Sequence and structure analysis
Sequence similarity was identified using Position-Specific Iterated
BLAST (PSI-BLAST) [12] on the set of “Refseq” dataset, and the
algorithm went through 12 iterations until convergence.
Protein with similar structured we identifies by structure comparison
programs DALI [15] and FATCAT [16] searching the PDB database.
The structure visualization was done with PyMOL [29] and Chimera
[30].
A multiple protein structure alignment was performed on the POSA
(Partial Order Structure Alignment) server [31], which provided a
superimposed PDB file of all studied proteins to view and individual
structurers were visualized using PyMOL.
The FATCAT server was used [16] to calculate pairwise alignments to
obtain RMSD values and database similarity searches.
The clan and the family of the FTT_1539 protein we identified using the
Pfam database of protein family Hidden Markov Models (HMM) [10] and
the local installation of the HMMER [32]. Pfam HMM identified the
SHS2 domain found in the N-terminus of the FTT_1539 protein, and the
Pfam database provided details of the nine other members of the SHS2
clan discussed here, such as GyrI-Like, Tip-alpha, and Dodecin type
proteins.