Link to Model organisms Autophagy Database
Classification (of LC3 interacting Region containing proteins)
Through this tab users can search through Canonical LIR motifs present in Viruses either through Legacy classification or by ICTV(International Committee on Taxonomy of Viruses) classification. Upon clicking for the information on a particular species, the users could see the predicted list of LIR containing proteins (LIRCPs) arranged alphabetically. For each LIRCP, LIR motif (sequence) along with its start and end positions, PSSM score, protein description and the species information is made available.
PSSM Score: Position Specific Scoring Matrix (PSSM) is a commonly used representation of motifs or patterns in biological sequences. The matrix is derived from a set of aligned sequences that are thought to be functionally related. Values in the matrix represent a log-odds score for the presence of a residue in the respective position of the alignment. While negative scores are assigned to rarely observed in the alignment and high positive scores are assigned to most frequent residues. (Further information).
BLAST(Basic Local Alignment Search Tool)
BLAST option helps Users to search against LIRCPs of viruses. PSI-BLAST with phi-pattern option is used for this.
a) Only one sequence in FASTA format can be searched at a time. Multiple sequences are not allowed.
b) Search against whole proteomes of viruses described in the website is available. This includes both Swiss-Prot and TrEMBL sequences.
c) Default e-value is set to 0.01 (When e-value textbox is left blank). If the user provides e-value greater than 0.1, it is limited to 0.1 to avoid longer search times.
d) PSI-BLAST whi Phi-Pattern is used to search against the proteomes of viruses.
Any combination in the LIR pattern [ADEFGLPRSK][DEGMSTV][FWY][DEILQTV][ADEFHIKLMPSTV][ILV] or WxxL pattern at a given position could appear in the result rather than an exact match with an aminoacid.
For example: a LIR pattern in the query protein sequence KEFEKL can match with a subject in the following way:
Here, in the Subject the first aminoacid 'S' is present within the enclosed first set of braces in the above mentioned LIR pattern where 'K' in the query sequence is present. The second aminoacid 'V' is present in the second set of braces in the LIR pattern where 'E' in the query was present. The same is matched for other residues as well.
The position of the pattern is mentioned in the query sequence submitted for BLAST search and in the matches the red colored asteriks (******) indicate the Query pattern. If multiple patterns are present, then all of their positions are also mentioned.
e) Clicking on the bitscore link takes the User to the respective alignment in the result.
Search tab has options to search the database using a keyword that which could be either Protein description (or) Uniprot ID (or) Virus taxons such as Order, Family, Subfamily, Genus or Species name.
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