Abstract:
:EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial focus. Both databases are queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc and MetaCyc are available at http://ecocyc.PangeaSystems.com/ecocyc/
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Karp PD,Riley M,Saier M,Paulsen IT,Paley SM,Pellegrini-Toole Adoi
10.1093/nar/28.1.56keywords:
subject
Has Abstractpub_date
2000-01-01 00:00:00pages
56-9issue
1eissn
0305-1048issn
1362-4962pii
gkd093journal_volume
28pub_type
杂志文章abstract::RNA structural complexity and flexibility present a challenge for computational modeling efforts. Experimental information and bioinformatics data can be used as restraints to improve the accuracy of RNA tertiary structure prediction. Regarding utilization of restraints, the fundamental questions are: (i) What is the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz427
更新日期:2019-06-20 00:00:00
abstract::Toxin-antitoxin systems are widespread in bacteria and archaea. They perform diverse functional roles, including the generation of persistence, maintenance of genetic loci and resistance to bacteriophages through abortive infection. Toxin-antitoxin systems have been divided into three types, depending on the nature of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks231
更新日期:2012-07-01 00:00:00
abstract::A small family of DNA sequences is rearranged during the development of the somatic nucleus in Tetrahymena. The family is defined by 266 bp of highly conserved sequence which restriction mapping, hybridization and sequence analysis have shown is shared by a cloned micronuclear fragment and three sequences which consti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.20.8007
更新日期:1986-10-24 00:00:00
abstract::The POU domain transcription factor, Oct-2, is essential for the B cell-specific expression of CD36 in mouse B cells. In order to determine how Oct-2 mediates expression of CD36 in B cells, we cloned and analysed the mouse CD36 promoter. In contrast to the human CD36 promoter, the mouse promoter contains a consensus o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.8.1767
更新日期:2002-04-15 00:00:00
abstract::Site-specific mutation was demonstrated in a shuttle vector system using nitrogen mustard-conjugated oligodeoxyribonucleotides (ODNs). Plasmid DNA was modified in vitro by ODNs containing all four DNA bases in the presence of Escherichia coli RecA protein. Up to 50% of plasmid molecules were alkylated in the targeted ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.24.e38
更新日期:1999-12-15 00:00:00
abstract::Ribosome biogenesis (RiBi) is an extremely energy intensive process that is critical for gene expression. It is thus highly regulated, including through the tightly coordinated expression of over 200 RiBi genes by positive and negative transcriptional regulators. We investigated RiBi regulation as cells initiated meio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz231
更新日期:2019-06-04 00:00:00
abstract::Apolipoprotein B (apoB) is a major protein component of low density and very low density lipoproteins. Because of its large size and heterogeneity, molecular studies of apoB have been difficult, and its structure and regulation remain poorly understood. We now report the identification of human apoB cDNA clones by ant...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.19.6937
更新日期:1985-10-11 00:00:00
abstract::Potential promoters in the genome of Escherichia coli were searched by pattern recognition software PlatProm and classified on the basis of positions relative to gene borders. Beside the expected promoters located in front of the coding sequences we found a considerable amount of intragenic promoter-like signals with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp490
更新日期:2009-08-01 00:00:00
abstract::Alternative RNA splicing is an essential process to yield proteomic diversity in eukaryotic cells, and aberrant splicing is often associated with numerous human diseases and cancers. We recently described serine/arginine-rich splicing factor 3 (SRSF3 or SRp20) being a proto-oncogene. However, the SRSF3-regulated splic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1500
更新日期:2016-02-29 00:00:00
abstract::The bacteriophage ø29 DNA packaging motor that assembles on the precursor capsid (prohead) contains an essential 174-nt structural RNA (pRNA) that forms multimers. To determine the structural features of the CE- and D-loops believed to be involved in multimerization of pRNA, 35- and 19-nt RNA molecules containing the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm874
更新日期:2008-02-01 00:00:00
abstract::Four pseudorevertants of a -10 region lacP mutation were isolated. Three of these mutations were found to activate nascent promoters. These mutations were: a -2 G/C----A/T change (-2A) promoting transcription at position +11, a +1 A/T----T/A change (+1T) promoting transcription initiation at position +13, and a +10 C/...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.10.3927
更新日期:1989-05-25 00:00:00
abstract::Chloroplast DNA, isolated from a synchronized culture of Chlamydomonas reinhardii, was digested with restriction endonucleases and examined in the electron microscope. Restriction fragments containing displacement loops (D-loop) were photographed and measured to determine the position of replicated sequences in relati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.9.3843
更新日期:1984-05-11 00:00:00
abstract::The last 82 nucleotides of the 6.3 kb genomic RNA of plant turnip yellow mosaic virus (TYMV), the so-called 'tRNA-like' domain, presents functional, structural and primary sequence homologies with canonical tRNAs. In particular, one of the stem-loops resembles the TPsi(pseudouridine)-branch of tRNA, except for the pre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.17.3991
更新日期:1998-09-01 00:00:00
abstract::The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are ...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkaa261
更新日期:2020-05-21 00:00:00
abstract::RJ2.2.5, a mutant derived from the human B-lymphoma cell, Raji, is unable to express the MHC class II genes because of a recessive transcriptional defect attributed to the lack of an activator function. We report the isolation of a RJ2.2.5 revertant, namely AR, in which the expression of the mRNAs encoded by these gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.3.381
更新日期:1993-02-11 00:00:00
abstract::The convergently transcribed restriction (R) and methylase (M) genes of the Restriction-Modification system Esp1396I are tightly regulated by a controller (C) protein that forms part of the CR operon. We have mapped the transcriptional start sites from each promoter and examined the regulatory role of C.Esp1396I in vi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp210
更新日期:2009-06-01 00:00:00
abstract::From a recombinant lambda phage, we have determined a 387 bp sequence containing a mouse lysine tRNA gene. The putative lys tRNA (anticodon UUU) differs from rabbit liver lys tRNA at five positions. The flanking regions of the mouse gene are not generally homologous to published human and Drosophila lys tRNA genes. Ho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.7.2053
更新日期:1983-04-11 00:00:00
abstract::Histone H2B O-GlcNAcylation is an important post-translational modification of chromatin during gene transcription. However, how this epigenetic modification is regulated remains unclear. Here we found that the energy-sensing adenosine-monophosphate-activated protein kinase (AMPK) could suppress histone H2B O-GlcNAcyl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku236
更新日期:2014-05-01 00:00:00
abstract::The transcriptional potential of the hsp70 heat shock gene promoter is established prior to induction by stress. It has been shown previously that the TBP subunit of TFIID is associated with the TATA element and that RNA polymerase II is paused downstream from the transcription start site. In order to identify new int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.16.3327
更新日期:1995-08-25 00:00:00
abstract::Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1-ORF2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl531
更新日期:2006-01-01 00:00:00
abstract::Mitochondrial DNA (mtDNA) resides in a high ROS environment and suffers more mutations than its nuclear counterpart. Increasing evidence suggests that mtDNA mutations are not the results of direct oxidative damage, rather are caused, at least in part, by DNA replication errors. To understand how the mtDNA replicase, P...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1018
更新日期:2020-01-24 00:00:00
abstract::Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with miss...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1319
更新日期:2019-04-08 00:00:00
abstract::The 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5' and 3' unt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.335
更新日期:2002-01-01 00:00:00
abstract::Secondary structure-sensitive chemical and enzymatic probes have been used to produce a model for the folding of the last 68 residues of the 3'-non-coding region of beet necrotic yellow vein benevirus RNA 3. The structure consists of two stem-loops separated by a single-stranded region. RNA 3-derived transcripts were ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.23.4723
更新日期:1997-12-01 00:00:00
abstract::RNA fragments from phage fr covering the complete or part of the replicase cistron initiation region have been used as templates in the formation of a ribosomal initiation complex in vitro. The results so obtained together with our earlier findings in a similar approach applied to fragments of the structurally related...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.23.7763
更新日期:1982-12-11 00:00:00
abstract::Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5'-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr031
更新日期:2011-05-01 00:00:00
abstract::Exposure of Schizosaccharomyces pombe cells to UV light results in increased uvi15(+) gene expression at both the mRNA and protein levels, leading to elevated cell survival. This UV-induced expression of the uvi15(+) gene was reduced in Deltasty1 and Deltawis1 cells lacking the stress-activated protein kinase pathway,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.17.3392
更新日期:2000-09-01 00:00:00
abstract::Methylthiotransferases (MTTases) are a closely related family of proteins that perform both radical-S-adenosylmethionine (SAM) mediated sulfur insertion and SAM-dependent methylation to modify nucleic acid or protein targets with a methyl thioether group (-SCH(3)). Members of two of the four known subgroups of MTTases...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq364
更新日期:2010-10-01 00:00:00
abstract::Escherichia coli mRNA translation is facilitated by sequences upstream and downstream of the initiation codon, called Shine-Dalgarno (SD) and downstream box (DB) sequences, respectively. In E.coli enhancing the complementarity between the DB sequences and the 16S rRNA penultimate stem resulted in increased protein acc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.4.970
更新日期:2001-02-15 00:00:00
abstract::In many eukaryotic mRNAs one or more short 'upstream' open reading frames, uORFs, precede the initiator of the main coding sequence. Upstream ORFs are functionally diverse as illustrated by their variety of features in polyamine pathway biosynthetic mRNAs. Their propensity to act as sensors for regulatory circuits and...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkp1037
更新日期:2010-01-01 00:00:00