Fig. 2: Gene neighborhoods analyses based on sequence similarity networks (SSNs) of DndC and SspD proteins essential for PT synthesis.
From: Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome
Sequence similarity networks (SSN) analysis was performed for the 3120 closest homologues of DndC (A) and 2132 homologues of SspD (B) in the UniProt database. Each node (circle) in the network represents one DndC or SspD protein. An edge is drawn between two nodes that have a BLAST E-value cutoff of ≤10−100 (alignment score of 100) in the DndC SSN or 10−50 (alignment score of 50) in the SspD SSN. Some nodes are filled with colors according to their genome neighborhood structure, with a representative species shown and indicated in the SSNs with a two-letter label. The node outlines are colored red when dndD is present in the genome neighborhood of dndC, and similarly for sspD when sspBC are present in the neighborhood. For better visualization, single nodes and clusters with only a few nodes were hidden. HEPN higher eukaryotes and prokaryotes nucleotide-binding, MTase methyltransferase, NTPase nucleoside triphosphatase, NTP transf, nucleotidyltransferase, top topoisomerase.
