1.TOP
The top page of the Autophagy database provides a brief introduction on autophagy and figures of autophagic processes.
2.Overview
This page gives an explanation of the database, the number of autophagy-related proteins in each type (see under 5 below for the definitions of the types), and a list of recent reviews.
3.New Refs
From this page, the user can get information on recently published papers on autophagy.
The first page shows articles published (i.e., registered at PubMed) on the previous day, while a click on "Papers published on the previous day" moves to a page showing a list of previously published ones. For each publication, the title (with a link to PubMed), author(s), journal, PubMed ID, abstract, and the average evaluation are displayed. All are invited to evaluate listed articles.
The first page shows articles published (i.e., registered at PubMed) on the previous day, while a click on "Papers published on the previous day" moves to a page showing a list of previously published ones. For each publication, the title (with a link to PubMed), author(s), journal, PubMed ID, abstract, and the average evaluation are displayed. All are invited to evaluate listed articles.
4.Protein List
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.
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.
5.Homologs
A table of orthologs and other homologs in the user-specified species is given.
Protein names in black are functional homologs taken from the literature, those in blue are orthologs so identified by a research article, while those in green are other homologs identified by our homology search.
Our homolog search was made among the protein sequences of the listed organisms in the GTOP database with the functional homologs and orthologs as queries.
We ran PSI-BLAST with three iterations setting the E-value at 0.1, and selected the resultant homologs with the E-value less than or equal to 1e-100.
Homologs without annotations are shown in grey.
The symbols are linked to detailed information.
Protein names in black are functional homologs taken from the literature, those in blue are orthologs so identified by a research article, while those in green are other homologs identified by our homology search.
Our homolog search was made among the protein sequences of the listed organisms in the GTOP database with the functional homologs and orthologs as queries.
We ran PSI-BLAST with three iterations setting the E-value at 0.1, and selected the resultant homologs with the E-value less than or equal to 1e-100.
Homologs without annotations are shown in grey.
The symbols are linked to detailed information.
6.Keyword Search
The user can specify keyword(s) to search for autophagy-related proteins.
If multiple keywords are entered, an AND search is conducted.A search at the default settings retrieves entries with the keywords that matched partially, while an exact match search limits the hits to those exactly matched the keywords. For example, a default search with the keyword BECN1 results in entries with BECN1L1 as well as BECN1, while an exact search with the same keyword displays entries containing BECN1 only.
If multiple keywords are entered, an AND search is conducted.A search at the default settings retrieves entries with the keywords that matched partially, while an exact match search limits the hits to those exactly matched the keywords. For example, a default search with the keyword BECN1 results in entries with BECN1L1 as well as BECN1, while an exact search with the same keyword displays entries containing BECN1 only.
7.Homology Search
The user can enter a protein sequence in one-letter notation to initiate a BLASTP search against all the autophagy-related proteins in the database, with the e-value cutoff set at 1e-10 and the SEG filter on.The ‘Filter by organism’ button allows the user to restrict homology search to the user-specified organism(s).
8.Original analyses
A list of proteins in a user-specified species that probably bind phosphatidylinositol 3-phosphate [PI3P] is displayed.
All the proteins with the FYVE domain are presented.
From the proteins with the PX domain, on the other hand, only those predicted to bind PI3P with high specificity are shown.
All the proteins with the FYVE domain are presented.
From the proteins with the PX domain, on the other hand, only those predicted to bind PI3P with high specificity are shown.
Proteins with the PX domain were judged to specifically bind PI3P if their sequences are more similar to proteins in the positive set (consisting of proteins whose UniProt accession numbers are
O60749, O60493, O95219, Q9UNH6, Q9Y5X2, Q9Y5X1, Q9Y5X0, Q9Y5W9, Q9UMY4, Q9Y5W7, Q9NRS6, P57768, Q15036, Q96RF0, Q92543, Q7Z614, Q969T3, Q96L94, Q9BQJ8, Q9Y343, Q9H3E2, O14559, Q96D79, Q8TEQ0, Q5VWJ9, Q8N9S9, Q8WV41, Q15080, Q53T59, Q6ZN39, Q9Y2I1, Q01846, Q08826, P32912 and P38815
) than those in the negative set (comprised of proteins with UniProt accession numbers
Q9UDV9, Q13596, Q13393, O14939, O00443, O00750, O75747, Q8NFA2 and P29366
).
Results of other original analyses will be added in the future.
9.Help
Help! Providing a description here will be a futile, self-referential act.
10.TPRP
A link is provided to the homepage of the Targeted Proteins Research Program, under which this database was built.
General Remarks
The protein and gene names, GO [Gene Ontology] annotations, references used in this database were taken from Entrez Gene of the NCBI, the UniProt knowledgebase, and the GTOP database of the National Institute of Genetics, Mishima, Japan.
As each screen has been optimized for Firefox 3 display, some pages may not appear properly with the use of other browsers such as the Internet Explorer.
We apologize for any inconvenience and promise to remedy defects in the future.
Whenever you research using this database produces publishable results, your citation of the autophagy database paper will be greatly appreciated: Homma, K., Suzuki, K., and Sugawara, H. 2011, Nucleic Acids Res. 39(Database issue): D986-990.
As each screen has been optimized for Firefox 3 display, some pages may not appear properly with the use of other browsers such as the Internet Explorer.
We apologize for any inconvenience and promise to remedy defects in the future.
Whenever you research using this database produces publishable results, your citation of the autophagy database paper will be greatly appreciated: Homma, K., Suzuki, K., and Sugawara, H. 2011, Nucleic Acids Res. 39(Database issue): D986-990.