highest similarity values will be valuable for our purpose in the
result page. According to the observed similarity values:(a) If the identity value between the first homolog(s) in the results
list andPQis 100% and the protein lengths are the same, the
user can directly check the UniProt page of this protein
(by clicking on the UniProt accession number of the
corresponding protein) to observe the experimental and
computational annotations, sincePQand the resulting homo-
log will possess the exact same functional properties. If the
highest ranked homolog is a UniProtKB/Swiss-Prot database
protein (marked by yellow document symbol at the “status”
column in the BLAST results table), the functional informa-
tion in UniProt will be richer and more reliable, since the
protein entries in UniProtKB/Swiss-Prot are reviewed with
manual curation. At this point, the user is advised to continue
from Subheading2.2.
(b) If the identity value is between 90 and 100% (together with a
very similar protein length), it will still be sufficient to transfer
generic whole-sequence and region based annotations from the
resulting protein to the query protein. The user can investigate
the UniProt protein page of the homologous protein(s) for
the generic functional annotations. However, active sites may
differ between the query and resulting sequences; as a result,Fig. 1The general flowchart to perform phylogenetic analysis to predict protein functional sites. The input is a
query sequence and the output is the active site information which are represented with parallelograms. The
processes and decisions involved in each approach is highlighted with a rectangular shade. Universal ET and
ConSurf are highlighted in light green, Trace Suite II in orange, and PROFisis in light blue. The common
processes and decisions across all these methods are shown in the intersection of the shaded rectangles
54 Heval Atas et al.