Structural Analyses of Xanthomonadaceae FimT3

FimT3 modeling was performed using the Phyre2 web portal [42 (link)] and visualized via PyMOL version 2.4.0 (Schrödinger, LLC). The surface electrostatics of FimT3 was predicted using the APBS Electrostatics plugin from PyMOL. Sequence alignments of FimT3 with ComP, VC0858 and FimT from A. baylyi and L. pneumophila were performed by retrieving the respective sequences from NCBI, aligning through the T-Coffee Multiple Sequence Alignment Server [21 (link)] and visualizing using the BoxShade webserver (https://embnet.vital-it.ch/software/BOX_form.html). For FimT3 analyses within the Xanthomonadaceae family, DNA sequences of different FimT homologs from Xylella, Xanthomonas, Lysobacter and Stenotrophomonas were used as query for screening genomes of Xanthomonadaceae using CRB-BLAST [4 (link)] with default settings. Nucleotide sequences for the CRB-BLAST hits were then retrieved and aligned using MAFFT [41 (link)], followed by RAxML version 8.0.24 [73 (link)] to build a phylogenetic tree, which was visualized using Fig Tree version 1.4.4 (http://tree.bio.ed.ac.uk/). FimT3-encoding sequences were retrieved from the phylogenetic tree using the TREE2FASTA Perl script [63 (link)], translated into amino acid sequences and aligned using Clustal Omega (Clustal 12.1) to determine percentage of identical amino acids [48 (link)]. The visualization of the alignment of representative FimT3 sequences among X. fastidiosa strains and representative bacterial species belonging to the Xanthomonadaceae family was performed using the BoxShade webserver. The FimT3 GRxR motif sequence logo was generated using the WebLogo webserver [16 (link)].