Literature DB >> 36043869

Genome Sequence of a Microvirus Recovered from Wastewater in Arizona, USA, in October 2020, Encodes a Previously Undescribed DNA-Binding Protein.

Abriana Smith1, Nicole Kaiser1, Allan Yanez2, Tyler Perleberg2, Amir Elyaderani1, Peter Skidmore1, Sangeet Adhikari2,3, Erin M Driver2, Rolf U Halden2,3,4, Arvind Varsani5, Matthew Scotch1,2, Temitope O C Faleye2.   

Abstract

We describe the genome of Microvirus-AZ-2020, which was identified from wastewater in Arizona, USA, in October 2020. Microvirus-AZ-2020 belongs to subfamily Gokushovirinae and contains six (five known and one hypothetical) open reading frames (ORFs), each with >40 codons. HHPred analysis and Colabfold structure prediction suggest that the hypothetical ORF encodes a previously undescribed putative DNA-binding protein.

Entities:  

Year:  2022        PMID： 36043869      PMCID： PMC9584320          DOI： 10.1128/mra.00337-22

Source DB:  PubMed          Journal:  Microbiol Resour Announc        ISSN： 2576-098X


  12 in total

1.  Protein homology detection by HMM-HMM comparison.

Authors:  Johannes Söding
Journal:  Bioinformatics       Date:  2004-11-05       Impact factor: 6.937

2.  Diverse single-stranded DNA viruses associated with honey bees (Apis mellifera).

Authors:  Simona Kraberger; Chelsea N Cook; Kara Schmidlin; Rafaela S Fontenele; Joshua Bautista; Brian Smith; Arvind Varsani
Journal:  Infect Genet Evol       Date:  2019-03-27       Impact factor: 3.342

3.  Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview.

Authors:  Welkin H Pope; Deborah Jacobs-Sera
Journal:  Methods Mol Biol       Date:  2018

4.  A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.

Authors:  Lukas Zimmermann; Andrew Stephens; Seung-Zin Nam; David Rau; Jonas Kübler; Marko Lozajic; Felix Gabler; Johannes Söding; Andrei N Lupas; Vikram Alva
Journal:  J Mol Biol       Date:  2017-12-16       Impact factor: 5.469

5.  DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues.

Authors:  Jing Yan; Lukasz Kurgan
Journal:  Nucleic Acids Res       Date:  2017-06-02       Impact factor: 16.971

6.  ColabFold: making protein folding accessible to all.

Authors:  Milot Mirdita; Sergey Ovchinnikov; Martin Steinegger; Konstantin Schütze; Yoshitaka Moriwaki; Lim Heo
Journal:  Nat Methods       Date:  2022-05-30       Impact factor: 47.990

7.  Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.

Authors:  Simon Roux; Mart Krupovic; Axel Poulet; Didier Debroas; François Enault
Journal:  PLoS One       Date:  2012-07-11       Impact factor: 3.240

8.  Organizing the Global Diversity of Microviruses.

Authors:  Paul C Kirchberger; Zachary A Martinez; Howard Ochman
Journal:  mBio       Date:  2022-05-02       Impact factor: 7.786

9.  KBase: The United States Department of Energy Systems Biology Knowledgebase.

Authors:  Adam P Arkin; Robert W Cottingham; Christopher S Henry; Nomi L Harris; Rick L Stevens; Sergei Maslov; Paramvir Dehal; Doreen Ware; Fernando Perez; Shane Canon; Michael W Sneddon; Matthew L Henderson; William J Riehl; Dan Murphy-Olson; Stephen Y Chan; Roy T Kamimura; Sunita Kumari; Meghan M Drake; Thomas S Brettin; Elizabeth M Glass; Dylan Chivian; Dan Gunter; David J Weston; Benjamin H Allen; Jason Baumohl; Aaron A Best; Ben Bowen; Steven E Brenner; Christopher C Bun; John-Marc Chandonia; Jer-Ming Chia; Ric Colasanti; Neal Conrad; James J Davis; Brian H Davison; Matthew DeJongh; Scott Devoid; Emily Dietrich; Inna Dubchak; Janaka N Edirisinghe; Gang Fang; José P Faria; Paul M Frybarger; Wolfgang Gerlach; Mark Gerstein; Annette Greiner; James Gurtowski; Holly L Haun; Fei He; Rashmi Jain; Marcin P Joachimiak; Kevin P Keegan; Shinnosuke Kondo; Vivek Kumar; Miriam L Land; Folker Meyer; Marissa Mills; Pavel S Novichkov; Taeyun Oh; Gary J Olsen; Robert Olson; Bruce Parrello; Shiran Pasternak; Erik Pearson; Sarah S Poon; Gavin A Price; Srividya Ramakrishnan; Priya Ranjan; Pamela C Ronald; Michael C Schatz; Samuel M D Seaver; Maulik Shukla; Roman A Sutormin; Mustafa H Syed; James Thomason; Nathan L Tintle; Daifeng Wang; Fangfang Xia; Hyunseung Yoo; Shinjae Yoo; Dantong Yu
Journal:  Nat Biotechnol       Date:  2018-07-06       Impact factor: 54.908

10.  Pan-Enterovirus Amplicon-Based High-Throughput Sequencing Detects the Complete Capsid of a EVA71 Genotype C1 Variant via Wastewater-Based Epidemiology in Arizona.

Authors:  Temitope O C Faleye; Erin Driver; Devin Bowes; Sangeet Adhikari; Deborah Adams; Arvind Varsani; Rolf U Halden; Matthew Scotch
Journal:  Viruses       Date:  2021-01-07       Impact factor: 5.048
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