{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T04:51:43Z","timestamp":1790398303686,"version":"4.1.0"},"reference-count":99,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T00:00:00Z","timestamp":1771804800000},"content-version":"vor","delay-in-days":18,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004504","name":"Research Council of Lithuania","doi-asserted-by":"publisher","award":["S-MIP-24-82"],"award-info":[{"award-number":["S-MIP-24-82"]}],"id":[{"id":"10.13039\/501100004504","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Lithuanian Research Library Consortium LMBA affiliated"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>DNA polymerases are key players in DNA replication, repair, and maintenance. However, the overall abundance, diversity, and distribution of bacterial DNA polymerases have not been systematically explored. To close this knowledge gap, we computationally identified and characterized DNA polymerases and their homologs from A, B, C, X, and Y families in over 3000 representative bacterial species with complete genomes. We found that Y-family is the most abundant, followed by C and A families, whereas B and X families are rare. All species have replicative C-family polymerases, 96% have A-family polymerases, and 88% have Y-family members. In each family, we identified and annotated distinct groups, proofreading nucleases, and interaction motifs. Based on conserved associations for DnaE2 and Y-family groups, we identified 11 types of putative multimeric error-prone DNA polymerases supported by AlphaFold modeling. Approximately 90% of the complexes belong to four major types, exemplified by Meiothermus silvanus PolY\u2013RecA complex, Mycobacterium tuberculosis ImuA\u2013ImuB\u2013DnaE2, Escherichia coli Pol V (UmuC\u2013UmuD\u20322\u2013RecA), and Bacillus subtilis YqjW\u2013YqjX\u2013RecA. We found that distribution patterns of distinct polymerase groups and multimeric complexes are shaped by bacterial lineages, replication-system types, and environmental factors. Our results thus provide a comprehensive picture of DNA polymerase diversity and distribution across the bacterial domain.<\/jats:p>","DOI":"10.1093\/nar\/gkag133","type":"journal-article","created":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T12:57:34Z","timestamp":1771505854000},"source":"Crossref","is-referenced-by-count":4,"title":["Diversity and distribution of bacterial DNA polymerases"],"prefix":"10.1093","volume":"54","author":[{"given":"K\u0119stutis","family":"Timinskas","sequence":"first","affiliation":[{"name":"Institute of Biotechnology, Life Sciences Center, Vilnius University , Saul\u0117tekio 7, Vilnius, LT-10257 ,","place":["Lithuania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6135-8549","authenticated-orcid":false,"given":"Darius","family":"Kazlauskas","sequence":"additional","affiliation":[{"name":"Institute of Biotechnology, Life Sciences Center, Vilnius University , Saul\u0117tekio 7, Vilnius, LT-10257 ,","place":["Lithuania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albertas","family":"Timinskas","sequence":"additional","affiliation":[{"name":"Institute of Biotechnology, Life Sciences Center, Vilnius University , Saul\u0117tekio 7, Vilnius, LT-10257 ,","place":["Lithuania"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4215-0213","authenticated-orcid":false,"given":"\u010ceslovas","family":"Venclovas","sequence":"additional","affiliation":[{"name":"Institute of Biotechnology, Life Sciences Center, Vilnius University , Saul\u0117tekio 7, Vilnius, LT-10257 ,","place":["Lithuania"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,2,23]]},"reference":[{"key":"2026022307382398800_B1","doi-asserted-by":"publisher","DOI":"10.1142\/7667","volume-title":"DNA polymerases: discovery, characterization, and functions in cellular DNA transactions","author":"H\u00fcbscher","year":"2010"},{"key":"2026022307382398800_B2","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1042\/BST20180579","article-title":"An updated structural classification of replicative DNA polymerases","volume":"47","author":"Raia","year":"2019","journal-title":"Biochem Soc Trans"},{"key":"2026022307382398800_B3","doi-asserted-by":"publisher","first-page":"D376","DOI":"10.1093\/nar\/gkz1064","article-title":"The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures","volume":"48","author":"Andreeva","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B4","doi-asserted-by":"publisher","first-page":"MDNA3","DOI":"10.1128\/microbiolspec.MDNA3-0058-2014","article-title":"An unexplored diversity of reverse transcriptases in bacteria","volume":"3","author":"Zimmerly","year":"2015","journal-title":"Microbiol Spectr"},{"key":"2026022307382398800_B5","doi-asserted-by":"publisher","first-page":"e29","DOI":"10.1093\/nar\/gkab1207","article-title":"Identification and classification of reverse transcriptases in bacterial genomes and metagenomes","volume":"50","author":"Sharifi","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B6","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/S1672-0229(07)60001-1","article-title":"Comparative analysis of eubacterial DNA polymerase III alpha subunits","volume":"4","author":"Zhao","year":"2006","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2026022307382398800_B7","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1093\/nar\/gkt900","article-title":"Comprehensive analysis of DNA polymerase III alpha subunits and their homologs in bacterial genomes","volume":"42","author":"Timinskas","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B8","volume-title":"DNA replication","author":"Kornberg","year":"2005","edition":"2nd edition"},{"key":"2026022307382398800_B9","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/j.molcel.2009.12.025","article-title":"Reconstitution of the B. subtilis replisome with 13 proteins including two distinct replicases","volume":"37","author":"Sanders","year":"2010","journal-title":"Mol Cell"},{"key":"2026022307382398800_B10","doi-asserted-by":"publisher","first-page":"1716","DOI":"10.1126\/science.1066351","article-title":"Two essential DNA polymerases at the bacterial replication fork","volume":"294","author":"Dervyn","year":"2001","journal-title":"Science"},{"key":"2026022307382398800_B11","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1007\/s004380100564","article-title":"Genetic identification of two distinct DNA polymerases, DnaE and PolC, that are essential for chromosomal DNA replication in Staphylococcus aureus","volume":"266","author":"Inoue","year":"2001","journal-title":"Mol Gen Genomics"},{"key":"2026022307382398800_B12","doi-asserted-by":"publisher","first-page":"3746","DOI":"10.1093\/nar\/26.16.3746","article-title":"Phosphoesterase domains associated with DNA polymerases of diverse origins","volume":"26","author":"Aravind","year":"1998","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B13","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1038\/nsmb1078","article-title":"A coproofreading Zn(2+)-dependent exonuclease within a bacterial replicase","volume":"13","author":"Stano","year":"2006","journal-title":"Nat Struct Mol Biol"},{"key":"2026022307382398800_B14","doi-asserted-by":"publisher","first-page":"855","DOI":"10.1038\/s41467-017-00886-w","article-title":"High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center","volume":"8","author":"Banos-Mateos","year":"2017","journal-title":"Nat Commun"},{"key":"2026022307382398800_B15","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1038\/ng.3269","article-title":"DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader","volume":"47","author":"Rock","year":"2015","journal-title":"Nat Genet"},{"key":"2026022307382398800_B16","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1093\/nar\/29.5.1017","article-title":"Exoribonuclease superfamilies: structural analysis and phylogenetic distribution","volume":"29","author":"Zuo","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B17","doi-asserted-by":"publisher","first-page":"7747","DOI":"10.1073\/pnas.81.24.7747","article-title":"A separate editing exonuclease for DNA replication: the epsilon subunit of Escherichia coli DNA polymerase III holoenzyme","volume":"81","author":"Scheuermann","year":"1984","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026022307382398800_B18","doi-asserted-by":"publisher","first-page":"2603","DOI":"10.1093\/nar\/gki551","article-title":"An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus","volume":"33","author":"Galhardo","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B19","doi-asserted-by":"publisher","first-page":"13093","DOI":"10.1073\/pnas.1002614107","article-title":"Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis","volume":"107","author":"Warner","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026022307382398800_B20","doi-asserted-by":"publisher","first-page":"408","DOI":"10.1038\/embor.2011.51","article-title":"Breaking the rules: bacteria that use several DNA polymerase IIIs","volume":"12","author":"McHenry","year":"2011","journal-title":"EMBO Rep"},{"key":"2026022307382398800_B21","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/0006-3002(56)90127-5","article-title":"Enzymic synthesis of deoxyribonucleic acid","volume":"21","author":"Bessman","year":"1956","journal-title":"Biochim Biophys Acta"},{"key":"2026022307382398800_B22","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1016\/S0968-0004(98)01259-6","article-title":"Structure-specific DNA cleavage by 5\u2032 nucleases","volume":"23","author":"Ceska","year":"1998","journal-title":"Trends Biochem Sci"},{"key":"2026022307382398800_B23","doi-asserted-by":"publisher","first-page":"6995","DOI":"10.1093\/nar\/gkx494","article-title":"Comprehensive classification of the PIN domain-like superfamily","volume":"45","author":"Matelska","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B24","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1002\/j.1460-2075.1991.tb07917.x","article-title":"Structural basis for the 3\u2032\u20135\u2032 exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism","volume":"10","author":"Beese","year":"1991","journal-title":"EMBO J"},{"key":"2026022307382398800_B25","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/0092-8674(89)90883-0","article-title":"A conserved 3\u2032\u20135\u2032 exonuclease active site in prokaryotic and eukaryotic DNA polymerases","volume":"59","author":"Bernad","year":"1989","journal-title":"Cell"},{"key":"2026022307382398800_B26","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1073\/pnas.65.1.168","article-title":"Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis","volume":"65","author":"Klenow","year":"1970","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026022307382398800_B27","doi-asserted-by":"publisher","first-page":"2954","DOI":"10.1073\/pnas.68.12.2954","article-title":"Slow joining of newly replicated DNA chains in DNA polymerase I-deficient Escherichia coli mutants","volume":"68","author":"Okazaki","year":"1971","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026022307382398800_B28","doi-asserted-by":"publisher","first-page":"1867","DOI":"10.1111\/j.1365-2958.2005.04513.x","article-title":"A new in vivo termination function for DNA polymerase I of Escherichia coli K12","volume":"55","author":"Markovitz","year":"2005","journal-title":"Mol Microbiol"},{"key":"2026022307382398800_B29","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1111\/j.1574-6976.2012.00338.x","article-title":"DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair","volume":"36","author":"Fijalkowska","year":"2012","journal-title":"FEMS Microbiol Rev"},{"key":"2026022307382398800_B30","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1093\/molbev\/mst078","article-title":"Lateral gene transfer of family A DNA polymerases between thermophilic viruses, aquificae, and apicomplexa","volume":"30","author":"Schoenfeld","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2026022307382398800_B31","doi-asserted-by":"publisher","first-page":"4488","DOI":"10.1093\/nar\/gkad242","article-title":"Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features","volume":"51","author":"Czernecki","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B32","doi-asserted-by":"publisher","first-page":"10142","DOI":"10.1093\/nar\/gkaa760","article-title":"Diversity and evolution of B-family DNA polymerases","volume":"48","author":"Kazlauskas","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B33","doi-asserted-by":"publisher","first-page":"6268","DOI":"10.1128\/jb.172.11.6268-6273.1990","article-title":"The Escherichia coli polB gene, which encodes DNA polymerase II, is regulated by the SOS system","volume":"172","author":"Iwasaki","year":"1990","journal-title":"J Bacteriol"},{"key":"2026022307382398800_B34","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1016\/j.cell.2009.11.043","article-title":"Structural insight into translesion synthesis by DNA pol II","volume":"139","author":"Wang","year":"2009","journal-title":"Cell"},{"key":"2026022307382398800_B35","doi-asserted-by":"publisher","first-page":"15327","DOI":"10.1074\/jbc.270.25.15327","article-title":"Purification and properties of wild-type and exonuclease-deficient DNA polymerase II from Escherichia coli","volume":"270","author":"Cai","year":"1995","journal-title":"J Biol Chem"},{"key":"2026022307382398800_B36","doi-asserted-by":"publisher","first-page":"8737","DOI":"10.1073\/pnas.092269199","article-title":"SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness","volume":"99","author":"Yeiser","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026022307382398800_B37","doi-asserted-by":"publisher","first-page":"354","DOI":"10.3389\/fmicb.2014.00354","article-title":"Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery","volume":"5","author":"Makarova","year":"2014","journal-title":"Front Microbiol"},{"key":"2026022307382398800_B38","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.3389\/fmicb.2020.01585","article-title":"A unique B-Family DNA polymerase facilitating error-prone DNA damage tolerance in crenarchaeota","volume":"11","author":"Feng","year":"2020","journal-title":"Front Microbiol"},{"key":"2026022307382398800_B39","doi-asserted-by":"publisher","first-page":"e0265921","DOI":"10.1128\/mbio.02659-21","article-title":"A well-conserved archaeal B-family polymerase functions as an extender in translesion synthesis","volume":"13","author":"Feng","year":"2022","journal-title":"mBio"},{"key":"2026022307382398800_B40","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1016\/j.csbj.2025.01.010","article-title":"Common themes in architecture and interactions of prokaryotic PolB2 and pol V mutasomes inferred from in silico studies","volume":"27","author":"Timinskas","year":"2025","journal-title":"Comput Struct Biotechnol J"},{"key":"2026022307382398800_B41","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1016\/j.bbapap.2009.07.008","article-title":"DNA polymerase family X: function, structure, and cellular roles","volume":"1804","author":"Yamtich","year":"2010","journal-title":"Biochim Biophys Acta"},{"key":"2026022307382398800_B42","first-page":"19219","article-title":"Intrinsic apurinic\/apyrimidinic (AP) endonuclease activity enables Bacillus subtilis DNA polymerase X to recognize, incise, and further repair abasic sites","volume-title":"Proc Natl Acad Sci USA","author":"Ba\u00f1os","year":"2010"},{"key":"2026022307382398800_B43","doi-asserted-by":"publisher","first-page":"1721","DOI":"10.1111\/j.1365-2958.2004.04233.x","article-title":"Involvement of an X family DNA polymerase in double-stranded break repair in the radioresistant organism Deinococcus radiodurans","volume":"53","author":"Lecointe","year":"2004","journal-title":"Mol Microbiol"},{"key":"2026022307382398800_B44","doi-asserted-by":"publisher","first-page":"9750","DOI":"10.1093\/nar\/gks702","article-title":"DNA stabilization at the Bacillus subtilis PolX core\u2014a binding model to coordinate polymerase, AP-endonuclease and 3\u2032\u20135\u2032 exonuclease activities","volume":"40","author":"Banos","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B45","doi-asserted-by":"publisher","first-page":"11992","DOI":"10.1074\/jbc.M809342200","article-title":"The family X DNA polymerase from Deinococcus radiodurans adopts a non-standard extended conformation","volume":"284","author":"Leulliot","year":"2009","journal-title":"J Biol Chem"},{"key":"2026022307382398800_B46","doi-asserted-by":"publisher","first-page":"6398","DOI":"10.1093\/nar\/gkac461","article-title":"Noncanonical prokaryotic X family DNA polymerases lack polymerase activity and act as exonucleases","volume":"50","author":"Prostova","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B47","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/S1097-2765(01)00278-7","article-title":"The Y-family of DNA polymerases","volume":"8","author":"Ohmori","year":"2001","journal-title":"Mol Cell"},{"key":"2026022307382398800_B48","doi-asserted-by":"publisher","first-page":"13792","DOI":"10.1073\/pnas.94.25.13792","article-title":"Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an overexpression of dinB\/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA","volume":"94","author":"Kim","year":"1997","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026022307382398800_B49","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1038\/nature08178","article-title":"The active form of DNA polymerase V is UmuD'(2)C-RecA-ATP","volume":"460","author":"Jiang","year":"2009","journal-title":"Nature"},{"key":"2026022307382398800_B50","doi-asserted-by":"publisher","first-page":"171","DOI":"10.3109\/10409238.2010.480968","article-title":"A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V","volume":"45","author":"Patel","year":"2010","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"2026022307382398800_B51","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/nrm3289","article-title":"Y-family DNA polymerases and their role in tolerance of cellular DNA damage","volume":"13","author":"Sale","year":"2012","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2026022307382398800_B52","doi-asserted-by":"publisher","first-page":"e75628","DOI":"10.7554\/eLife.75628","article-title":"Investigating the composition and recruitment of the mycobacterial ImuA'-ImuB-DnaE2 mutasome","volume":"12","author":"Gessner","year":"2023","journal-title":"eLife"},{"key":"2026022307382398800_B53","doi-asserted-by":"publisher","first-page":"4393","DOI":"10.1093\/nar\/gkz198","article-title":"New insights into the structures and interactions of bacterial Y-family DNA polymerases","volume":"47","author":"Timinskas","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B54","doi-asserted-by":"publisher","first-page":"108108","DOI":"10.1016\/j.jbc.2024.108108","article-title":"The RecA-NT homology motif in ImuB mediates the interaction with ImuA', which is essential for DNA damage-induced mutagenesis","volume":"301","author":"Santos","year":"2025","journal-title":"J Biol Chem"},{"key":"2026022307382398800_B55","doi-asserted-by":"publisher","first-page":"D73","DOI":"10.1093\/nar\/gkv1226","article-title":"Assembly: a resource for assembled genomes at NCBI","volume":"44","author":"Kitts","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B56","doi-asserted-by":"publisher","first-page":"D957","DOI":"10.1093\/nar\/gkac974","article-title":"Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9","volume":"51","author":"Mukherjee","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B57","doi-asserted-by":"publisher","first-page":"D748","DOI":"10.1093\/nar\/gkae959","article-title":"BacDive in 2025: the core database for prokaryotic strain data","volume":"53","author":"Schober","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B58","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1186\/s12866-018-1320-7","article-title":"Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures","volume":"18","author":"Engqvist","year":"2018","journal-title":"BMC Microbiol"},{"key":"2026022307382398800_B59","doi-asserted-by":"publisher","first-page":"ME20074","DOI":"10.1264\/jsme2.ME20074","article-title":"TEMPURA: database of growth TEMPeratures of usual and RAre prokaryotes","volume":"35","author":"Sato","year":"2020","journal-title":"Microb Environ"},{"key":"2026022307382398800_B60","doi-asserted-by":"publisher","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":"2026022307382398800_B61","doi-asserted-by":"publisher","first-page":"2237","DOI":"10.1016\/j.jmb.2017.12.007","article-title":"A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core","volume":"430","author":"Zimmermann","year":"2018","journal-title":"J Mol Biol"},{"key":"2026022307382398800_B62","doi-asserted-by":"publisher","first-page":"D488","DOI":"10.1093\/nar\/gkac1077","article-title":"RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence\/machine learning","volume":"51","author":"Burley","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B63","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B64","doi-asserted-by":"publisher","first-page":"166943","DOI":"10.1016\/j.jmb.2021.166943","article-title":"GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts","volume":"433","author":"Pereira","year":"2021","journal-title":"J Mol Biol"},{"key":"2026022307382398800_B65","doi-asserted-by":"publisher","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":"Frickey","year":"2004","journal-title":"Bioinformatics"},{"key":"2026022307382398800_B66","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1038\/s41587-023-01953-y","article-title":"Identification of mobile genetic elements with geNomad","volume":"42","author":"Camargo","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2026022307382398800_B67","doi-asserted-by":"publisher","first-page":"6968","DOI":"10.1038\/s41467-022-34630-w","article-title":"Muscle5: high-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny","volume":"13","author":"Edgar","year":"2022","journal-title":"Nat Commun"},{"key":"2026022307382398800_B68","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2026022307382398800_B69","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2026022307382398800_B70","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Gutierrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2026022307382398800_B71","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B72","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1186\/1471-2105-11-431","article-title":"Hidden Markov model speed heuristic and iterative HMM search procedure","volume":"11","author":"Johnson","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2026022307382398800_B73","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1093\/bioinformatics\/bti125","article-title":"Protein homology detection by HMM\u2013HMM comparison","volume":"21","author":"S\u00f6ding","year":"2005","journal-title":"Bioinformatics"},{"key":"2026022307382398800_B74","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"2026022307382398800_B75","doi-asserted-by":"publisher","article-title":"Protein complex prediction with AlphaFold-multimer","author":"Evans","DOI":"10.1101\/2021.10.04.463034"},{"key":"2026022307382398800_B76","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026022307382398800_B77","doi-asserted-by":"publisher","first-page":"W437","DOI":"10.1093\/nar\/gkz367","article-title":"VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes","volume":"47","author":"Olechnovi\u010d","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B78","doi-asserted-by":"publisher","first-page":"4873","DOI":"10.1093\/bioinformatics\/btab448","article-title":"VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures","volume":"37","author":"Olechnovi\u010d","year":"2021","journal-title":"Bioinformatics"},{"key":"2026022307382398800_B79","doi-asserted-by":"publisher","first-page":"W210","DOI":"10.1093\/nar\/gkac387","article-title":"Dali server: structural unification of protein families","volume":"50","author":"Holm","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B80","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J Comput Chem"},{"key":"2026022307382398800_B81","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat Methods"},{"key":"2026022307382398800_B82","doi-asserted-by":"publisher","DOI":"10.25080\/Majora-92bf1922-011","article-title":"Statsmodels: econometric and statistical modeling with Python","volume-title":"Proceedings of the 9th Python in Science Conference","author":"Seabold","year":"2010"},{"key":"2026022307382398800_B83","doi-asserted-by":"publisher","first-page":"3109","DOI":"10.1111\/j.1742-4658.2011.08236.x","article-title":"The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III tau subunit","volume":"278","author":"Timinskas","year":"2011","journal-title":"FEBS J"},{"key":"2026022307382398800_B84","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1472-6807-13-8","article-title":"A structural role for the PHP domain in E. coli DNA polymerase III","volume":"13","author":"Barros","year":"2013","journal-title":"BMC Struct Biol"},{"key":"2026022307382398800_B85","doi-asserted-by":"publisher","first-page":"5354","DOI":"10.1093\/nar\/gkt162","article-title":"Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits alpha, epsilon, theta and beta reveals a highly flexible arrangement of the proofreading domain","volume":"41","author":"Ozawa","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B86","doi-asserted-by":"publisher","first-page":"e2322938121","DOI":"10.1073\/pnas.2322938121","article-title":"An additional proofreader contributes to DNA replication fidelity in mycobacteria","volume":"121","author":"Deng","year":"2024","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026022307382398800_B87","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.1002\/prot.25278","article-title":"VoroMQA: assessment of protein structure quality using interatomic contact areas","volume":"85","author":"Olechnovi\u010d","year":"2017","journal-title":"Proteins"},{"key":"2026022307382398800_B88","doi-asserted-by":"publisher","first-page":"8575","DOI":"10.1128\/JB.00653-07","article-title":"Reassessment of the in vivo functions of DNA polymerase I and RNase H in bacterial cell growth","volume":"189","author":"Fukushima","year":"2007","journal-title":"J Bacteriol"},{"key":"2026022307382398800_B89","doi-asserted-by":"publisher","first-page":"e4981","DOI":"10.1002\/pro.4981","article-title":"Myxococcus xanthus translesion DNA synthesis protein ImuA is an ATPase enhanced by DNA","volume":"33","author":"Lichimo","year":"2024","journal-title":"Protein Sci"},{"key":"2026022307382398800_B90","doi-asserted-by":"publisher","first-page":"1118","DOI":"10.1093\/nar\/gkr856","article-title":"Translesion-synthesis DNA polymerases participate in replication of the telomeres in Streptomyces","volume":"40","author":"Tsai","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B91","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/1745-6150-8-20","article-title":"Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems","volume":"8","author":"Aravind","year":"2013","journal-title":"Biol Direct"},{"key":"2026022307382398800_B92","doi-asserted-by":"publisher","first-page":"e70327","DOI":"10.1002\/pro.70327","article-title":"Assessing scoring metrics for AlphaFold2 and AlphaFold3 protein complex predictions","volume":"34","author":"Genz","year":"2025","journal-title":"Protein Sci"},{"key":"2026022307382398800_B93","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1016\/j.cell.2006.07.027","article-title":"The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases","volume":"126","author":"Bailey","year":"2006","journal-title":"Cell"},{"key":"2026022307382398800_B94","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1016\/j.cell.2006.07.028","article-title":"Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III","volume":"126","author":"Lamers","year":"2006","journal-title":"Cell"},{"key":"2026022307382398800_B95","doi-asserted-by":"publisher","first-page":"11056","DOI":"10.1093\/nar\/gku752","article-title":"Characterization of three mycobacterial DinB (DNA polymerase IV) paralogs highlights DinB2 as naturally adept at ribonucleotide incorporation","volume":"42","author":"Ordonez","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026022307382398800_B96","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1016\/j.cbpa.2011.07.018","article-title":"Bacterial replicases and related polymerases","volume":"15","author":"McHenry","year":"2011","journal-title":"Curr Opin Chem Biol"},{"key":"2026022307382398800_B97","doi-asserted-by":"crossref","first-page":"170146","DOI":"10.1098\/rsob.170146","article-title":"Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity","volume":"7","author":"Paschalis","year":"2017","journal-title":"Open Biol"},{"key":"2026022307382398800_B98","doi-asserted-by":"publisher","first-page":"e1002152","DOI":"10.1371\/journal.pgen.1002152","article-title":"Unexpected role for Helicobacter pylori DNA polymerase I as a source of genetic variability","volume":"7","author":"Garcia-Ortiz","year":"2011","journal-title":"PLoS Genet"},{"key":"2026022307382398800_B99","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1111\/j.1365-2958.2005.04725.x","article-title":"DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis","volume":"57","author":"Duigou","year":"2005","journal-title":"Mol Microbiol"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/4\/gkag133\/67072033\/gkag133.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/4\/gkag133\/67072033\/gkag133.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T12:38:35Z","timestamp":1771850315000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkag133\/8494767"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,5]]},"references-count":99,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,2,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkag133","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,2,27]]},"published":{"date-parts":[[2026,2,5]]},"article-number":"gkag133"}}