AspGD Help: PDB Homolog Page

Contents

• Page Description and Navigation
• Organization of the Results Table
  • PDB protein structure(s) homologous to query protein
  • PDB Homolog Source
  • Protein Alignment: query vs. PDB Homolog
  • External Links
• Related AspGD Help Documents

Page Description and Navigation

The PDB Homolog Page presents information for proteins of known structure homologous to the specified AspGD protein, identified in a BLASTP search of The RCSB Protein Databank (PDB). All BLAST hits with a P-value less than 1E-5 are displayed. The search results and associated informational links are displayed in a large table.

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.

Organization of the Results Table

PDB protein structure(s) homologous to query protein

This column summarizes the homologous PDB structures in two sub-columns:

• PDB identifier and description.
• Links to summary (PDB_Info) and structure (PDB_Structure) for the PDB homolog. Clicking on the latter initiates an interactive viewing session at PDB's site using the Jmol structure viewer.

PDB Homolog Source

This column identifies the source organism(s) for the PDB homolog.

Protein Alignment: query vs. PDB Homolog

This column summarizes the alignment between the query protein and PDB homolog in four sub-columns:

• P-Value. The significance score of the BLAST hit.
• % Identical. The percent of aligned residues that are identical between the query and PDB homolog.
• % Similar. The percent of aligned residues that are physicochemically similar between the query and PDB homolog.
• Alignment. Link to view the pairwise alignment between the query and PDB homolog.

External Links

This column provides links to external resources providing additional information on the 3D-structure of the homolog. The resources are:

• CATH (Class, Architecture, Topology, Homologous superfamily site)
• MMDB (Molecular Modeling Database at NCBI)
• SCOP (Structural Classification of Proteins site)

Related AspGD Help Documents

• Locus Summary Help Page
• Protein Information Help Page
• Protein Domain/Motif Help Page
• Physicochemical Properties Help Page
• PDB Alignment Help Page

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