Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements
Fig 2
C domain subtype analysis and representative NRPS organizations in bacteria and fungi.
A. Maximum-likelihood phylogenetic tree of the condensation domain superfamily. Subtype classification and sequences are described in the main text and the Method. Different subtypes are indicated by colors, with subtypes exclusive to fungi marked by underlines, and subtypes found predominantly in bacteria marked by asterisks. This tree is rooted, taking papA and WES as outgroups [65] (black shading). L-clade and D-clade are indicated by blue and red shading, respectively. B. Domains adjacent to different C domain subtypes in bacteria and fungi. C. The statistics of subtype distribution in 83,489 bacterial C domains and 34,269 fungal C domains. C domains with HMM scores above the empirical threshold of 200 were annotated by their predictions, otherwise marked as “Low-confidence”. D. The sequence logo for the C3 or E2 motif from different C domain subtypes and the T1 or ACP1 motif adjacent to each subtype. Sequences from bacteria were marked by red, while sequences from fungi were marked by blue. E. Frequent NRPS organizations with known representative examples in bacteria and fungi.