Enzyme annotation in UniProtKB using Rhea

Morgat, Anne; Lombardot, Thierry; Coudert, Elisabeth; Axelsen, Kristian B.; Neto, Teresa Batista; Géhant, Sébastien; Bansal, Parit; Bolleman, Jerven; Gasteiger, Elisabeth; Castro, Edouard de; Baratin, Delphine; Pozzato, Monica; Xénarios, Ioannis; Poux, Sylvain; Redaschi, Nicole; Bridge, Alan

doi:10.1101/709899

Cited by 8 publications

(2 citation statements)

References 36 publications

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“…The lytic module of vB_HmeY_H4907 comprises only two ORFs. P51770 is a member of the spanin complex, homologous to ORF 32, and plays a crucial role in disrupting the host outer membrane during viral efflux and causing cell lysis ( 36 ). The spanin complex completes host lysis by rupturing the outer membrane after the actions of holin and endolysin penetrate the inner membrane and break down the host peptidoglycan.…”

Section: Resultsmentioning

confidence: 99%

“…We manually screened the start and end sites repeated in multiple programs and the sequences with start and stop codons to determine the open reading frame. The conserved domain was detected by finding homologs in the non-redundant database ( http://blast.ncbi.nlm.nih.gov/ ), the InterPro database ( 57 ), the Conserved Domain Database Suite (CDD/SPARCLE) ( 58 ), the UniProtKB database ( 36 ), the Pfam database ( http://pfam.xfam.org/ ), and the HHpred server ( 59 ). To identify the start and end of the phage genome’s replication, the cumulative GC skew ( https://genskew.csb.univie.ac.at/webskew ) analysis was applied ( 29 ).…”

Section: Methodsmentioning

confidence: 99%

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Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m

Su,

Zhang,

Liang

et al. 2023

Microbiol Spectr

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Viruses play crucial roles in the ecosystem by modulating the host community structure, mediating biogeochemical cycles, and compensating for the metabolism of host cells. Mariana Trench, the world’s deepest hadal habitat, harbors a variety of unique microorganisms that have adapted to its extreme conditions of low temperatures, high pressure, and nutrient scarcity. However, our knowledge about isolated hadal phage strains in the hadal trench is still limited. This study reported the discovery of a temperate phage, vB_HmeY_H4907, infecting Halomonas meridiana H4907, isolated from surface sediment from the Mariana Trench at a depth of 8,900 m. To our best knowledge, it is the deepest isolated siphovirus from the ocean. Its 40,452 bp linear dsDNA genome has 57.64% GC content and 55 open reading frames, and it is highly homologous to its host. Phylogenetic analysis and average nucleotide sequence identification reveal that vB_HmeY_H4907 is separated from the isolated phages and represents a new family, Suviridae , with eight predicted proviruses and six uncultured viral genomes. They are widely distributed in the ocean, suggesting a prevalence of this viral family in the deep sea. These findings expand our understanding of the phylogenetic diversity and genomic features of hadal lysogenic phages, provide essential information for further studies of phage-host interactions and evolution, and may reveal new insights into the lysogenic lifestyles of viruses inhabiting the hadal ocean. IMPORTANCE Halomonas phage vB_HmeY_H4907 is the deepest isolated siphovirus from the ocean, and it represents a novel abundant viral family in the ocean. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral family, namely, Suviridae .

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m

Su,

Zhang,

Liang

et al. 2023

Microbiol Spectr

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An integrative docking and simulation-based approach towards the development of epitope-based vaccine against enterotoxigenic Escherichia coli

Khan

Kumar

2021

Netw Model Anal Health Inform Bioinforma

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Enterotoxigenic E.coli is causing diarrheal illness in children as well as adults with the majority of the cases occurring in developing countries. To reduce the number of cases occurring worldwide, the development of an effectual vaccine against these bacteria can be the only prevention. This conjectural work was performed using modern bioinformatics tools for investigation of proteome of ETEC strain E24377A. Different computational vaccinology approaches were deployed to assess several parameters including antigenicity, allergenicity, stability, localization, molecular weight and toxicity of the predicted epitopes required for good vaccine candidate to elicit immune response against diarrhea. We estimated two known control antigens, epitope 141 STLPETTVV 149 of Hepatitis B virus and epitope 265 ILRGSVAHK 273 of H1N1 Nucleoprotein in an attempt to corroborate our research work. Furthermore molecular docking was performed to evaluate the interaction between HLA allele and peptide, the peptide QYGGGNSAL and peptide LPYFELRWL were considered to be the most promiscuous T cell epitopes with the highest binding energy value of −2.09 kcal/mol and −1.84 kcal/mol, respectively. In addition, dynamic simulation revealed good stability of the vaccine construct as well as population coverage analysis exhibits the highest population coverage in the regions of East Asia, India, Northeast Asia, South Asia and North America. Therefore, these two epitopes can be further synthesized for wet lab analysis and could be considered as a promising vaccine against diarrhea. Supplementary Information The online version contains supplementary material available at 10.1007/s13721-021-00287-6.

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OrganelX web server for sub-peroxisomal and sub-mitochondrial protein localization and peroxisomal target signal detection

Anteghini

Haja

Santos

et al. 2023

Computational and Structural Biotechnology Journal

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Enzyme annotation in UniProtKB using Rhea

Cited by 8 publications

References 36 publications

Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m

Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m

An integrative docking and simulation-based approach towards the development of epitope-based vaccine against enterotoxigenic Escherichia coli

OrganelX web server for sub-peroxisomal and sub-mitochondrial protein localization and peroxisomal target signal detection

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