Inter-Modular Linkers

Within Bacterial NRP Biosynthetic Pathways

Tutorials

Everyday, new bacteria are being sequenced and added to the genomic database. Some of them might have novel and unique inter-modular linkers (IMLs). Thus NRPS Parser will help users to identify and extract all new IMLs and in turn this will help us expanding and updating our IMLs database.

IMLs Database

IMLs database consist of two Libraries:

MIBiG IMLs library: which contains 586 inter-modular linkers retrieved from 408 non-ribosomal peptide BGCs.
NCBI IMLs library: which contains 17445 inter-modular linkers retrieved from 51810 non-ribosomal peptide BGCs.

Both libraries share the following columns:

A1: The adenylation substrate of module one.
Linker: The inter-modular linker between two successive modules
A2: The adenylation substrate of module two
Length: The length of the linker
Organism_name: The name of the organism the BGC belongs to.

Both libraries are searchable and the data can be sorted in multiple ways. Moreover, if users are interested in a particular section of the table, they get to export that section as a CSV file.

NRPS-Linker Workflow:

Download all known NRP biosynthetic gene clusters from the MIBiG repository.
Download the whole NCBI RefSeq Bacterial genomes.^{As of Jan. 2017}
Each database was scanned for NRP gene clusters using the AntiSMASH tool, that allows rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
Analyze all extracted IMLs for selectivity, sgnificance, and determine their level of conservation within and across species.
Run NRPS Parser on all identified NRP gene clusters, extract all possible IMLs and update our IMLs database