For the species specified, a list of autophagy-related proteins is given. The user can also choose the display items by checking the boxes.
A link from the SYMBOL column provides detailed information on the protein (with a copy button that saves the sequence on the clipboard), while other links give information from the original databases.
The CASA db link gives the user an opportunity to conduct a keyword search in the CASA database, which provides information on all existing protein sequences. The PDB column shows PDB IDs of proteins whose 3D structures have been determined, registered, and made publicly available.
The TPRP logo is placed to the left if the structure was determined within the Targeted Proteins Research Program. The protein localization column represents the subcellular localization predicted by WoLF PSORT.
Protein-protein interaction information
-If the user is examining the human protein list: A click on the PPI button displays a new sub-window that shows a list of human proteins that interact with each protein. You can search for the orthologs of each interacting protein (‘interactant’) in other species by selecting an organism and then press the BLAST search button. The results of a BLASTP search with SEG filter on and the cut-off e-value set at 1e-10 will appear in a new sub-window.
-If the user is examining a non-human protein list: A click on the PPI button displays a new sub-window that shows a list of human orthologs and human interactant that interact with each human ortholog. You can search for the orthologs of each interactant in other species by selecting an organism and then press the BLAST search button. The results of a BLASTP search with SEG filter on and the cut-off e-value set at 1e-10 will appear in a new sub-window.
-Information on intrinsically structured regions and structural domains. The “Predicted disordered regions” column indicates predicted intrinsically structured regions. The prediction was made by the DICHOT system that divides the entire protein sequences into intrinsically structured regions and structural domains with an accuracy exceeding 97% (Fukuchi et al. 2009, BMC Struct Biol. 9:26). A click on the “Show DICHOT result” button will display details of DICHOT analysis. Structural domains having homology with existing sequences whose structures have been registered in the PDB database are regarded as known structural domains, while the rest are considered as novel (‘cryptic’) structural domains.