{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T15:53:35Z","timestamp":1769270015346,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005652","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,7,31]],"date-time":"2017-07-31T00:00:00Z","timestamp":1501459200000}}],"reference-count":88,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2017,7,17]],"date-time":"2017-07-17T00:00:00Z","timestamp":1500249600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["201505\/Z\/16\/Z"],"award-info":[{"award-number":["201505\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["Oxford Life Sciences Interface Doctoral Training Centre"],"award-info":[{"award-number":["Oxford Life Sciences Interface Doctoral Training Centre"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["MLST database"],"award-info":[{"award-number":["MLST database"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005652","type":"journal-article","created":{"date-parts":[[2017,7,17]],"date-time":"2017-07-17T17:35:11Z","timestamp":1500312911000},"page":"e1005652","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":60,"title":["Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models"],"prefix":"10.1371","volume":"13","author":[{"given":"Connor","family":"Sharp","sequence":"first","affiliation":[]},{"given":"James","family":"Bray","sequence":"additional","affiliation":[]},{"given":"Nicholas G.","family":"Housden","sequence":"additional","affiliation":[]},{"given":"Martin C. J.","family":"Maiden","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3273-0302","authenticated-orcid":true,"given":"Colin","family":"Kleanthous","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2017,7,17]]},"reference":[{"issue":"93","key":"ref1","first-page":"1040","article-title":"Sur un remarquable exemple d'antagonisme entre deux souches de colibacille","author":"A Gratia","year":"1925","journal-title":"CR SocBiol (Paris)"},{"issue":"6894","key":"ref2","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nature00823","article-title":"Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors","volume":"418","author":"B Kerr","year":"2002","journal-title":"Nature"},{"issue":"10","key":"ref3","doi-asserted-by":"crossref","first-page":"6324","DOI":"10.1073\/pnas.78.10.6324","article-title":"Structured habitats and the evolution of anticompetitor toxins in bacteria","volume":"78","author":"L Chao","year":"1981","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/ismej.2010.90","article-title":"Competitive interactions in Escherichia coli populations: the role of bacteriocins","volume":"5","author":"H Majeed","year":"2011","journal-title":"The ISME journal"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"e63837","DOI":"10.1371\/journal.pone.0063837","article-title":"The weak shall inherit: bacteriocin-mediated interactions in bacterial populations","volume":"8","author":"H Majeed","year":"2013","journal-title":"PloS one"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/S0966-842X(99)01459-6","article-title":"The ecological role of bacteriocins in bacterial competition","volume":"7","author":"Ma Riley","year":"1999","journal-title":"Trends in microbiology"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1498","DOI":"10.1042\/BST20120206","article-title":"Bacteriocins active against plant pathogenic bacteria","volume":"40","author":"R Grinter","year":"2012","journal-title":"Biochemical Society transactions"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"E5454","DOI":"10.1073\/pnas.1513311112","article-title":"Broad and efficient control of major foodborne pathogenic strains of Escherichia coli by mixtures of plant-produced colicins","volume":"112","author":"S Schulz","year":"2015","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/nrmicro2937","article-title":"Bacteriocins\u2014a viable alternative to antibiotics?","volume":"11","author":"PD Cotter","year":"2013","journal-title":"Nature reviews Microbiology"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"30201","DOI":"10.1038\/srep30201","article-title":"Efficacy of species-specific protein antibiotics in a murine model of acute Pseudomonas aeruginosa lung infection","volume":"6","author":"LC McCaughey","year":"2016","journal-title":"Sci Rep"},{"issue":"Pt 6","key":"ref11","doi-asserted-by":"crossref","first-page":"1783","DOI":"10.1099\/mic.0.2007\/016139-0","article-title":"The role of SOS boxes in enteric bacteriocin regulation","volume":"154","author":"O Gillor","year":"2008","journal-title":"Microbiology"},{"issue":"1","key":"ref12","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1111\/j.1365-2958.2012.08179.x","article-title":"Double locking of an Escherichia coli promoter by two repressors prevents premature colicin expression and cell lysis","volume":"86","author":"M Butala","year":"2012","journal-title":"Molecular microbiology"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1128\/MMBR.00036-06","article-title":"Colicin biology","volume":"71","author":"E Cascales","year":"2007","journal-title":"Microbiology and molecular biology reviews: MMBR"},{"issue":"2","key":"ref14","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1046\/j.1365-2958.1998.00811.x","article-title":"Immunity proteins and their specificity for endonuclease colicins: telling right from wrong in protein-protein recognition","volume":"28","author":"C Kleanthous","year":"1998","journal-title":"Molecular microbiology"},{"issue":"3","key":"ref15","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/6683","article-title":"Structural and mechanistic basis of immunity toward endonuclease colicins","volume":"6","author":"C Kleanthous","year":"1999","journal-title":"Nature structural biology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1017\/S0033583511000114","article-title":"Nuclease colicins and their immunity proteins","volume":"45","author":"G Papadakos","year":"2012","journal-title":"Quarterly reviews of biophysics"},{"issue":"28","key":"ref17","doi-asserted-by":"crossref","first-page":"18932","DOI":"10.1074\/jbc.M806149200","article-title":"Energy-dependent immunity protein release during tol-dependent nuclease colicin translocation","volume":"284","author":"M Vankemmelbeke","year":"2009","journal-title":"The Journal of biological chemistry"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"3415","DOI":"10.1099\/13500872-142-12-3415","article-title":"Structural and functional organization of the Yersinia pestis bacteriocin pesticin gene cluster","volume":"142","author":"A Rakin","year":"1996","journal-title":"Microbiology"},{"key":"ref19","first-page":"2253","article-title":"Characterization of three group A klebicin plasmids: localization of their E colicin immunity genes","volume":"133","author":"R James","year":"1987","journal-title":"Journal of general microbiology"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"6179","DOI":"10.1128\/jb.175.19.6179-6185.1993","article-title":"Functional domains of S-type pyocins deduced from chimeric molecules","volume":"175","author":"Y Sano","year":"1993","journal-title":"Journal of bacteriology"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1186\/s12915-014-0068-2","article-title":"Nutrient-responsive regulation determines biodiversity in a colicin-mediated bacterial community","volume":"12","author":"FJH Hol","year":"2014","journal-title":"BMC biology"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1099\/jmm.0.037234-0","article-title":"Colicin insensitivity correlates with a higher prevalence of extraintestinal virulence factors among Escherichia coli isolates from skin and soft-tissue infections","volume":"61","author":"Z Petkovsek","year":"2012","journal-title":"Journal of medical microbiology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1186\/1471-2180-14-109","article-title":"Bacteriocin-encoding genes and ExPEC virulence determinants are associated in human fecal Escherichia coli strains","volume":"14","author":"L Micenkov\u00e1","year":"2014","journal-title":"BMC microbiology"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e1003844","DOI":"10.1371\/journal.ppat.1003844","article-title":"Inflammation fuels colicin Ib-dependent competition of Salmonella serovar Typhimurium and E. coli in enterobacterial blooms","volume":"10","author":"LP Nedialkova","year":"2014","journal-title":"PLoS pathogens"},{"issue":"43","key":"ref25","doi-asserted-by":"crossref","first-page":"17522","DOI":"10.1073\/pnas.1308632110","article-title":"Tracking the establishment of local endemic populations of an emergent enteric pathogen","volume":"110","author":"KE Holt","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7","key":"ref26","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1099\/00221287-138-7-1345","article-title":"A survey of Col plasmids in natural isolates of Escherichia coli and an investigation into the stability of Col-plasmid lineages","volume":"138","author":"MA Riley","year":"1992","journal-title":"Journal of general microbiology"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated Profile HMM Searches","volume":"7","author":"SR Eddy","year":"2011","journal-title":"PLoS computational biology"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1603","DOI":"10.1110\/ps.04658504","article-title":"Identification of the catalytic motif of the microbial ribosome inactivating cytotoxin colicin E3","volume":"13","author":"D Walker","year":"2004","journal-title":"Protein science: a publication of the Protein Society"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1016\/j.bbrc.2004.07.206","article-title":"Relation between tRNase activity and the structure of colicin D according to X-ray crystallography","volume":"322","author":"S Yajima","year":"2004","journal-title":"Biochemical and biophysical research communications"},{"key":"ref30","article-title":"Homing Endonucleases and Inteins. Nucleic acids and molecular biology","volume":"16","author":"AH Keeble","year":"2005"},{"issue":"1","key":"ref31","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.jmb.2004.07.032","article-title":"DNA binding and cleavage by the HNH homing endonuclease I-HmuI","volume":"342","author":"BW Shen","year":"2004","journal-title":"J Mol Biol"},{"issue":"3","key":"ref32","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/nbt.2508","article-title":"RNA-guided editing of bacterial genomes using CRISPR-Cas systems","volume":"31","author":"W Jiang","year":"2013","journal-title":"Nature biotechnology"},{"key":"ref33","article-title":"Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium","author":"LP Nedialkova","year":"2015","journal-title":"Environmental microbiology"},{"issue":"33","key":"ref34","doi-asserted-by":"crossref","first-page":"34763","DOI":"10.1074\/jbc.M403719200","article-title":"Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases","volume":"279","author":"MJ Mate","year":"2004","journal-title":"The Journal of biological chemistry"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1093\/infdis\/jit480","article-title":"Escherichia coli uropathogenic-specific protein, USP, is a bacteriocin-like genotoxin","volume":"208","author":"D Nipi\u010d","year":"2013","journal-title":"Journal of Infectious Diseases"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1093\/infdis\/jit482","article-title":"Uropathogenic Escherichia coli colicin-like usp and associated proteins: their evolution and role in pathogenesis","volume":"208","author":"GD Armstrong","year":"2013","journal-title":"The Journal of infectious diseases"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"4532","DOI":"10.1093\/nar\/gkr036","article-title":"A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems","volume":"39","author":"D Zhang","year":"2011","journal-title":"Nucleic acids research"},{"key":"ref38","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.1406110111","article-title":"Marker for type VI secretion system effectors","volume":"111","author":"D Salomon","year":"2014","journal-title":"PNAS"},{"issue":"1","key":"ref39","doi-asserted-by":"crossref","first-page":"e1004592","DOI":"10.1371\/journal.ppat.1004592","article-title":"A new family of secreted toxins in pathogenic Neisseria species","volume":"11","author":"A Jamet","year":"2015","journal-title":"PLoS pathogens"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"D581","DOI":"10.1093\/nar\/gkt1099","article-title":"PATRIC, the bacterial bioinformatics database and analysis resource","volume":"42","author":"AR Wattam","year":"2014","journal-title":"Nucleic acids research"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1007\/BF01574688","article-title":"The ecology and evolution of bacteriocins","volume":"17","author":"Ma Riley","year":"1996","journal-title":"Journal of Industrial Microbiology & Biotechnology"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/S0300-9084(02)01422-0","article-title":"The pyocins of Pseudomonas aeruginosa","volume":"84","author":"Y Michel-Briand","year":"2002","journal-title":"Biochimie"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"3239","DOI":"10.1099\/mic.0.28690-0","article-title":"Bacteriocin diversity and the frequency of multiple bacteriocin production in Escherichia coli","volume":"152","author":"DM Gordon","year":"2006","journal-title":"Microbiology (Reading, England)"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1111\/1574-6976.12079","article-title":"Ribosomally encoded antibacterial proteins and peptides from Pseudomonas","volume":"38","author":"MGK Ghequire","year":"2014","journal-title":"Fems Microbiol Rev"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"A Carattoli","year":"2014","journal-title":"Antimicrobial agents and chemotherapy"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1128\/AEM.01780-06","article-title":"Prevalence of ColE1-like plasmids and colicin K production among uropathogenic Escherichia coli strains and quantification of inhibitory activity of colicin K","volume":"73","author":"M Rijavec","year":"2007","journal-title":"Applied and environmental microbiology"},{"issue":"2","key":"ref47","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/0147-619X(86)90072-7","article-title":"The complete nucleotide sequence of the bacteriocinogenic plasmid CloDF13","volume":"16","author":"HJ Nijkamp","year":"1986","journal-title":"Plasmid"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"17368","DOI":"10.1038\/srep17368","article-title":"Distinct colicin M-like bacteriocin-immunity pairs in Burkholderia","volume":"5","author":"MGK Ghequire","year":"2015","journal-title":"Scientific reports"},{"issue":"3","key":"ref49","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1089\/mdr.2011.0230","article-title":"Characterization of colicin M and its orthologs targeting bacterial cell wall peptidoglycan biosynthesis","volume":"18","author":"H Barreteau","year":"2012","journal-title":"Microbial drug resistance (Larchmont, NY)"},{"issue":"8","key":"ref50","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1038\/ismej.2009.43","article-title":"Abundance, composition, diversity and novelty of soil Proteobacteria","volume":"3","author":"AM Spain","year":"2009","journal-title":"The ISME journal"},{"issue":"18","key":"ref51","doi-asserted-by":"crossref","first-page":"3702","DOI":"10.1093\/bioinformatics\/bth444","article-title":"CLANS: a Java application for visualizing protein families based on pairwise similarity","volume":"20","author":"T Frickey","year":"2004","journal-title":"Bioinformatics"},{"issue":"33","key":"ref52","doi-asserted-by":"crossref","first-page":"29397","DOI":"10.1074\/jbc.M111.242354","article-title":"FtsH-dependent processing of RNase colicins D and E3 means that only the cytotoxic domains are imported into the cytoplasm","volume":"286","author":"M Chauleau","year":"2011","journal-title":"The Journal of biological chemistry"},{"issue":"5","key":"ref53","doi-asserted-by":"crossref","first-page":"e96549","DOI":"10.1371\/journal.pone.0096549","article-title":"In vivo processing of DNase colicins E2 and E7 is required for their import into the cytoplasm of target cells","volume":"9","author":"L Mora","year":"2014","journal-title":"PLoS One"},{"issue":"11","key":"ref54","doi-asserted-by":"crossref","first-page":"3989","DOI":"10.1073\/pnas.73.11.3989","article-title":"Colicin E2 is DNA endonuclease","volume":"73","author":"K Schaller","year":"1976","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ref55","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1073\/pnas.70.1.156","article-title":"Colicin E3: a unique endoribonuclease","volume":"70","author":"B Meyhack","year":"1973","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref56","article-title":"Structural and biophysical analysis of nuclease protein antibiotics","author":"A Klein","year":"2016","journal-title":"Biochem J"},{"issue":"5","key":"ref57","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.jmb.2012.01.039","article-title":"Kinetic basis for the competitive recruitment of TolB by the intrinsically disordered translocation domain of colicin E9","volume":"418","author":"G Papadakos","year":"2012","journal-title":"J Mol Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"1570","DOI":"10.1126\/science.1237864","article-title":"Intrinsically disordered protein threads through the bacterial outer membrane porin OmpF","volume":"340","author":"NG Housden","year":"2013","journal-title":"Science"},{"issue":"50","key":"ref59","doi-asserted-by":"crossref","first-page":"21412","DOI":"10.1073\/pnas.1010780107","article-title":"Directed epitope delivery across the Escherichia coli outer membrane through the porin OmpF","volume":"107","author":"NG Housden","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5\u20136","key":"ref60","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/S0300-9084(02)01426-8","article-title":"Importation of nuclease colicins into E coli cells: endoproteolytic cleavage and its prevention by the immunity protein","volume":"84","author":"M de Zamaroczy","year":"2002","journal-title":"Biochimie"},{"issue":"43","key":"ref61","doi-asserted-by":"crossref","first-page":"31389","DOI":"10.1074\/jbc.M705883200","article-title":"The role of electrostatics in colicin nuclease domain translocation into bacterial cells","volume":"282","author":"D Walker","year":"2007","journal-title":"The Journal of biological chemistry"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1007\/s00239-004-0263-9","article-title":"Phage associated bacteriocins reveal a novel mechanism for bacteriocin diversification in Klebsiella","volume":"60","author":"M Chavan","year":"2005","journal-title":"Journal of molecular evolution"},{"issue":"7","key":"ref63","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1038\/sj.emboj.7600162","article-title":"Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein","volume":"23","author":"M Graille","year":"2004","journal-title":"The EMBO journal"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1179\/joc.2009.21.5.493","article-title":"Serratia marcescens infections and outbreaks in neonatal intensive care units","volume":"21","author":"A Dessi","year":"2009","journal-title":"Journal of chemotherapy (Florence, Italy)"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/jac\/dku482","article-title":"Pathogenicity of pan-drug-resistant Serratia marcescens harbouring blaNDM-1","volume":"70","author":"TM Gruber","year":"2015","journal-title":"The Journal of antimicrobial chemotherapy"},{"issue":"Pt 8","key":"ref66","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1099\/00221287-138-8-1737","article-title":"Cloning and DNA sequence analysis of a bacteriocin gene of Serratia marcescens","volume":"138","author":"MB Viejo","year":"1992","journal-title":"Journal of general microbiology"},{"key":"ref67","first-page":"1","article-title":"New Players in the Toxin Field: Polymorphic Toxin Systems in","volume":"6","author":"A Jamet","year":"2015","journal-title":"New Players in the Toxin Field: Polymorphic Toxin Systems in"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.1128\/JB.05885-11","article-title":"Novel colicin FY of Yersinia frederiksenii inhibits pathogenic Yersinia strains via YiuR-mediated reception, TonB import, and cell membrane pore formation","volume":"194","author":"J Bos\u00e1k","year":"2012","journal-title":"Journal of bacteriology"},{"issue":"5","key":"ref69","doi-asserted-by":"crossref","first-page":"1580","DOI":"10.1128\/jb.179.5.1580-1583.1997","article-title":"Pesticin displays muramidase activity","volume":"179","author":"W Vollmer","year":"1997","journal-title":"Journal of bacteriology"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.drup.2015.08.002","article-title":"The increasing threat of Pseudomonas aeruginosa high-risk clones","volume":"21\u201322","author":"A Oliver","year":"2015","journal-title":"Drug resistance updates: reviews and commentaries in antimicrobial and anticancer chemotherapy"},{"issue":"3","key":"ref71","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1111\/2049-632X.12033","article-title":"Pseudomonas aeruginosa: new insights into pathogenesis and host defenses","volume":"67","author":"SL Gellatly","year":"2013","journal-title":"Pathogens and disease"},{"issue":"15","key":"ref72","doi-asserted-by":"crossref","first-page":"2345","DOI":"10.1042\/BCJ20160470","article-title":"Discovery, characterization and in vivo activity of pyocin SD2, a protein antibiotic from Pseudomonas aeruginosa","volume":"473","author":"L C McCaughey","year":"2016","journal-title":"Biochem J"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME Suite: Tools for motif discovery and searching","volume":"37","author":"TL Bailey","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"ref74","first-page":"103","article-title":"Construction and Characterization of Pyocin-Colicin Chimeric Proteins","volume":"178","author":"M Kageyama","year":"1996","journal-title":"Construction and Characterization of Pyocin-Colicin Chimeric Proteins"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"4751","DOI":"10.1128\/IAI.67.9.4751-4756.1999","article-title":"The gene locus yijP contributes to Escherichia coli K1 invasion of brain microvascular endothelial cells","volume":"67","author":"Y Wang","year":"1999","journal-title":"Infection and immunity"},{"key":"ref76","first-page":"703","article-title":"Sequence Analysis of the Escherichia coli O15 Antigen Gene Cluster and Development of a PCR Assay for Rapid Detection of Intestinal and Extraintestinal Pathogenic E. coli O15 Strains","volume":"43","author":"L Beutin","year":"2005","journal-title":"Society"},{"issue":"Pt 4","key":"ref77","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1099\/mic.0.055459-0","article-title":"Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain","volume":"158","author":"KA Jolley","year":"2012","journal-title":"Microbiology"},{"issue":"5","key":"ref78","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"DR Zerbino","year":"2008","journal-title":"Genome research"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1006\/jmbi.2001.5080","article-title":"Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure","volume":"313","author":"J Gough","year":"2001","journal-title":"Journal of molecular biology"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"ref81","doi-asserted-by":"crossref","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"F Sievers","year":"2011","journal-title":"Molecular Systems Biology"},{"issue":"7","key":"ref82","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements","volume":"14","author":"ACE Darling","year":"2004","journal-title":"Genome research"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1126\/science.252.5009.1162","article-title":"Predicting coiled coils from protein sequences","volume":"252","author":"A Lupas","year":"1991","journal-title":"Science (New York, NY)"},{"issue":"4","key":"ref84","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1016\/j.jmb.2005.01.071","article-title":"The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins","volume":"347","author":"Z Dosztanyi","year":"2005","journal-title":"J Mol Biol"},{"issue":"8","key":"ref85","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1101\/gr.205245.116","article-title":"Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland","volume":"26","author":"D Moradigaravand","year":"2016","journal-title":"Genome research"},{"key":"ref86","first-page":"btv421","article-title":"Roary: Rapid large-scale prokaryote pan genome analysis","volume":"31","author":"AJ Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1093\/bioinformatics\/bti191","article-title":"RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees","volume":"21","author":"a Stamatakis","year":"2005","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1093\/bioinformatics\/bth250","article-title":"BAPS 2: enhanced possibilities for the analysis of genetic population structure","volume":"20","author":"J Corander","year":"2004","journal-title":"Bioinformatics (Oxford, England)"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005652","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,7,31]],"date-time":"2017-07-31T00:00:00Z","timestamp":1501459200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005652","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,31]],"date-time":"2022-07-31T02:39:37Z","timestamp":1659235177000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005652"}},"subtitle":[],"editor":[{"given":"Christine A.","family":"Orengo","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,7,17]]},"references-count":88,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2017,7,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005652","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1005652","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,7,17]]}}}