5‐Online‐version
Online platform can be visited in NRPS motif Finder.
User need register an account (It's very simple and no restriction). The history of results can be visited in the account.
Waring: The headers of input fasta file must be different!!!
Demonstration on the result panel of the NRPS Motif Finder
The NRPS Motif Finder result panel provides an interactive interface. The whole result could be navigated by scrolling the page, and details about motif and intermotif could be viewed by clicking the corresponding components. Especially, the predicted subtype and confidence score are displayed for C domains. The general statistics about the NRPS architecture are displayed on the right for comparison. The results could be downloaded in table format.
Take test.fasta as example.
The csv output is NRPSMotifFinder__1710245201012.csv.
Each row is one motif or intermotif of C/A/T/E/TE domain.
Column1 seq:the Header in the input seq.
Column2 S_code: Stachelhaus code proposed by Torsten Stachelhaus in 1999.
Column2 domain: The domain where motif or intermotif from. It can be Condensation, AMP-binding, PP-binding, Epimerization and Thioesterase.
Column3 start: The start of motif or intermotif in the input seq.
Column4 end: The end of motif or intermotif in the input seq.
Column5 motif_name: For A domain, it can be 1-10, Aalpha and G motif. For C and E domain, it's 1-7. For T domain, it can be Talpha and 1. For intermotif, there will be "inter".
Column6 motif_seq: For motif, there is motif sequence. For intermotif, there is empty.
Column7 inter_motif_seq: For motif, there is empty. For intermotif, there is intermotif sequence.
Colum8 C_subtype: For C domain, there is subtype prediction. Details for C domain subtype see here. For other domain, there is -.
Column9 C_score: For C domain, there is the HMM profile alignment score for predicted C subtype. For other domain, there is -.
Column10 loop_group: For C domain, there is loop group. There are 5 loop groups. For other domain, there is empty.
Column11 loop_length: For C domain, there is length of 5 loops:[A3-A4),[A4,S4),[S4,S6),[S6,A5),[A5,G). [ means inclusion, ) mean exclusion. [A3-A4) means the length includes A3 but not A4. For other domain, there is empty.
Column12 loop_seq: For C domain, there is sequence of 5 loops. For other domain, there is empty.
Loop length and loop group are proposed in our paper. And we found loop group is related with A domain substrate specificity.