Manual of the HTP server

Entry Viewer Panel

Entry Viewer

This panel is for summarize the information collected and/or predicted for each protein in the human proteome. The screenshot of an example Entry Viewer Panel is in the right side, the main areas are the following:

  1. The UniProt name of the protein.
  2. Navigation panel. In the middle there is the HTP code of the given entry. The meanings of the components from left to right are
    • Link to the first entry in the current search result list
    • Link to the previous entry in the current result list
    • Label containing HTP code of the given entry
    • Link to the next entry in the current result list
    • Link to the last entry in the current result list
  3. PDB cross references of the given entry. By clicking the codes, user can select each PDB entry for visualization.

    Note, this area is visible for entries of which evidence type is 3D.

  4. Main area. The content of this panel depends on the selected tab, which are the following:
    • Summary tab
      It contains basic informations about the entry, such as gene name, cross references, reliability of the predicted topology, number of transmembrane segments, and the download buttons for getting the xml file of the given entry.
    • 1D tab
      It contains the color-coded amino acid sequence of the given human transmembrane protein based on the determined or predicted topology (red: inside/cytosolic; yellow: membrane; orange: re-entrant loop; blue: outside/extra-cytosolic region).
    • 2D tab
      It contains a graphical representation of the determined and predicted topology of the given entry. The graph consists of three parts: the results of the final HTP prediction, the results of the various topology and topography prediction methods and the collected constraints aligned to the amino acid sequence of the given entry.
      The x-axes on the graph are the sequence, lower red lines represent inside/cytosolic regions, yellow rectangles code transmembrane regions, orange rectangles show membrane re-entrant loops and upper blue lines represent outside/extra-cytosolic regions. Thin gray lines indicate regions, where the topology information is not predicted/determined.
    • 3D tab
      This tab is selectable for entries of which have the evidence level 3D. It contains the 3D representation of the structure of the given entry positioned in the membrane bilayer. For the 3D representation, the Open Astex Viewer is used. The membrane orientation is determined by the TMDET algorithm. Data are taken from PDBTM database.
    • XML
      This tab shows the raw xml description of the given entry. The XSD schema definition for the xml files can be found here.