LIR: [WFY]..[LIV] xLIR: [ADEFGLPRSK][DEGMSTV][WFY][DEILQTV][ADEFHIKLMPSTV][ILV] hfAIM1: .[DE][DE][WFY][ADCQEIGNLMFPSTWYV].[LIV] hfAIM2: [DE][DE][ADCQEIGNLMFPSTWYV][WFY][ADCQEIGNLMFPSTWYV].[LIV] hfAIM3: ..[ADCQEIGNLMFPSTWYV][WFY][DE][DE][LIV] hfAIM4: [DE].[DE][WFY][ADCQEIGNLMFPSTWYV].[LIV] hfAIM5: ..[DE][WFY][DE].[LIV]
This is the landing page of LIRcentral, providing a brief introduction.
Two graphs summarize the current content of the database. On wide displays
these graphs are plotted side by side, while on smaller screens (e.g. mobile
phones) they are plotted vertically arranged.
Left/Top: The distribution of experimentally verified LIR-motifs per species. Species names are automatically exctracted from the underlying UniProt entries.
Right/Bottom: The number of instances of different type of LIR-motif entries, as defined by LIRcentral curators based on the literature. See LIR definitions.
The "Search" functionality allows generic keyword-based search across all the fields of the LIRcentral database.
On the search page, users can perform keyword search in any field of the database, such as: UniProt ACC (e.g. O15040), UniProt ID (e.g. TCPR2_HUMAN), LIR motif sequence (e.g. YIAV), xLIR motif sequence (e.g. GDYIAV), any one of the five hfAIM motif sequences (e.g. EDEWEVI), species (e.g. Homo sapiens), protein/gene name (e.g. Tectonin beta-propeller repeat-containing protein 2, CALCOCO), motif type (e.g. LIR), Up-stream (e.g. YLTALDTNGD) and Down-stream (e.g. GSSIGMLYLY). It is worth noting that searches are also executed against synonyms for protein/gene-names, as available in the underlying UniProt records.
Under the search bar, there are additional options for the user:
Note: By clicking the “Search” button without any keywords, all available entries in the database will be retrieved.
To get detailed information on the results returned by a "Search" operation, see Results Table.
The "Browse" functionality allows targeted search in different fields of the LIRcentral database.
First, users need to select a field from the drop down list (e.g. "Species") and then, in the text box on the right, write a term which corresponds to the drop down selection (e.g. Homo sapiens).
Complex queries can be formed by clicking the “Add More” button, enabling the selection of additional field/keyword combinations. By default, additional terms are used with the "OR" Boolean operator. This behaviour can be altered by selecting the appropriate operator from the dropdown selection on the left.
Selecting “AND” will show results that fulfill the first and the second conditions. You can add more rows with more conditions.
To get detailed information on the results returned by a "Browse" operation, see Results Table.
A detailed description of the fields present in the results table is given below:
Each Protein Entry view is organised in three sections.
Important note: LIRcentral curators save the exact UniProt sequence version based on which the LIRcentral annotations are derived. In cases where the current UniProt entry differs, a warning message is displayed in the header section; in those cases, only the header and table sections become available, to avoid confusion. Currently (April 2022), two UniProt entries show such discrepancies and are marked by the LIRcentral database:
The header and table sections are always rendered at the top of the page. The relative position of the graphical panel depends on monitor settings: on wide screens the graphical panel appears next to the table, while on small screens (e.g. tablets) it appears below the table.
Most columns in this table correspond to the columns in the Results table. The only aditional piece of information here, refers to the "Type" of predicted LIR-motifs and is displayed in an additional column (column 6). In this field LIRcentral records the type of regular expression pattern (if any) that matches the particular LIR-motif. Superscripts (if available) in the last columns correspond to comments for this particular protein, displayed below the table. See Definitions for more details.
ProtVista graphical panel
Instances of different types of LIR-motifs are organized in individual "tracks", under "Lir motifs" on the top left of the visual display. Each of them is displayed with a colored box in the respective position under the sequence. Boxes are selectable and display positional and sequence information.
More ProtVista features: