Abstract：
:The products of many bacterial non-ribosomal peptide synthetases (NRPS) are highly important secondary metabolites, including vancomycin and other antibiotics. The ability to predict substrate specificity of newly detected NRPS Adenylation (A-) domains by genome sequencing efforts is of great importance to identify and annotate new gene clusters that produce secondary metabolites. Prediction of A-domain specificity based on the sequence alone can be achieved through sequence signatures or, more accurately, through machine learning methods. We present an improved predictor, based on previous work (NRPSpredictor), that predicts A-domain specificity using Support Vector Machines on four hierarchical levels, ranging from gross physicochemical properties of an A-domain's substrates down to single amino acid substrates. The three more general levels are predicted with an F-measure better than 0.89 and the most detailed level with an average F-measure of 0.80. We also modeled the applicability domain of our predictor to estimate for new A-domains whether they lie in the applicability domain. Finally, since there are also NRPS that play an important role in natural products chemistry of fungi, such as peptaibols and cephalosporins, we added a predictor for fungal A-domains, which predicts gross physicochemical properties with an F-measure of 0.84. The service is available at http://nrps.informatik.uni-tuebingen.de/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Röttig M,Medema MH,Blin K,Weber T,Rausch C,Kohlbacher Odoi
10.1093/nar/gkr323subject
Has Abstractpub_date
2011-07-01 00:00:00pages
W362-7issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkr323journal_volume
39pub_type
杂志文章abstract：:Melibiose uptake and hydrolysis in E.coli is performed by the MelB and MelA proteins, respectively. We report the cloning and sequencing of the melA gene. The nucleotide sequence data showed that melA codes for a 450 amino acid long protein with a molecular weight of 50.6 kd. The sequence data also supported the assum...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.5.2213
更新日期：1987-03-11 00:00:00
abstract：:The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics--indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provid...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp477
更新日期：2009-07-01 00:00:00
abstract：:Expression of the wild-type p53 tumor suppressor gene has been found to play an important role in the regulation of cellular proliferation and differentiation. In addition, in many transformed cells and primary tumors, the gene has undergone allelic deletions and mutant forms of the p53 gene are expressed at elevated ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.2.345
更新日期：1993-01-25 00:00:00
abstract：:The purine rich oligodeoxyribonucleotides 1C, d(ATGACGGAATA) and 2C, d(ATGAGCGAATA) alone exhibit highly cooperative melting transitions. Analysis of the concentration dependence of melting, and electrophoretic studies indicate that these oligomers can form an unusual purine rich offset double helix. The unusual duple...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.11.5137
更新日期：1988-06-10 00:00:00
abstract：:The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to g...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki317
更新日期：2005-03-23 00:00:00
abstract：:The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr981
更新日期：2012-01-01 00:00:00
abstract：:Nonsense-mediated mRNA decay (NMD) is a molecular pathway of mRNA surveillance that ensures rapid degradation of mRNAs containing premature translation termination codons (PTCs) in eukaryotes. NMD has been shown to also regulate normal gene expression and thus emerged as one of the key post-transcriptional mechanisms ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm461
更新日期：2007-01-01 00:00:00
abstract：:To successfully infect plants, viruses must counteract small RNA-based host defense responses. During infection of Arabidopsis, Cauliflower mosaic pararetrovirus (CaMV) is transcribed into pregenomic 35S and subgenomic 19S RNAs. The 35S RNA is both reverse transcribed and also used as an mRNA with highly structured 60...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr119
更新日期：2011-07-01 00:00:00
abstract：:We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky024
更新日期：2018-02-28 00:00:00
abstract：:Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laborious in vitro DNA splicing. In Vibrio cholerae, we uncover that this requirement is due to cytopl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx496
更新日期：2017-07-07 00:00:00
abstract：:Chromatin modulation at various cis-acting elements is critical for V(D)J recombination during T and B cell development. MARbeta, a matrix-associated region (MAR) located upstream of the T cell receptor beta (TCRbeta) enhancer (Ebeta), serves a crucial role in silencing Ebeta-mediated TCR activation. By DNaseI hyperse...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh807
更新日期：2004-09-15 00:00:00
abstract：:EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1235
更新日期：2013-01-01 00:00:00
abstract：:A Fortran computer algorithm has been used to analyze the nucleotide sequence of several structural genes. The analysis performed on both coding and complementary DNA strands shows that whereas open reading frames shorter than 100 codons are randomly distributed on both DNA strands, open reading frames longer than 100...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.6.1499
更新日期：1981-03-25 00:00:00
abstract：:Human lung epithelioid cells were treated with Benzo (a) pyrene diol epoxide (anti) in order to establish the binding and removal of covalent adducts in chromosomal components. Isolating two different classes of mononucleosomes, it was found that their DNA contained different concentrations of B(a)PDE-DNA adducts, whi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.24.9897
更新日期：1986-12-22 00:00:00
abstract：:Zar1 was one of the earliest mammalian maternal-effect genes to be identified. Embryos derived from Zar1-null female mice are blocked before zygotic genome activation; however, the underlying mechanism remains unclear. By knocking out Zar1 and its homolog Zar2 in mice, we revealed a novel function of these genes in oo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz863
更新日期：2019-12-02 00:00:00
abstract：:With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh046
更新日期：2004-03-26 00:00:00
abstract：:RNA sequencing has become an important method to perform hypothesis-free characterization of global gene expression. One of the limitations of RNA sequencing is that most sequence reads represent highly expressed transcripts, whereas low level transcripts are challenging to detect. To combine the benefits of tradition...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks816
更新日期：2013-01-07 00:00:00
abstract：:Predicting molecular interactions is a major goal in rational drug design. Pharmacophore, which is the spatial arrangement of features that is essential for a molecule to interact with a specific target receptor, is an important model for achieving this goal. We present a freely available web server, named PharmaGist,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn187
更新日期：2008-07-01 00:00:00
abstract：:The GenBank(R) sequence database (http://www.ncbi.nlm.nih.gov/) incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (WWW) or Sequin programs to send t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.1
更新日期：1998-01-01 00:00:00
abstract：:The advent of jellyfish green fluorescent protein and its spectral variants, together with promising new fluorescent proteins from other classes of the Cnidarian phylum (coral and anemones), has greatly enhanced and promises to further boost the detection and localization of proteins in cell biology. It has been less ...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/29.5.1013
更新日期：2001-03-01 00:00:00
abstract：:Non-selenocysteine-containing phospholipid hydroperoxide glutathione peroxidase (NPGPx or GPx7) is an oxidative stress sensor that modulates the antioxidative activity of its target proteins through intermolecular disulfide bond formation. Given NPGPx's role in protecting cells from oxidative damage, identification of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1010
更新日期：2015-10-30 00:00:00
abstract：:Restriction fragments of T7 DNA which selectively bind E. coli RNA polymerase have been identified. These include fragments located close to the beginning of gene 1 where according to Minkley and Pribnow (1973) there is a promoter called C. The smallest fragment from this region which binds RNA polymerase has been seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.2.525
更新日期：1979-02-01 00:00:00
abstract：:We have examined the expression and structure of several genes belonging to two classes of vegetative specific genes of the simple eukaryote, Dictyostelium discoideum. In amebae grown on bacteria, deactivation of all vegetative specific genes occurred at the onset of development and very little mRNA exists by 8 to 10 ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.23.9679
更新日期：1989-12-11 00:00:00
abstract：:The 80S ribosome from Saccharomyces cerevisiae has been reconstructed from cryo electron micrographs to a resolution of 35 A. It is strikingly similar to the 70S ribosome from Escherichia coli, while displaying the characteristic eukaryotic features familiar from reconstructions of ribosomes from higher eukaryotes. As...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.2.655
更新日期：1998-01-15 00:00:00
abstract：:The dominant kanr marker gene plays an important role in gene disruption experiments in budding yeast, as this marker can be used in a variety of yeast strains lacking the conventional yeast markers. We have developed a loxP-kanMX-loxP gene disruption cassette, which combines the advantages of the heterologous kanr ma...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.13.2519
更新日期：1996-07-01 00:00:00
abstract：:The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1133
更新日期：2017-01-04 00:00:00
abstract：:The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, se...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw796
更新日期：2017-01-04 00:00:00
abstract：:Alu insertions have contributed to >11% of the human genome and ∼30-35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1089
更新日期：2015-12-02 00:00:00
abstract：:Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to techn...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz474
更新日期：2019-09-05 00:00:00
abstract：:We have developed a new method for analysis of complex genetic systems by a combination of the Amplification Refractory Mutation System (ARMS) and Single-Strand Conformation Polymorphism (SSCP) analysis: ARMS-SSCP. Thus, a complex allelic series is subdivided into a number of groups by ARMS followed by the identificat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.5.1005
更新日期：1992-03-11 00:00:00
