{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T12:33:11Z","timestamp":1761741191742,"version":"build-2065373602"},"reference-count":82,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T00:00:00Z","timestamp":1761696000000},"content-version":"vor","delay-in-days":301,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Direcci\u00f3n General de Asuntos del Personal Acad\u00e9mico-Universidad Nacional Aut\u00f3noma de M\u00e9xico","award":["IN-220523"],"award-info":[{"award-number":["IN-220523"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>DNA-binding transcription factors (TFs) have a central role in regulation of gene expression at the transcription initiation level. These proteins have been experimentally described in multiple bacterial and archaeal genomes. These descriptions have allowed their prediction in complete genomes. In this work, we collected 1784 experimentally validated TFs across 25 bacterial and seven archaeal phyla, including Gammaproteobacteria, Bacillota, and Actinomycetota in bacteria and Thermoproteota and Thermococci in archaea. The collection of regulatory proteins was organized into a relational database, named ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes or ENTRAF. The database shows the experimental evidence for all the TFs [protein structure information (X-ray or NMR structural data); binding of purified proteins; footprinting assays; site mutation; in vitro transcription assay; and PRiMer extension analysis, among others], their global regulatory roles (carbon source assimilation, virulence, antibiotic resistance, stress, and DNA damage), evolutionary families, and structural classifications. In addition, we achieved a global description of the collection in terms of their regulatory mechanisms (activation, repression, and dual activities), structural diversity, functional categories, and protein families. We consider that this collection of well-annotated TFs could be used as a benchmark, enhancing the predictions for this class of proteins in complete genomes. The complete collection of TFs is available at https:\/\/entraf.iimas.unam.mx and https:\/\/github.com\/BioIIMAS\/ENTRAF.<\/jats:p>","DOI":"10.1093\/database\/baaf071","type":"journal-article","created":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T12:17:14Z","timestamp":1759925834000},"source":"Crossref","is-referenced-by-count":0,"title":["ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0"],"prefix":"10.1093","volume":"2025","author":[{"given":"Silvia","family":"Tenorio-Salgado","sequence":"first","affiliation":[{"name":"Tecnol\u00f3gico Nacional de M\u00e9xico, Instituto Tecnol\u00f3gico de M\u00e9rida , Av. Tecnol\u00f3gico km. 4.5, 97118, Merida, Yucatan ,","place":["M\u00e9xico"]}]},{"given":"Cinthia Rodr\u00edguez","family":"Maya","sequence":"additional","affiliation":[{"name":"Centro de Estudios en Computaci\u00f3n Avanzada, Coordinaci\u00f3n de la Investigaci\u00f3n Cient\u00edfica, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Avenida Universidad 3000. Col. UNAM-CU.Coyoacan. 04510, Ciudad de M\u00e9xico ,","place":["M\u00e9xico"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9165-1241","authenticated-orcid":false,"given":"Edgardo","family":"Galan-Vasquez","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas, UNAM , Avenida Universidad 3000. Col. UNAM-CU.Coyoacan. 04510, Ciudad de M\u00e9xico ,","place":["M\u00e9xico"]}]},{"given":"Andr\u00e9 Borges","family":"Farias","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica\u2014LNCC , Avenida Get\u00falio Vargas, 25651075, Petr\u00f3polis, Rio de Janeiro ,","place":["Brazil"]}]},{"given":"Dulce","family":"\u00c1lvarez-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas, Unidad Acad\u00e9mica del Estado de Yucat\u00e1n, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Carretera Sierra Papacal - Chuburn\u00e1. Km. 5.5. CP. 97302, M\u00e9rida, Yucat\u00e1n ,","place":["M\u00e9xico"]}]},{"given":"Jose Luis","family":"Villalpando-Aguilar","sequence":"additional","affiliation":[{"name":"Tecnol\u00f3gico Nacional de M\u00e9xico, Instituto Tecnol\u00f3gico de Campeche , Carretera Campeche\u2014Esc\u00e1rcega Km. 9 C.P. 24500 Lerma, Campeche ,","place":["M\u00e9xico"]}]},{"given":"Alberto J","family":"Martin","sequence":"additional","affiliation":[{"name":"Laboratorio de Redes Biol\u00f3gicas, Centro Cient\u00edfico y Tecnol\u00f3gico de Excelencia Ciencia & Vida, Fundaci\u00f3n Ciencia & Vida , Av. del Valle Nte. 725, 8580704 Huechuraba, Regi\u00f3n Metropolitana ,","place":["Chile"]},{"name":"Escuela de Ingenier\u00eda, Facultad de Ingenier\u00eda, Arquitectura y Dise\u00f1o, Universidad San Sebasti\u00e1n , Bellavista 7, Recoleta, 8580704, Santiago ,","place":["Chile"]}]},{"given":"Leonardo","family":"Ledesma-Dominguez","sequence":"additional","affiliation":[{"name":"Facultad de Ingenier\u00eda, Divisi\u00f3n de Ingenier\u00eda El\u00e9ctrica, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Avenida Universidad 3000. Col. UNAM-CU.Coyoacan. 04510, Ciudad de M\u00e9xico ,","place":["M\u00e9xico"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6879-0673","authenticated-orcid":false,"given":"Ernesto","family":"Perez-Rueda","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas, Unidad Acad\u00e9mica del Estado de Yucat\u00e1n, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Carretera Sierra Papacal - Chuburn\u00e1. Km. 5.5. 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