{"id":"https://openalex.org/W1583586808","doi":"https://doi.org/10.1186/1471-2105-6-172","title":"The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function","display_name":"The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function","publication_year":2005,"publication_date":"2005-07-12","ids":{"openalex":"https://openalex.org/W1583586808","doi":"https://doi.org/10.1186/1471-2105-6-172","mag":"1583586808","pmid":"https://pubmed.ncbi.nlm.nih.gov/16011798"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-6-172","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-172","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-172","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-172","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030398825","display_name":"Jan Kosi\u0144ski","orcid":"https://orcid.org/0000-0002-3641-0322"},"institutions":[{"id":"https://openalex.org/I4210120699","display_name":"International Institute of Molecular and Cell Biology","ror":"https://ror.org/01y3dkx74","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120699"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Jan Kosinski","raw_affiliation_strings":["Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland. kosa@genesilico.pl","Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland. kosa@genesilico.pl","institution_ids":["https://openalex.org/I4210120699"]},{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland","institution_ids":["https://openalex.org/I4210120699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055108552","display_name":"Marcin Feder","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120699","display_name":"International Institute of Molecular and Cell Biology","ror":"https://ror.org/01y3dkx74","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120699"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Marcin Feder","raw_affiliation_strings":["Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109, Warsaw, Poland","Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109, Warsaw, Poland","institution_ids":["https://openalex.org/I4210120699"]},{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland","institution_ids":["https://openalex.org/I4210120699"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003280938","display_name":"Janusz M. Bujnicki","orcid":"https://orcid.org/0000-0002-6633-165X"},"institutions":[{"id":"https://openalex.org/I4210120699","display_name":"International Institute of Molecular and Cell Biology","ror":"https://ror.org/01y3dkx74","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120699"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Janusz M Bujnicki","raw_affiliation_strings":["Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109, Warsaw, Poland","Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109, Warsaw, Poland","institution_ids":["https://openalex.org/I4210120699"]},{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland","institution_ids":["https://openalex.org/I4210120699"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.6545,"has_fulltext":true,"cited_by_count":111,"citation_normalized_percentile":{"value":0.89477831,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"6","issue":"1","first_page":"172","last_page":"172"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10123","display_name":"DNA Repair Mechanisms","score":0.6377999782562256,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10123","display_name":"DNA Repair Mechanisms","score":0.6377999782562256,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.19030000269412994,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.022199999541044235,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6656001210212708},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6634800434112549},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.615533709526062},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5883221626281738},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5662150382995605},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5075200796127319},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4750107228755951},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.41680800914764404},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.34379899501800537},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1896151602268219},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09939634799957275}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6656001210212708},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6634800434112549},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.615533709526062},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5883221626281738},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5662150382995605},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5075200796127319},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4750107228755951},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.41680800914764404},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34379899501800537},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1896151602268219},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09939634799957275},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015252","descriptor_name":"Deoxyribonucleases, Type II Site-Specific","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015252","descriptor_name":"Deoxyribonucleases, Type II Site-Specific","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015252","descriptor_name":"Deoxyribonucleases, Type II Site-Specific","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015252","descriptor_name":"Deoxyribonucleases, Type II Site-Specific","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015252","descriptor_name":"Deoxyribonucleases, Type II Site-Specific","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015252","descriptor_name":"Deoxyribonucleases, Type II Site-Specific","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-6-172","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-172","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-172","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16011798","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16011798","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:0eab4a6139b14100b58d35f847577e8f","is_oa":true,"landing_page_url":"https://doaj.org/article/0eab4a6139b14100b58d35f847577e8f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 6, Iss 1, p 172 (2005)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1802320","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1189080","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-6-172","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-172","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-172","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6899999976158142,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337356","display_name":"Fogarty International Center","ror":"https://ror.org/02xey9a22"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1583586808.pdf","grobid_xml":"https://content.openalex.org/works/W1583586808.grobid-xml"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W10876090","https://openalex.org/W95544650","https://openalex.org/W136476865","https://openalex.org/W164481364","https://openalex.org/W205578041","https://openalex.org/W1480952678","https://openalex.org/W1569201777","https://openalex.org/W1583990459","https://openalex.org/W1603399877","https://openalex.org/W1947762817","https://openalex.org/W1963534925","https://openalex.org/W1969247268","https://openalex.org/W1971596502","https://openalex.org/W1981153702","https://openalex.org/W1985017723","https://openalex.org/W1985301707","https://openalex.org/W1985924549","https://openalex.org/W1991877881","https://openalex.org/W1995277701","https://openalex.org/W1996242834","https://openalex.org/W1996819283","https://openalex.org/W2001054940","https://openalex.org/W2004228538","https://openalex.org/W2005402849","https://openalex.org/W2009367968","https://openalex.org/W2011700794","https://openalex.org/W2018272332","https://openalex.org/W2021466856","https://openalex.org/W2026478054","https://openalex.org/W2030748296","https://openalex.org/W2030960641","https://openalex.org/W2032574084","https://openalex.org/W2039405645","https://openalex.org/W2049044001","https://openalex.org/W2053621743","https://openalex.org/W2058713270","https://openalex.org/W2060039190","https://openalex.org/W2062123114","https://openalex.org/W2062166748","https://openalex.org/W2063973770","https://openalex.org/W2066076971","https://openalex.org/W2067248093","https://openalex.org/W2068599914","https://openalex.org/W2071326813","https://openalex.org/W2072313340","https://openalex.org/W2084466582","https://openalex.org/W2085207106","https://openalex.org/W2089611019","https://openalex.org/W2093435081","https://openalex.org/W2095126902","https://openalex.org/W2099886875","https://openalex.org/W2104759327","https://openalex.org/W2106066024","https://openalex.org/W2110863368","https://openalex.org/W2113677672","https://openalex.org/W2119195082","https://openalex.org/W2120157253","https://openalex.org/W2133391421","https://openalex.org/W2139582206","https://openalex.org/W2140455347","https://openalex.org/W2141885858","https://openalex.org/W2142529984","https://openalex.org/W2144483796","https://openalex.org/W2145268834","https://openalex.org/W2146763898","https://openalex.org/W2147423231","https://openalex.org/W2147667050","https://openalex.org/W2155606054","https://openalex.org/W2158714788","https://openalex.org/W2164843630","https://openalex.org/W2166458835","https://openalex.org/W2188699182","https://openalex.org/W2911680748","https://openalex.org/W4210400672","https://openalex.org/W4246188361"],"related_works":["https://openalex.org/W2898732673","https://openalex.org/W2410053581","https://openalex.org/W2383658677","https://openalex.org/W3123203398","https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W623104033","https://openalex.org/W1972473893","https://openalex.org/W1802639773","https://openalex.org/W2118505788"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,102,191],"PD-(D/E)XK":[2,57,119,165,221],"nuclease":[3,222],"superfamily,":[4],"initially":[5],"identified":[6,60],"in":[7,14,18,224,228,277],"type":[8],"II":[9],"restriction":[10,296],"endonucleases":[11],"and":[12,21,34,173,205,236,268,276,315,343],"later":[13],"many":[15,328],"enzymes":[16],"involved":[17],"DNA":[19,231,245,261],"recombination":[20],"repair,":[22],"is":[23,44,71],"one":[24],"of":[25,49,55,105,112,114,117,140,161,164,207,219,238,273,304,311,323,326,331,337,345],"the":[26,38,50,56,63,77,110,118,168,171,220,269,302,308,312,320,334,341,346],"most":[27,48],"challenging":[28],"targets":[29],"for":[30,137,194,279,295,333],"protein":[31,79,144,185,251,256,272,313],"sequence":[32,39,124],"analysis":[33],"structure":[35,235],"prediction.":[36],"Typically,":[37],"similarity":[40],"between":[41,52,143],"these":[42],"proteins":[43,226,278],"so":[45],"low,":[46],"that":[47,75,85,339],"relationships":[51],"known":[53,127,162],"members":[54,116],"superfamily":[58,120],"were":[59,66,197],"only":[61],"after":[62],"corresponding":[64,176],"structures":[65],"determined":[67],"experimentally.":[68],"Thus,":[69],"it":[70],"tempting":[72],"to":[73,87,126,167,177,187,258,285,301,318],"speculate":[74],"among":[76],"uncharacterized":[78,184],"families,":[80],"there":[81],"are":[82],"potential":[83,208],"nucleases":[84,166,196],"remain":[86],"be":[88,259,330],"discovered,":[89],"but":[90,232],"their":[91],"identification":[92,113,206,218],"requires":[93],"more":[94],"sensitive":[95,138],"tools":[96],"than":[97],"traditional":[98],"PSI-BLAST":[99],"searches.":[100],"RESULTS:":[101],"low":[103],"degree":[104],"amino":[106],"acid":[107],"conservation":[108],"hampers":[109],"possibility":[111],"new":[115,195,324],"based":[121],"solely":[122],"on":[123,307],"comparisons":[125],"members.":[128],"Therefore,":[129],"we":[130,216],"used":[131],"a":[132,159,249,253,260],"recently":[133],"developed":[134],"method":[135],"HHsearch":[136],"detection":[139],"remote":[141],"similarities":[142],"families":[145,163,186],"represented":[146],"as":[147,181,183,241,288],"profile":[148],"Hidden":[149],"Markov":[150],"Models":[151],"enhanced":[152],"by":[153,200],"secondary":[154],"structure.":[155],"We":[156],"carried":[157],"out":[158],"comparison":[160],"database":[169],"comprising":[170],"COG":[172],"PFAM":[174],"profiles":[175],"both":[178],"functionally":[179],"characterized":[180],"well":[182],"detect":[188],"significant":[189],"similarities.":[190],"initial":[192],"candidates":[193,294],"subsequently":[198],"verified":[199],"sequence-structure":[201],"threading,":[202],"comparative":[203],"modeling,":[204],"active":[209],"site":[210],"residues.":[211],"CONCLUSION:":[212],"In":[213],"this":[214],"article,":[215],"report":[217],"domain":[223],"numerous":[225],"implicated":[227],"interactions":[229],"with":[230,233],"unknown":[234],"mechanism":[237],"action":[239],"(such":[240,287],"putative":[242],"recombinase":[243],"RmuC,":[244],"competence":[246],"factor":[247],"CoiA,":[248],"DNA-binding":[250],"SfsA,":[252],"large":[254],"human":[255],"predicted":[257,264],"repair":[262],"enzyme,":[263],"archaeal":[265],"transcription":[266],"regulators,":[267],"head":[270],"completion":[271],"phage":[274,291],"T4)":[275],"which":[280,327],"no":[281],"function":[282],"was":[283],"assigned":[284],"date":[286],"YhcG,":[289],"various":[290],"proteins,":[292],"novel":[293],"enzymes).":[297],"Our":[298],"results":[299],"contributes":[300],"reduction":[303],"\"white":[305],"spaces\"":[306],"sequence-structure-function":[309],"map":[310],"universe":[314],"will":[316],"help":[317],"jump-start":[319],"experimental":[321],"characterization":[322],"nucleases,":[325],"may":[329],"importance":[332],"complete":[335],"understanding":[336],"mechanisms":[338],"govern":[340],"evolution":[342],"stability":[344],"genome.":[347]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}