The PDB Alignment Page displays the alignment between the AspGD protein and a homolog of known structure identified in a BLASTP search of The RCSB Protein Databank (PDB). Additional information about the homolog and its structure is presented at the bottom of the page.
The top of the page provides a site-wide quick search, links to the major AspGD informational resources, and a bar with links to popular tools, such as a local BLAST search.
The Page is divided into several sections:
This section gives summary statistics for the alignment between the query protein and PDB homolog, including:
An overview showing the protein regions aligned between the query (numeric scale and blue bar) and the PDB homolog (red bar).
The Smith-Waterman local pairwise sequence alignment between the query (upper sequence) and the PDB homolog (lower sequence). The residues shaded yellow are identical between the two sequences, and those shaded green are physicochemically similar. The identifiers to the left of the sequence link to the AspGD Locus Summary page of the query and to PDB's summary page for the homolog.
This section gives details about the PDB homolog structure, including:
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AspGD Copyright © 2008-2013 The Board of Trustees, Leland Stanford Junior University, and Broad Institute.
Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
To cite AspGD, please use the following reference: Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2013). The Aspergillus Genome Database (AspGD): multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 42(Database issue):D705-D710; see How to cite AspGD.