.

References

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. PMID: 10592235; PMC: PMC102472