Schema for PDB Structures - Protein Data Bank (PDB) Sequence Matches
  Database: wuhCor1    Primary Table: pdb Data last updated: 2020-12-03
Big Bed File: /gbdb/wuhCor1/bbi/pdb.bb
Item Count: 819
Format description: Browser Extensible Data
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart19617Start position in chromosome
chromEnd20655End position in chromosome
name2h85Name of item.
score764Score (0-1000)
strand++ or - for strand
thickStart19617Start of where display should be thick (start codon)
thickEnd20655End of where display should be thick (stop codon)
reserved0Used as itemRgb as of 2004-11-22
blockCount1Number of blocks
blockSizes1038,Comma separated list of block sizes
chromStarts0,Start positions relative to chromStart

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
NC_045512v219617206552h85764+1961720655011038,0,
NC_045512v219620206587kf41000+1962020658011038,0,
NC_045512v219620206587keh1000+1962020658011038,0,
NC_045512v219620206587keg1000+1962020658011038,0,
NC_045512v219620206587k9p1000+1962020658011038,0,
NC_045512v219620206587k1o1000+1962020658011038,0,
NC_045512v219620206587k1l1000+1962020658011038,0,
NC_045512v219620206586xdh1000+1962020658011038,0,
NC_045512v219620206586x4i1000+1962020658011038,0,
NC_045512v219620206586x1b1000+1962020658011038,0,

PDB Structures (pdb) Track Description
 

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