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NRPSpredictor specifications

Information


Unique identifier OMICS_16625
Name NRPSpredictor
Alternative name Non-Ribosomal Peptide Synthetases predictor
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Version 2.0
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_16625
Name NRPSpredictor
Alternative name Non-Ribosomal Peptide Synthetases predictor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained No

Versioning


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Maintainer


This tool is not available anymore.

Publications for Non-Ribosomal Peptide Synthetases predictor

NRPSpredictor citations

 (67)
library_books

An Optimized Synthetic Bioinformatic Natural Product Antibiotic Sterilizes Multidrug Resistant Acinetobacter baumannii Infected Wounds

2018
PMCID: 5784245
PMID: 29404414
DOI: 10.1128/mSphere.00528-17

[…] after twice-daily treatments and the rats showed no rebound infection after 5 days.Two commonly used bioinformatic algorithms for prediction of peptide sequence from an NRPS gene cluster (Minowa and NRPSPredictor2) (, ) yielded peptides that only differed by Phe-for-Trp exchanges at both positions 5 and 9. Although the bioinformatics prediction of the peptide sequence appeared robust, the identit […]

library_books

Asperphenamate biosynthesis reveals a novel two module NRPS system to synthesize amino acid esters in fungi† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc02396k

2018
PMCID: 5897882
PMID: 29719714
DOI: 10.1039/c7sc02396k

[…] r catalysing its formation. By searching the genome of P. brevicompactum, we found 73 biosynthetic gene clusters (BGCs), including 14 NRPSs. The NRPS domain prediction was performed using the service NRPSpredictor2. The prediction indicated that 6 NRPSs containing two A-domains matched our previous predictions. Interestingly, cluster 1 contained two NRPSs harbouring four A-domains. It was also pos […]

library_books

The insect pathogenic bacterium Xenorhabdus innexi has attenuated virulence in multiple insect model hosts yet encodes a potent mosquitocidal toxin

2017
BMC Genomics
PMCID: 5709968
PMID: 29191166
DOI: 10.1186/s12864-017-4311-4

[…] edict the putative function, and then analyzed through the conserved domain search to identify PKS, NRPS and non-PKS/NRPS domains. Protein sequences of A-domains in NRPS modules were analyzed through NRPSpredictor2 [] and AT- domains identified in PKS modules were analyzed using I-TASSER server []. […]

library_books

Nonribosomal Peptides from Marine Microbes and Their Antimicrobial and Anticancer Potential

2017
Front Pharmacol
PMCID: 5702503
PMID: 29209209
DOI: 10.3389/fphar.2017.00828

[…] ani et al., ). The search database for NRPquest generates all possible orders of NRPS assembly lines within each detected NRP BGC hence, predicting the amino acids encoded by each of its module using NRPSPredictor2 (Röttig et al., ). A chemoinformatic based library and informatic search strategy for natural products (iSNAP) has also been doveloped for true nontargeted dereplication across a spectr […]

library_books

Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds

2017
Front Microbiol
PMCID: 5563371
PMID: 28868049
DOI: 10.3389/fmicb.2017.01494

[…] module, since it lacked AT and ACP domains. Two additional genes containing an ACPS domain and a Te domain were also determined to be part of these clusters (Supplementary Table ). antiSMASH uses (i) NRPSPredictor2 (ii) the method of and (iii) the specificity conferring code proposed by to predict the consensus substrate which binds at the A domain in NRPS clusters. All predictions are then inte […]

library_books

An L threonine transaldolase is required for L threo β hydroxy α amino acid assembly during obafluorin biosynthesis

2017
Nat Commun
PMCID: 5490192
PMID: 28649989
DOI: 10.1038/ncomms15935

[…] and we predict that it catalyses release of the resulting enzyme bound pseudo-dipeptide with concomitant formation of the β-lactone moiety to yield 1. Analysis of the A domain sequences of ObaI using NRPSpredictor2 (ref. ) identified 5 as the likely substrate of A1, whereas L-threonine is predicted to be the substrate of A2. This means that the domain architecture of ObaI () is further unusual as […]

Citations

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NRPSpredictor institution(s)
Applied Bioinformatics, Center for Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany; Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands; Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands; Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany; Algorithms in Bioinformatics Group, Center for Bioinformatics/Department of Computer Science, University of Tübingen, Tübingen, Germany
NRPSpredictor funding source(s)
Supported by German Ministry for Education and Research (BMBF) [0315585A (GenBioCom)]; by the Dutch Technology Foundation (STW), which is the applied-science division of The Netherlands Organisation for Scientific Research (NWO) and the Technology Programme of the Ministry of Economic Affairs (grant STW 10463).

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