CGD Help: PDB Alignment Page

Contents

Page Description and Navigation
Organization of the PDB Alignment Page

Alignment Details
Alignment Position
Sequence Alignment
Homolog Structure

Related CGD Help Documents

Page Description and Navigation

The PDB Alignment Page displays the alignment between the CGD 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 CGD informational resources, and a bar with links to popular tools, such as a local BLAST search.

Organization of the PDB Alignment Page

The Page is divided into several sections:

Alignment Details
This section gives summary statistics for the alignment between the query protein and PDB homolog, including:
- Query length. The full length, in amino acids, of the query protein.
- Alignment length. The total number of aligned residues between the query protein and homolog.
- 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 Position

An overview showing the protein regions aligned between the query (numeric scale and blue bar) and the PDB homolog (red bar).
Sequence Alignment

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 CGD Locus Summary page of the query and to PDB's summary page for the homolog.
Homolog Structure

This section gives details about the PDB homolog structure, including:
- PDB identifier and description, with a link to the PDB summary page (PDB_Info).
- The source organism for the PDB homolog.
- 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)
- A thumbnail image of the PDB structure. Clicking on the thumbnail initiates an interactive viewing session at PDB's site using the Jmol structure viewer.