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Tool: Blast Protein

Blast Protein runs a protein sequence similarity search using a BLAST web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI). See also: matchmaker

The Blast Protein tool can be opened from the Sequence section of the Tools menu and manipulated like other panels (more...). It is also implemented as the blastprotein command.

Search Parameters

Clicking the Blast button initiates the search.

BLAST Protein Results

When results are returned, the hits are listed in a table below the search parameters in the Blast Protein window. The Blast Protein tool including search results (but not window size or location) is saved in ChimeraX sessions.

A text-search box allows finding hits that contain terms of interest. Pull-down menus to the right of the search box allow adjusting the number of hits shown at a time and which columns of information are shown in the table. Clicking a column header sorts by the values in that column.

Some columns are available for NR sequences regardless of whether they are in the PDB subset:

Additional columns of information are available for PDB sequences:


Pseudo-multiple alignment. The pseudo-multiple alignment from BLAST is not a true multiple alignment, but a consolidation of the pairwise alignments of individual hits to the query. This output corresponds to the BLAST formatting option (alignment view) “flat query-anchored with letters for identities.”

Basic Local Alignment Search Tool (BLAST). The BLAST software is provided by the NCBI and described in:

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.

Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. J Mol Biol. 1990 Oct 5;215(3):403-10.

UCSF Resource for Biocomputing, Visualization, and Informatics / December 2019