UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View

Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Schneider, Michel; Bansal, Parit; Bridge, Alan; Poux, Sylvain; Bougueleret, Lydie; Xénarios, Ioannis

doi:10.1007/978-1-4939-3167-5_2

Cited by 624 publications

(489 citation statements)

References 15 publications

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“…Briefly, the contigs were assembled using Newbler 2.6 [32]. Open reading frames and pseudogenes were predicted using RAST 2.0 [33] combined with BLASTP/BLASTN searches [34] against the UniProtKB/Swiss-Prot database [35] and the RefSeq database [36]. Annotation of resistance genes, mobile elements, and other features was carried out using the online databases including CARD [37], ResFinder [38], BacMet [39], ISfinder [40], INTEGRALL [41], and the Tn Number Registry [42].…”

Section: Sequencing and Annotationmentioning

confidence: 99%

WITHDRAWN: Structure genomics of two chimera plasmids p675920-1 and p675920-2 coexisting in a multi-drug resistant Klebsiella pneumoniae isolate

Feng¹,

Yin²,

Zhan³

et al. 2018

Oncotarget

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This study dealt with detailed genomic characterization of two multidrug resistant (MDR) plasmids p675920-1 and p675920-2 from a single clinical Klebsiella pneumoniae isolate 675920. p675920-1 was essentially a hybrid of the IncFII plasmid pHN7A8 and the IncR plasmid pKPC-LK30, and functioned as an IncFII plasmid with inactivation of the IncR replication gene. The backbone of p675920-2 was a hybrid of a novel replicon, three maintenance regions (22.0-, 2.7-, 2.6-kb in length, respectively) as found in pKPYL2, p10164-3 and pK1HV, respectively, and the entire 25.9-kb conjugal transfer region of pKPYL2. p675920-1 and p675920-2 carried a large number of resistance genes, which contributed to resistance to at least seven classes of antibiotics (β-lactams, quinolones, aminoglycosides, fosfomycins, sulphonamides, trimethoprims, and tetracyclines) and one kind of heavy mental (mercury). All of these resistance genes are associated with mobile elements such as insertion sequences, insertion sequence-based transposition units, and transposons, which constituted a total of three novel MDR regions, two in p675920-1 and another in p675920-2. Coexistence of two MDR plasmids p675920-1 and p675920-2 made K. pneumoniae 675920 tend to become extensively drug-resistant.

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Section: Sequencing and Annotationmentioning

confidence: 99%

WITHDRAWN: Structure genomics of two chimera plasmids p675920-1 and p675920-2 coexisting in a multi-drug resistant Klebsiella pneumoniae isolate

Feng¹,

Yin²,

Zhan³

et al. 2018

Oncotarget

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“…transcript alignment for each database entry above a specified significance threshold), compared to Mus musculus RefSeq transcripts, UniProtKB/SwissProt database 19,20 and UniRef90 database 21,22 (Figs 9, 10 and 11). Gene Ontology (GO) terms corresponding to annotated transcripts were well distributed between the categories of biological process, cellular component and molecular function (Supplementary Figure S4).…”

Section: Resultsmentioning

confidence: 99%

De novotranscriptome assembly for the spiny mouse (Acomys cahirinus)

Mamrot

Legaie

Ellery

et al. 2016

Preprint

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Spiny mice of the genus Acomys display several unique physiological traits, including menstruation and scar-free wound healing; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique attributes, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research, however little genetic information is accessible for this species. This project aimed to generate a draft transcriptome for the Common spiny mouse (Acomys cahirinus). Illumina sequencing of RNA from 15 organ types (male and female) produced 451 million, 150 bp paired-end reads (92.4Gbp). An extensive survey of de novo transcriptome assembly approaches using Trinity, SOAPdenovo-Trans, and Oases at multiple kmer lengths was conducted, producing 50 single-kmer assemblies from this dataset. Nonredundant transcripts from all assemblies were merged into a meta-assembly using the EvidentialGene tr2aacds pipeline, producing the largest gene catalogue to date for Acomys cahirinus. This study provides the first detailed characterization of the spiny mouse transcriptome. It validates use of the EvidentialGene tr2aacds pipeline in mammals to augment conventional de novo assembly approaches, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys.The Common or Cairo spiny mouse (Acomys cahirinus) is a small rodent species endemic to the semi-arid deserts of Africa and the Middle East . Used in research to model human disease, spiny mice exhibit physiological characteristics not typically found in rodents: they exhibit a precocial pattern of development 2, 3 , atypical synthesis of hormones such as cortisol and dehydroepiandosterone [4][5][6] , and a menstrual cycle 7 . These traits are common to humans and other higher order primates, but rare in other mammals. For example, menstruation has been identified in only six non-primate species (from >5,000 extant mammals), none of which are rodents 8 . The discovery of human-like physiological characteristics in a rodent is highly valuable for those in the scientific community looking to model human conditions, however fundamental aspects of their biology remain unexplored; for instance, there is little genetic information accessible for this species.Publically available genetic information for the spiny mouse consists of the mitochondrial genome 9 , and two RNA sequencing (RNA-Seq) datasets: PRJNA184055 10 , and PRJNA292021 11 . These next-generation sequencing (NGS) datasets were created with specific aims: to establish incipient sympatric speciation as a mode of natural selection in mammals inhabiting divergent microclimates 9 , to examine the molecular basis for natural variation in mammalian lifespan 10 , and to characterize and investigate another characteristic unique to Acomys: scar-free wound healing and skin regeneration 11 . De novo assembly of NGS reads was conducted for each specific organ/...

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“…The selected structure was required to be present in humans (homo sapiens), include a complete amino acid sequence at the active site, and be in complex with a ligand. The structure could not be a mutant protein or have a resolution of more than 2.5 Å. UniProt, InterPro, and protein model portal were used to compare the sequences and lengths of the amino acid chains [28][29][30]. The selected structure was then downloaded and optimized.…”

Section: Preparing the Target Protein Structurementioning

confidence: 99%

Virtual Screening of Indonesian Herbal Database for Dna Methyltransferase Inhibitors

Bhaskarawilaputraka

Azminah

Erlina

et al. 2017

Asian J Pharm Clin Res

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Objective: DNA hypermethylation is an abnormal epigenetic process catalyzed by DNA methyltransferase 1 (DNMT1). It is also one of the factors that cause non-communicable diseases such as cancer, diabetes, and other metabolic diseases. DNA hypermethylation can be reversed by suppressing DNMT1 activity using a DNMT inhibitor. This study was conducted to seek out inhibitor candidates among natural products. Methods:The search for potential inhibitors was conducted through a virtual screening of the Indonesian Herbal Database using AutoDockVina as docking software. Twenty-five compounds known for their inhibitory activity against DNMT1 were used as actives and as a reference for generating decoys, which was done using the Directory of Useful Decoys, Enhanced. Results:The 12 compounds with binding energies below the cutoff value were cassiamin C (A1), procyanidin B2 (B2), ent-epicatechin-(4alpha->8)-ent-epicatechin (C3), epicatechin-(4beta->8)-epicatechin-3-O-gallate (D4), neorhusflavanone (E5), 3-O-galloylepicatechin-(4beta->6)-epicatechin-3-O-gallate (F6), withanolide (G7), 3-O-galloylepigallocatechin-(4beta->6)-epigallocatechin-3-O-gallate (H8), cyanidin 3-(6''-caffeylsophoroside)-5-glucoside (I9), epifriedelanol (J10), gallocatechin-(4alpha->8)-epicatechin (K11), and scutellarein 7-glucosyl-(1->4)-rhamnoside (L12). A1 had the lowest binding energy of −12.7 kcal/mol, whereas K11 had the highest of −11.5 kcal/mol. Conclusions:The virtual screening yielded five potential DNMT1 inhibitors: Procyanidin B2, ent-epicatechin-(4alpha->8)-ent-epicatechin, epicatechin-(4beta->8)-epicatechin-3-O-gallate, neorhusflavanone, and cyanidin 3-(6''-caffeylsophoroside)-5-glucoside.Keywords: Epigenetic, DNA methyltransferase inhibitor, Indonesian Herbal Database, Virtual screening, AutoDockVina. INTRODUCTIONEpigenetic modification is one of the factors that cause noncommunicable diseases. Living environment, lifestyle, exposure to toxic chemicals, and nutrition may influence an individual's epigenetic profile. Epigenetic modification can alter gene expression [1]. One type of epigenetic modification is DNA methylation. DNA methylation, catalyzed by DNA methyltransferases (DNMTs), is the addition of a methyl (CH3) group to the DNA strand, specifically to the fifth carbon atom of a cytosine ring. Methylated cytosine, called 5-methylcytosine, usually occurs to a cytosine base that lies adjacent to a guanine base, at what is called a CpG site. The reason for this name is that cytosine is bonded to guanine through a phosphate bond. These sites normally occur in clusters; an area rich in CpG sites is called a CpG island. CpG islands are usually located near a gene regulator such as a promoter. DNA methylation that affects a gene promoter may repress the transcription of said gene and ultimately its expression. This process of turning a gene on and off through methylation is part of normal eukaryotic cell function [2,3].There are several types of DNMTs. Based on their functions, they can be grouped into two categories: De novo DNMTs...

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UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View

Cited by 624 publications

References 15 publications

WITHDRAWN: Structure genomics of two chimera plasmids p675920-1 and p675920-2 coexisting in a multi-drug resistant Klebsiella pneumoniae isolate

WITHDRAWN: Structure genomics of two chimera plasmids p675920-1 and p675920-2 coexisting in a multi-drug resistant Klebsiella pneumoniae isolate

De novotranscriptome assembly for the spiny mouse (Acomys cahirinus)

Virtual Screening of Indonesian Herbal Database for Dna Methyltransferase Inhibitors

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