Enter a query protein or nucleotide sequence in raw format (no fasta header, use one-letter codes) or a UniProt Knowledgebase (Swiss-Prot or TrEMBL) accession number.
UniProt (Universal Protein Resource) is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
The UniProt Knowledgebase consists of two sections: Swiss-Prot, containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis, and TrEMBL, a section with computationally analyzed records that await full manual annotation. Updated monthly and includes splice variants.
Since UniProtKB contains a huge number of sequences, it may be useful to restrict the search to a certain taxonomy division or to curated sequences (i.e. Swiss-Prot), only.
All nucleotide databases are subdivided into taxonomic sections, selectable from the Taxonomic groups drop-down list, below.
The matrix assigns a probability score for each position in an alignment. The BLOSUM matrix assigns a probability score for each position in an alignment that is based on the frequency with which that substitution is known to occur among consensus blocks within related proteins.
BLOSUM62 is among the best of the available matrices for detecting weak protein similarities. The PAM set of matrices is also available.
If the "Auto-select" option is selected (default), the matrix will be selected depending on the query sequence length, based on the following (empirically constructed) table:
Low-complexity regions (e.g. stretches of cysteine in CSP_DROME (Q03751), hydrophobic regions in membrane proteins) tend to produce spurious, insignificant matches with sequences in the database which have the same kind of low-complexity regions, but are unrelated biologically.
If this option is checked, the query sequence will be run through the program SEG, and all amino acids in low-complexity regions will be replaced by X's which will appear in the alignment. The masked regions will also be visible as slashed regions in the PaintBlast image.