{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T05:34:23Z","timestamp":1775799263397,"version":"3.50.1"},"reference-count":91,"publisher":"Oxford University Press (OUP)","issue":"4","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000092","name":"National Library of Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008893","name":"University of Iowa","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008893","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of Biomedical Engineering"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>For the past 20\u2009years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and\/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis.<\/jats:p>","DOI":"10.1093\/bib\/bbx117","type":"journal-article","created":{"date-parts":[[2017,9,5]],"date-time":"2017-09-05T15:09:50Z","timestamp":1504624190000},"page":"1063-1070","source":"Crossref","is-referenced-by-count":273,"title":["Microbial genome analysis: the COG approach"],"prefix":"10.1093","volume":"20","author":[{"given":"Michael Y","family":"Galperin","sequence":"first","affiliation":[]},{"given":"David M","family":"Kristensen","sequence":"additional","affiliation":[]},{"given":"Kira S","family":"Makarova","sequence":"additional","affiliation":[]},{"given":"Yuri I","family":"Wolf","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3943-8299","authenticated-orcid":false,"given":"Eugene V","family":"Koonin","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2017,9,14]]},"reference":[{"key":"2019100807383968900_bbx117-B1","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families","volume":"278","author":"Tatusov","year":"1997","journal-title":"Science"},{"key":"2019100807383968900_bbx117-B2","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/S0959-440X(98)80070-5","article-title":"Beyond complete genomes: from sequence to structure and function","volume":"8","author":"Koonin","year":"1998","journal-title":"Curr Opin Struct Biol"},{"key":"2019100807383968900_bbx117-B3","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1093\/nar\/28.1.33","article-title":"The COG database: a tool for genome-scale analysis of protein functions and evolution","volume":"28","author":"Tatusov","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B4","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/nar\/29.1.22","article-title":"The COG database: new developments in phylogenetic classification of proteins from complete genomes","volume":"29","author":"Tatusov","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B5","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2019100807383968900_bbx117-B6","doi-asserted-by":"crossref","first-page":"D261","DOI":"10.1093\/nar\/gku1223","article-title":"Expanded microbial genome coverage and improved protein family annotation in the COG database","volume":"43","author":"Galperin","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B7","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1146\/annurev.genet.39.073003.114725","article-title":"Orthologs, paralogs, and evolutionary genomics","volume":"39","author":"Koonin","year":"2005","journal-title":"Annu Rev Genet"},{"key":"2019100807383968900_bbx117-B8","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/nrg3456","article-title":"Functional and evolutionary implications of gene orthology","volume":"14","author":"Gabaldon","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2019100807383968900_bbx117-B9","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1093\/bib\/bbr030","article-title":"Computational methods for gene orthology inference","volume":"12","author":"Kristensen","year":"2011","journal-title":"Brief Bioinform"},{"key":"2019100807383968900_bbx117-B10","doi-asserted-by":"crossref","first-page":"818","DOI":"10.3390\/life5010818","article-title":"Archaeal Clusters of Orthologous Genes (arCOGs): an update and application for analysis of shared features between Thermococcales, Methanococcales, and Methanobacteriales","volume":"5","author":"Makarova","year":"2015","journal-title":"Life"},{"key":"2019100807383968900_bbx117-B11","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","author":"Kanehisa","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B12","doi-asserted-by":"crossref","first-page":"D363","DOI":"10.1093\/nar\/gkj123","article-title":"OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups","volume":"34","author":"Chen","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B13","doi-asserted-by":"crossref","first-page":"D270","DOI":"10.1093\/nar\/gku1152","article-title":"MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data","volume":"43","author":"Uchiyama","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B14","doi-asserted-by":"crossref","first-page":"D240","DOI":"10.1093\/nar\/gku1158","article-title":"The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements","volume":"43","author":"Altenhoff","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B15","doi-asserted-by":"crossref","first-page":"e766","DOI":"10.1371\/journal.pone.0000766","article-title":"The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists","volume":"2","author":"Heinicke","year":"2007","journal-title":"PLoS One"},{"key":"2019100807383968900_bbx117-B16","doi-asserted-by":"crossref","first-page":"D897","DOI":"10.1093\/nar\/gkt1177","article-title":"PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome","volume":"42","author":"Huerta-Cepas","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B17","doi-asserted-by":"crossref","first-page":"D250","DOI":"10.1093\/nar\/gku1220","article-title":"OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software","volume":"43","author":"Kriventseva","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B18","doi-asserted-by":"crossref","first-page":"D231","DOI":"10.1093\/nar\/gkt1253","article-title":"eggNOG v4.0: nested orthology inference across 3686 organisms","volume":"42","author":"Powell","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B19","doi-asserted-by":"crossref","first-page":"D234","DOI":"10.1093\/nar\/gku1203","article-title":"InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic","volume":"43","author":"Sonnhammer","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B20","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gkw923","article-title":"HieranoiDB: a database of orthologs inferred by Hieranoid","volume":"45","author":"Kaduk","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B21","doi-asserted-by":"crossref","first-page":"D250","DOI":"10.1093\/nar\/gkm796","article-title":"eggNOG: automated construction and annotation of orthologous groups of genes","volume":"36","author":"Jensen","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B22","doi-asserted-by":"crossref","first-page":"D286","DOI":"10.1093\/nar\/gkv1248","article-title":"eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences","volume":"44","author":"Huerta-Cepas","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B23","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B24","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"2019100807383968900_bbx117-B25","doi-asserted-by":"crossref","first-page":"55","DOI":"10.3233\/ISB-00007","article-title":"Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption","volume":"1","author":"Galperin","year":"1998","journal-title":"In Silico Biol"},{"key":"2019100807383968900_bbx117-B26","doi-asserted-by":"crossref","first-page":"e1000605","DOI":"10.1371\/journal.pcbi.1000605","article-title":"Annotation error in public databases: misannotation of molecular function in enzyme superfamilies","volume":"5","author":"Schnoes","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"2019100807383968900_bbx117-B27","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/bioinformatics\/18.12.1641","article-title":"Modeling the percolation of annotation errors in a database of protein sequences","volume":"18","author":"Gilks","year":"2002","journal-title":"Bioinformatics"},{"key":"2019100807383968900_bbx117-B28","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1016\/j.sbi.2005.05.010","article-title":"Automatic annotation of protein function","volume":"15","author":"Valencia","year":"2005","journal-title":"Curr Opin Struct Biol"},{"key":"2019100807383968900_bbx117-B29","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1093\/bib\/bbr042","article-title":"Phylogenetic-based propagation of functional annotations within the Gene Ontology Consortium","volume":"12","author":"Gaudet","year":"2011","journal-title":"Brief Bioinform"},{"key":"2019100807383968900_bbx117-B30","doi-asserted-by":"crossref","first-page":"D183","DOI":"10.1093\/nar\/gkw1138","article-title":"PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements","volume":"45","author":"Mi","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B31","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"The UniProt Consortium","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B32","doi-asserted-by":"crossref","first-page":"D257","DOI":"10.1093\/nar\/gku949","article-title":"SMART: recent updates, new developments and status in 2015","volume":"43","author":"Letunic","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B33","doi-asserted-by":"crossref","first-page":"D227","DOI":"10.1093\/nar\/gku1041","article-title":"The SUPERFAMILY 1.75 database in 2014: a doubling of data","volume":"43","author":"Oates","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B34","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: towards a more sustainable future","volume":"44","author":"Finn","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B35","doi-asserted-by":"crossref","first-page":"D190","DOI":"10.1093\/nar\/gkw1107","article-title":"InterPro in 2017-beyond protein family and domain annotations","volume":"45","author":"Finn","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B36","doi-asserted-by":"crossref","first-page":"D200","DOI":"10.1093\/nar\/gkw1129","article-title":"CDD\/SPARCLE: functional classification of proteins via subfamily domain architectures","volume":"45","author":"Marchler-Bauer","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B37","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/S0168-9525(02)02793-2","article-title":"Orthology, paralogy and proposed classification for paralog subtypes","volume":"18","author":"Sonnhammer","year":"2002","journal-title":"Trends Genet"},{"key":"2019100807383968900_bbx117-B38","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1093\/bioinformatics\/btq229","article-title":"A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches","volume":"26","author":"Kristensen","year":"2010","journal-title":"Bioinformatics"},{"key":"2019100807383968900_bbx117-B39","doi-asserted-by":"crossref","first-page":"e105015","DOI":"10.1371\/journal.pone.0105015","article-title":"Orthology detection combining clustering and synteny for very large datasets","volume":"9","author":"Lechner","year":"2014","journal-title":"PLoS One"},{"key":"2019100807383968900_bbx117-B40","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1093\/bib\/bbr040","article-title":"Positional orthology: putting genomic evolutionary relationships into context","volume":"12","author":"Dewey","year":"2011","journal-title":"Brief Bioinform"},{"key":"2019100807383968900_bbx117-B41","doi-asserted-by":"crossref","first-page":"D348","DOI":"10.1093\/nar\/gks1243","article-title":"CDD: conserved domains and protein three-dimensional structure","volume":"41","author":"Marchler-Bauer","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B42","doi-asserted-by":"crossref","first-page":"e9","DOI":"10.1093\/bioinformatics\/btl213","article-title":"Automatic clustering of orthologs and inparalogs shared by multiple proteomes","volume":"22","author":"Alexeyenko","year":"2006","journal-title":"Bioinformatics"},{"key":"2019100807383968900_bbx117-B43","doi-asserted-by":"crossref","first-page":"e383","DOI":"10.1371\/journal.pone.0000383","article-title":"Assessing performance of orthology detection strategies applied to eukaryotic genomes","volume":"2","author":"Chen","year":"2007","journal-title":"PLoS One"},{"key":"2019100807383968900_bbx117-B44","doi-asserted-by":"crossref","first-page":"e1000262","DOI":"10.1371\/journal.pcbi.1000262","article-title":"Phylogenetic and functional assessment of orthologs inference projects and methods","volume":"5","author":"Altenhoff","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"2019100807383968900_bbx117-B45","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1007\/978-1-61779-582-4_9","article-title":"Inferring orthology and paralogy","volume":"855","author":"Altenhoff","year":"2012","journal-title":"Methods Mol Biol"},{"key":"2019100807383968900_bbx117-B46","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1745-6150-3-13","article-title":"Evolutionary primacy of sodium bioenergetics","volume":"3","author":"Mulkidjanian","year":"2008","journal-title":"Biol Direct"},{"key":"2019100807383968900_bbx117-B47","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1006\/abbi.1994.1352","article-title":"Tartrate dehydrogenase, a new member of the family of metal-dependent decarboxylating R-hydroxyacid dehydrogenases","volume":"313","author":"Tipton","year":"1994","journal-title":"Arch Biochem Biophys"},{"key":"2019100807383968900_bbx117-B48","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1094\/MPMI-9-0401","article-title":"Characterization and distribution of tartrate utilization genes in the grapevine pathogen Agrobacterium vitis","volume":"9","author":"Salomone","year":"1996","journal-title":"Mol Plant Microbe Interact"},{"key":"2019100807383968900_bbx117-B49","doi-asserted-by":"crossref","first-page":"5013","DOI":"10.1128\/JB.182.17.5013-5016.2000","article-title":"Identification of enzymes homologous to isocitrate dehydrogenase that are involved in coenzyme B and leucine biosynthesis in methanoarchaea","volume":"182","author":"Howell","year":"2000","journal-title":"J Bacteriol"},{"key":"2019100807383968900_bbx117-B50","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gks1234","article-title":"TIGRFAMs and genome properties in 2013","volume":"41","author":"Haft","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B51","doi-asserted-by":"crossref","first-page":"D216","DOI":"10.1093\/nar\/gkn734","article-title":"The national center for biotechnology information's protein clusters database","volume":"37","author":"Klimke","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B52","doi-asserted-by":"crossref","first-page":"e36972","DOI":"10.1371\/journal.pone.0036972","article-title":"Phylogenomics of prokaryotic ribosomal proteins","volume":"7","author":"Yutin","year":"2012","journal-title":"PLoS One"},{"key":"2019100807383968900_bbx117-B53","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1023\/A:1004031323748","article-title":"Using the COG database to improve gene recognition in complete genomes","volume":"108","author":"Natale","year":"2000","journal-title":"Genetica"},{"key":"2019100807383968900_bbx117-B54","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-3783-7","volume-title":"Sequence\u2014Evolution\u2014Function: Computational Approaches in Comparative Genomics","author":"Koonin","year":"2003"},{"key":"2019100807383968900_bbx117-B55","doi-asserted-by":"crossref","first-page":"D553","DOI":"10.1093\/nar\/gkt1274","article-title":"RefSeq microbial genomes database: new representation and annotation strategy","volume":"42","author":"Tatusova","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B56","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B57","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1023\/A:1003705601428","article-title":"Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes","volume":"106","author":"Galperin","year":"1999","journal-title":"Genetica"},{"key":"2019100807383968900_bbx117-B58","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1016\/j.copbio.2006.08.007","article-title":"New metrics for comparative genomics","volume":"17","author":"Galperin","year":"2006","journal-title":"Curr Opin Biotechnol"},{"key":"2019100807383968900_bbx117-B59","doi-asserted-by":"crossref","first-page":"4169","DOI":"10.1128\/JB.01887-05","article-title":"Structural classification of bacterial response regulators: diversity of output domains and domain combinations","volume":"188","author":"Galperin","year":"2006","journal-title":"J Bacteriol"},{"key":"2019100807383968900_bbx117-B60","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.mib.2010.01.005","article-title":"Diversity of structure and function of response regulator output domains","volume":"13","author":"Galperin","year":"2010","journal-title":"Curr Opin Microbiol"},{"key":"2019100807383968900_bbx117-B61","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1128\/JB.01010-10","article-title":"argC orthologs from Rhizobiales show diverse profiles of transcriptional efficiency and functionality in Sinorhizobium meliloti","volume":"193","author":"Diaz","year":"2011","journal-title":"J Bacteriol"},{"key":"2019100807383968900_bbx117-B62","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1099\/mic.0.000255","article-title":"Evidence that COG0325 proteins are involved in PLP homeostasis","volume":"162","author":"Prunetti","year":"2016","journal-title":"Microbiology"},{"key":"2019100807383968900_bbx117-B63","doi-asserted-by":"crossref","first-page":"12","DOI":"10.3390\/biom7010012","article-title":"The Escherichia coli COG1738 member YhhQ is involved in 7-cyanodeazaguanine (preQ0) transport","volume":"7","author":"Zallot","year":"2017","journal-title":"Biomolecules"},{"key":"2019100807383968900_bbx117-B64","doi-asserted-by":"crossref","first-page":"D210","DOI":"10.1093\/nar\/gkw934","article-title":"ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation","volume":"45","author":"Kristensen","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B65","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"2019100807383968900_bbx117-B66","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/j.mib.2008.09.006","article-title":"Comparative genomics: the bacterial pan-genome","volume":"11","author":"Tettelin","year":"2008","journal-title":"Curr Opin Microbiol"},{"key":"2019100807383968900_bbx117-B67","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s12915-014-0066-4","article-title":"Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes","volume":"12","author":"Puigbo","year":"2014","journal-title":"BMC Biol"},{"key":"2019100807383968900_bbx117-B68","doi-asserted-by":"crossref","first-page":"16208","DOI":"10.1038\/nmicrobiol.2016.208","article-title":"Two fundamentally different classes of microbial genes","volume":"2","author":"Wolf","year":"2016","journal-title":"Nat Microbiol"},{"key":"2019100807383968900_bbx117-B69","doi-asserted-by":"crossref","first-page":"99","DOI":"10.2307\/2412448","article-title":"Distinguishing homologous from analogous proteins","volume":"19","author":"Fitch","year":"1970","journal-title":"Syst Zool"},{"key":"2019100807383968900_bbx117-B70","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1745-6150-2-33","article-title":"Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea","volume":"2","author":"Makarova","year":"2007","journal-title":"Biol Direct"},{"key":"2019100807383968900_bbx117-B71","doi-asserted-by":"crossref","first-page":"D744","DOI":"10.1093\/nar\/gkw1119","article-title":"OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs","volume":"45","author":"Zdobnov","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B72","doi-asserted-by":"crossref","first-page":"11819","DOI":"10.1073\/pnas.94.22.11819","article-title":"Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation","volume":"94","author":"Curnow","year":"1997","journal-title":"Proc Natl Acad Sci USA"},{"key":"2019100807383968900_bbx117-B73","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/1745-6150-7-46","article-title":"Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer","volume":"7","author":"Wolf","year":"2012","journal-title":"Biol Direct"},{"key":"2019100807383968900_bbx117-B74","doi-asserted-by":"crossref","first-page":"13126","DOI":"10.1073\/pnas.0605709103","article-title":"The cyanobacterial genome core and the origin of photosynthesis","volume":"103","author":"Mulkidjanian","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"2019100807383968900_bbx117-B75","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1128\/JB.01351-06","article-title":"Evolutionary genomics of lactic acid bacteria","volume":"189","author":"Makarova","year":"2007","journal-title":"J Bacteriol"},{"key":"2019100807383968900_bbx117-B76","doi-asserted-by":"crossref","first-page":"D448","DOI":"10.1093\/nar\/gkn684","article-title":"ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes","volume":"37","author":"Novichkov","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B77","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1128\/JB.01237-08","article-title":"Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes","volume":"191","author":"Novichkov","year":"2009","journal-title":"J Bacteriol"},{"key":"2019100807383968900_bbx117-B78","doi-asserted-by":"crossref","first-page":"e00956-14","DOI":"10.1128\/mBio.00956-14","article-title":"Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea","volume":"5","author":"Ran","year":"2014","journal-title":"MBio"},{"key":"2019100807383968900_bbx117-B79","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1186\/1743-422X-10-106","article-title":"Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family","volume":"10","author":"Yutin","year":"2013","journal-title":"Virol J"},{"key":"2019100807383968900_bbx117-B80","doi-asserted-by":"crossref","first-page":"D491","DOI":"10.1093\/nar\/gkw975","article-title":"Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation","volume":"45","author":"Grazziotin","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B81","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1093\/nar\/30.2.482","article-title":"A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis","volume":"30","author":"Makarova","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B82","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1745-6150-1-7","article-title":"A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action","volume":"1","author":"Makarova","year":"2006","journal-title":"Biol Direct"},{"key":"2019100807383968900_bbx117-B83","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1101\/gr.162001","article-title":"Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach","volume":"11","author":"Koonin","year":"2001","journal-title":"Genome Res"},{"key":"2019100807383968900_bbx117-B84","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1111\/j.1574-6968.2001.tb10814.x","article-title":"Novel domains of the prokaryotic two-component signal transduction systems","volume":"203","author":"Galperin","year":"2001","journal-title":"FEMS Microbiol Lett"},{"key":"2019100807383968900_bbx117-B85","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/bioinformatics\/bti739","article-title":"PilZ domain is part of the bacterial c-di-GMP binding protein","volume":"22","author":"Amikam","year":"2006","journal-title":"Bioinformatics"},{"key":"2019100807383968900_bbx117-B86","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1745-6150-4-19","article-title":"Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes","volume":"4","author":"Makarova","year":"2009","journal-title":"Biol Direct"},{"key":"2019100807383968900_bbx117-B87","doi-asserted-by":"crossref","first-page":"3743","DOI":"10.1093\/nar\/gkq054","article-title":"Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families","volume":"38","author":"Fozo","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B88","doi-asserted-by":"crossref","first-page":"6039","DOI":"10.1128\/JB.05535-11","article-title":"Defense islands in bacterial and archaeal genomes and prediction of novel defense systems","volume":"193","author":"Makarova","year":"2011","journal-title":"J Bacteriol"},{"key":"2019100807383968900_bbx117-B89","doi-asserted-by":"crossref","first-page":"667","DOI":"10.3389\/fmicb.2016.00667","article-title":"Diversity and evolution of type IV pili systems in Archaea","volume":"7","author":"Makarova","year":"2016","journal-title":"Front Microbiol"},{"key":"2019100807383968900_bbx117-B90","doi-asserted-by":"crossref","first-page":"5452","DOI":"10.1093\/nar\/gkh885","article-title":"\u2032Conserved hypothetical\u2032 proteins: prioritization of targets for experimental study","volume":"32","author":"Galperin","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2019100807383968900_bbx117-B91","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1016\/j.tibtech.2010.05.006","article-title":"From complete genome sequence to \u2032complete\u2032 understanding?","volume":"28","author":"Galperin","year":"2010","journal-title":"Trends Biotechnol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/20\/4\/1063\/30119612\/bbx117.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/20\/4\/1063\/30119612\/bbx117.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,25]],"date-time":"2025-06-25T11:50:22Z","timestamp":1750852222000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/20\/4\/1063\/4158183"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,9,14]]},"references-count":91,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2017,9,14]]},"published-print":{"date-parts":[[2019,7,19]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbx117","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.731288498.793537176","asserted-by":"object"}]},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,7]]},"published":{"date-parts":[[2017,9,14]]}}}