Protein Feature View: Overview

The Protein Feature View provides a graphical summary of a full-length protein sequence from UniProtKB and how it relates to PDB entries. It also loads annotations from external databases such as Pfam, Phosphosite, domain annotations from SCOP and SCOPe, or regions for which homology models are available from the Protein Model Portal. There are also tracks of annotations available that visualize predicted regions of protein disorder (computed with JRONN) and hydrophobic regions, as computed using a sliding window approach. Predicted disordered and hydrophobic regions are in red, ordered and hydrophilic regions are in blue. For human proteins, that can be mapped to the human genome, a track describes the projection of the protein structure onto the genome.

By default representative PDB entries are being displayed that give an overview for which regions of the UniProtKB sequence PDB entries are available. The view can be expanded to show all available PDB entries (which can be many in some cases) by pressing the "+" icon or by selecting the "Extended" menu option.

View An example Protein Feature View.

 

Protein Feature Header Section

Learn more about the protein

The header section of the Protein Feature View shows information about the Function, Catalytic Activity and subunit structure (if available) from UniProtKB. It also has an option to select Protein Feature Views from related organisms with the same gene name.


Protein Feature View for Ribulose bisphosphate carboxylase large chain (P23755). Other organisms with the same gene name can be selected from the menu (the number of available PDB structures is shown in gray circles).

The Action button has an option to map sequence motifs in the Protein Feature View as shown below.


Active site sequence motif Gx[DN]FxKxDE (Ribulose bisphosphate carboxylase large chain active site) mapped onto protein feature view (red box around mapped region). Note, X matches any amino acid and [DN] matches either D or N. See Sequence Motif help page for details

Legend

What do all the tracks on the Protein Feature View represent?
Data origin/color codes
The vertical color bar on the left side indicates data provenance.
Data in green originates from UniProtKB  
Data in yellow originates from Pfam  , by interacting with the HMMER3 web site  
Data in purple originates from Phosphosite  .
Data in orange originates from the SCOP   (version 1.75) and SCOPe   (version 2.04) classifications.
Data in grey has been calculated using BioJava  . Protein disorder predictions are based on JRONN (Troshin, P. and Barton, G. J. unpublished), a Java implementation of RONN  
Hydropathy has been calculated using a sliding window of 15 residues and summing up scores from standard hydrophobicity tables.
Data in lilac represent the genomic exon structure projected onto the UniProt sequence.
Data in blue originates from PDB
Data in red indicates combined ranges of Homology Models from SBKB   and the Protein Model Portal