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.