Sequence (BLAST, PSI-BLAST, FASTA)
Searches protein and nucleic acid sequences using the BLAST or FASTA method. Both methods find similar protein or nucleic acid chains in the PDB. PSI-BLAST is used to find more distantly related sequences.
Sequences can be searched in two ways:
- By PDB ID and Chain ID. Type in a PDB ID in the Structure ID text box and select a Chain ID from the pull-down menu. This is useful to find all sequences that are similar to the sequence from the specified chain.
- By sequence. Paste the sequence in the Sequence text box.
Note: sequences must be at least 12 residues long. For shorter sequences try the Sequence Motif Search.
The E value, or Expect value, is a parameter that describes the number of hits one can expect to see just by chance when searching a database of a particular size. For example, an E value of one indicates that a result will contain one sequence with similar score simply by chance. The scoring takes chain length into consideration and therefore shorter sequences can have identical matches with high E value.
The Low Complexity filter masks low complexity regions in a sequence to filter out avoid spurious alignments. Low complexity regions in the sequence are displayed as X in the query sequence.
Sequence Identity Cutoff (%) filter removes the entries of low sequence similarity. The cutoff value is a percentage value between 0 to 100.
BLAST: Sequence searching using NCBI's BLAST (Basic Local Alignment Search Tool) Program , Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215: 403-410 (1990)
PSI-BLAST: Sequence searching to detect distantly related evolutionary relationships using NCBI's PSI-BLAST (Position-Specific Iterated BLAST). http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/psi1.html
FASTA: Sequence search using the program of W.R. Pearson, Pearson, W.R. and Lipman, D.J. Improved tools for biological sequence comparison. PNAS 85: 2444-2448 (1988)