Inter-Modular Linkers

Within Bacterial NRP Biosynthetic Pathways


MIBiG Linkers

Number of MIBiG NRP Biosynthetic Gene Clusters 408
Number of Inter-Modular Linkers 586, 902*
Number of Unique Inter-Modular Linkers 556, 859*
Number of unique Adenylation Domain Substrate Pairs 182, 224*
selectivity
Fig1. MIBiG IMLs length distribution.

NCBI Linkers

Number of NCBI RefSeq Bacterial Genomes 39232
Number of NRP Biosynthetic Gene Clusters 51810
Number of Inter-Modular Linkers 17445, 38902*
Number of Unique Inter-Modular Linkers 8143, 12905*
Number of Unique Adenylation Domain Substrate Pairs 352, 398*
selectivity
Fig2. NCBI IMLs length distribution.


* Our tool processes non-ribosomal peptide biosynthetic gene clusters after being identified using the AntiSMASH tool. In the process of scanning and identifying NRP BGCs, AntiSMASH uses three algorithms to predict the specificity of the NRPS adenylation domain (Minowa .et.al, Roettig, M et.al, Stachelhaus et.al). If all three algorithms agree on the same predicted substrate then it will be used as the substrate of choice by AntiSMASH, otherwise, AntiSMASH uses the term 'nrp' for all unidentified NRPS substrates. Hence, some IMLs may look as follows (e.g Ala-linker-Ser), if both substrates are well identified, others will look like (nrp-linker-Ser) or even sometimes (nrp-linker-nrp), with one or two unidentified substrates. Thus under each Data (MIBiG and NCBI), there are two tables, one where all linkers are included (larger data) and the other one lacks all "nrp containing linkers" (smaller data).


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