Fig. 3

(a) Apicidin (APS) subnetwork generated from feature-based molecular network analysis of APS-like signals using GNPS (release_23) [47], visualized in cytoscape. Nodes represent distinct features (peaks) with unique retention times and m/z, and are either connected by cosine similarity score (threshold = 0.7, blue line) or adduct identity match generated using IIN module [48] in MZMine2 [49] (red line). Nodes are coloured based on ion identity, and node outlines are coloured by annotation method: red annotations derive from top hit from in silico MS² structural prediction using Sirius / CSI Finger-ID [50], green annotations derive from spectral matching to GNPS database, grey outlines represent spectra whose adducts were annotated by manual inspection of raw data. Potentially novel APS-like signals are annotated with exact masses (< 5 ppm). Node size represents relative size of signal calculated by precursor intensity (sum of all spectra in MS² scan). (b) Mirror plot comparing MS² spectra of predicted APS and APS-G signals. Substructures are coloured based on association with m/z motifs: blue m/z occur in nearly all APS-associated mass feature MS² scans, purple fragments are detected in most spectra associated with tryptophan-bearing apicidins, red fragments correspond to predicted phenylalanine moiety-associated fragments and appear only in putative APS-G spectra. For detailed information see Additional file 11. (c) Synteny visualization of FpAPS gene cluster residing on putative accessory chromosome of Fp157 as compared to homologous cluster in F. incarnatum KCTC 16676 (Genbank accession GQ331953) [51]. Blue arrows are predicted genes, red squares are predicted transposable elements. Predicted APS gene functions: 1, NRPS; 2, transcription factor; 3, pyrroline reductase; 4, aminotransferase; 5, fatty acid synthase; 6, O-methyl transferase; 7, cytochrome P450; 8, cytochrome P450; 9, FAD-dependent oxidase; 10, short-chain reductase; 11, efflux pump; 12, reductase