Extended Data Fig. 9: Sequence similarity network (SSN) and genome neighborhood network (GNN) of NegJ. | Nature Chemical Biology

Extended Data Fig. 9: Sequence similarity network (SSN) and genome neighborhood network (GNN) of NegJ.

From: A heme-dependent enzyme forms the hydrazine in the antibiotic negamycin

Extended Data Fig. 9

The networks were visualized and analyzed using Cytoscape 3.10.3. a) SSN of NegJ was constructed using the EFI-EST online tool (https://efi.igb.illinois.edu/efi-est)56. The BLAST query e-value and the alignment score threshold for generating the SSN were set to 5 and 100 respectively. Three NegJ homologs for genome mining (Extended Data Fig. 10) were indicated with arrows. b) GNN was constructed based on SSN of NegJ and created by EFI-GNT web tool (https://efi.igb.illinois.edu/efi-gnt)57. The values for Neighborhood Size and Minimal Co-occurrence Percentage Lower Limit were 10 and 20 respectively. Three GNN clusters (No. 1, 3, and 6) with SSN cluster-hub nodes with Pfam family spoke nodes were randomly selected for genome mining of potential N–N-bond-containing natural products (see Extended Data Fig. 10). The SSN cluster-hub nodes were colored.

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