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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

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Publications for Non-Ribosomal Peptide Synthetases predictor

NRPSpredictor in publications

 (59)
PMCID: 5784245
PMID: 29404414
DOI: 10.1128/mSphere.00528-17

[…] 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, […]

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

[…] coding genes closely resembled both fcl and zmn synthesis genes, and this further suggested that the candidate xlt biosynthesis gene cluster is homologous to the fcl and zmn clusters. in x. innexi, nrpspredictor2 predicted a1 through a6 to be a1: serine, a2: phenylalanine, a3: asparagine, a4: asparagine, a5: threonine, and a6: valine (fig. ). also, some programs predicted an epimerization […]

PMCID: 5702503
PMID: 29209209
DOI: 10.3389/fphar.2017.00828

[…] 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 […]

PMCID: 5563371
PMID: 28868049
DOI: 10.3389/fmicb.2017.01494

[…] 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 […]

PMCID: 5490192
PMID: 28649989
DOI: 10.1038/ncomms15935

[…] 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 […]


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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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