Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
Figure 3
PSI-BLAST input panel (top) and PSI-BLAST output iteration (bottom).
(Top) Default parameters are used. The fasta sequence of query protein with UniProt accession O67940 from Aquifex aeolicus is blasted against NCBI's nr database. (Bottom) The query protein O67940_ AQUAE hits several structures (tagged with S in a red box). Only two of the non-redundant structures with PDB-ids 2Q6O and 1RQP (marked by a pink box) are functionally characterized with e-values 3e-20 and 3e-17 and percent identities of 32% and 26%, respectively. (The Expect value (E) or an e-value is a parameter that describes the number of hits one can “expect” to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases.)