{"id":"https://openalex.org/W1995452806","doi":"https://doi.org/10.1371/journal.pcbi.0020173","title":"Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems","display_name":"Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems","publication_year":2006,"publication_date":"2006-01-01","ids":{"openalex":"https://openalex.org/W1995452806","doi":"https://doi.org/10.1371/journal.pcbi.0020173","mag":"1995452806","pmid":"https://pubmed.ncbi.nlm.nih.gov/17140285"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0020173","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0020173","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020173&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020173&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079660157","display_name":"Duccio Medini","orcid":"https://orcid.org/0000-0001-6041-2603"},"institutions":[{"id":"https://openalex.org/I4210139938","display_name":"Novartis (Italy)","ror":"https://ror.org/04rcxhq50","country_code":"IT","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210139938"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Duccio Medini","raw_affiliation_strings":["Cellular Microbiology and BioInformatics Unit, Novartis Vaccines and Diagnostics, Siena, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cellular Microbiology and BioInformatics Unit, Novartis Vaccines and Diagnostics, Siena, Italy","institution_ids":["https://openalex.org/I4210139938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054576678","display_name":"Antonello Covacci","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139938","display_name":"Novartis (Italy)","ror":"https://ror.org/04rcxhq50","country_code":"IT","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210139938"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Antonello Covacci","raw_affiliation_strings":["Cellular Microbiology and BioInformatics Unit, Novartis Vaccines and Diagnostics, Siena, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cellular Microbiology and BioInformatics Unit, Novartis Vaccines and Diagnostics, Siena, Italy","institution_ids":["https://openalex.org/I4210139938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040360763","display_name":"Claudio Donati","orcid":"https://orcid.org/0000-0001-8688-1651"},"institutions":[{"id":"https://openalex.org/I4210139938","display_name":"Novartis (Italy)","ror":"https://ror.org/04rcxhq50","country_code":"IT","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210139938"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Claudio Donati","raw_affiliation_strings":["Cellular Microbiology and BioInformatics Unit, Novartis Vaccines and Diagnostics, Siena, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cellular Microbiology and BioInformatics Unit, Novartis Vaccines and Diagnostics, Siena, Italy","institution_ids":["https://openalex.org/I4210139938"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054576678"],"corresponding_institution_ids":["https://openalex.org/I4210139938"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.0448,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.85258046,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2","issue":"12","first_page":"e173","last_page":"e173"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.995199978351593,"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":0.9911999702453613,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6814862489700317},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.6386385560035706},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.5949158072471619},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5725575089454651},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5517162084579468},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5422871708869934},{"id":"https://openalex.org/keywords/effector","display_name":"Effector","score":0.5171117782592773},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.49982786178588867},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4993565082550049},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4255402088165283},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.41761842370033264},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32760339975357056},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.16753685474395752},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.0979563295841217}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6814862489700317},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.6386385560035706},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.5949158072471619},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5725575089454651},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5517162084579468},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5422871708869934},{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.5171117782592773},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.49982786178588867},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4993565082550049},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4255402088165283},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.41761842370033264},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32760339975357056},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.16753685474395752},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.0979563295841217}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.0020173","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0020173","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020173&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:17140285","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17140285","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.280.7922","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.280.7922","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/d0/6e/PLoS_Comput_Biol_2006_Dec_1_2(12)_e173.tar.gz","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:6369bd626ec34198a49ceda490d5de41","is_oa":true,"landing_page_url":"https://doaj.org/article/6369bd626ec34198a49ceda490d5de41","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":"PLoS Computational Biology, Vol 2, Iss 12, p e173 (2006)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2622178","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC1676029","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":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/152690","is_oa":true,"landing_page_url":"https://figshare.com/articles/Protein_Homology_Network_Families_Reveal_Step_Wise_Diversification_of_Type_III_and_Type_IV_Secretion_Systems/152690","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:1676029","is_oa":true,"landing_page_url":"http://doi.org/10.1371/journal.pcbi.0020173","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0020173","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0020173","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0020173&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1995452806.pdf","grobid_xml":"https://content.openalex.org/works/W1995452806.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1493206838","https://openalex.org/W1496547366","https://openalex.org/W1875969639","https://openalex.org/W1909944853","https://openalex.org/W1973092868","https://openalex.org/W1989660766","https://openalex.org/W1990453950","https://openalex.org/W2005360556","https://openalex.org/W2014141216","https://openalex.org/W2018045523","https://openalex.org/W2069992928","https://openalex.org/W2089594628","https://openalex.org/W2095293504","https://openalex.org/W2098558111","https://openalex.org/W2115043726","https://openalex.org/W2124637492","https://openalex.org/W2130916082","https://openalex.org/W2135771899","https://openalex.org/W2137749186","https://openalex.org/W2141885858","https://openalex.org/W2142276846","https://openalex.org/W2144878722","https://openalex.org/W2147512361","https://openalex.org/W2148606196","https://openalex.org/W2150550043","https://openalex.org/W2152495216","https://openalex.org/W2158714788","https://openalex.org/W2168069424","https://openalex.org/W2168513931","https://openalex.org/W2169690786","https://openalex.org/W4210400672"],"related_works":["https://openalex.org/W216150590","https://openalex.org/W2002335391","https://openalex.org/W2103040549","https://openalex.org/W2045258636","https://openalex.org/W2370709181","https://openalex.org/W2045342173","https://openalex.org/W2386553998","https://openalex.org/W2152847734","https://openalex.org/W2018030091","https://openalex.org/W2153173907"],"abstract_inverted_index":{"From":[0],"the":[1,11,27,34,40,43,46,54,59,63,72,77,105,112,163,197,218],"analysis":[2],"of":[3,22,58,65,95,114,131,144,162,202,221],"251":[4],"prokaryotic":[5],"genomes":[6],"stored":[7],"in":[8,76,111],"public":[9],"databases,":[10],"761,260":[12],"deduced":[13],"proteins":[14,41,135,172],"were":[15],"used":[16],"to":[17,98,107,151,156,166,217,224],"reconstruct":[18],"a":[19,83,99,129,141,167,191],"complete":[20],"set":[21,143],"bacterial":[23],"proteic":[24],"families.":[25,178],"Using":[26],"new":[28],"Overlap":[29],"algorithm,":[30],"we":[31,87,103],"have":[32,187],"partitioned":[33],"Protein":[35],"Homology":[36],"Network":[37],"(PHN),":[38],"where":[39],"are":[42,173],"nodes":[44],"and":[45,117,123,185,210],"links":[47],"represent":[48],"homology":[49],"relationships.":[50],"The":[51,179],"algorithm":[52,92],"identifies":[53],"densely":[55],"connected":[56],"regions":[57],"PHN":[60],"that":[61,89,183],"define":[62],"families":[64,109],"homologous":[66],"proteins,":[67],"here":[68],"called":[69],"PHN-Families,":[70],"recognizing":[71],"phylogenetic":[73],"relationships":[74],"embedded":[75],"network.":[78],"By":[79],"direct":[80],"comparison":[81],"with":[82,200],"manually":[84],"curated":[85],"dataset,":[86],"assessed":[88],"this":[90],"classification":[91,181],"generates":[93],"data":[94],"quality":[96],"similar":[97],"human":[100],"expert.":[101],"Then,":[102],"explored":[104],"network":[106],"identify":[108],"involved":[110],"assembly":[113],"Type":[115,118],"III":[116],"IV":[119],"secretion":[120],"systems":[121],"(T3SS":[122],"T4SS).":[124,159],"We":[125],"noticed":[126],"that,":[127],"beside":[128],"core":[130,164,199],"conserved":[132,198],"functions":[133],"(eight":[134],"for":[136,139,153,158],"T3SS,":[137,154],"seven":[138],"T4SS),":[140],"variable":[142],"accessory":[145,171],"components":[146],"is":[147],"always":[148],"present":[149],"(one":[150],"nine":[152],"one":[155],"five":[157],"Each":[160],"member":[161],"corresponds":[165],"single":[168],"PHN-Family,":[169],"while":[170],"distributed":[174],"among":[175],"different":[176,225],"pure":[177],"PHN-Family":[180],"suggests":[182],"T3SS":[184],"T4SS":[186],"been":[188],"assembled":[189],"through":[190],"step-wise,":[192],"discontinuous":[193],"process,":[194],"by":[195],"complementing":[196],"subgroups":[201],"nonconserved":[203],"proteins.":[204],"Such":[205],"genetic":[206],"modules,":[207],"independently":[208],"recruited":[209],"probably":[211],"tuned":[212],"on":[213],"specific":[214],"effectors,":[215],"contribute":[216],"functional":[219],"specialization":[220],"these":[222],"organelles":[223],"microenvironments.":[226]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}