ENTRAF

An Encyclopedia of well-annotated DNA-binding TRanscription factors in Bacteria and Archaea.

Gold standard resource for experimentally validated TFs

Regulatory proteins were retrieved from Uniprot and other databases and depurated by using experimental evidences from literature. All records were systematically and manually evaluated. From these searches, proteins with not experimental evidences and annotated with functions beyond gene regulation were excluded. These data enabled us to present a dataset of well-characterized proteins devoted to regulate gene expression at the transcriptional level. Overall, the project provides insights into the organization and regulation of genes in prokaryotes, and is an expansive resource of functional annotations for biological and biomedical research.

MEET THE TEAM

Ernesto Pérez Rueda
Researcher of the Research Institute in Applied Mathematics and Systems (IIMAS) of the Autonomous National University of México (UNAM), Mérida headquarters, as well as the Institute of Biotechnology of the UNAM. He belongs to the National System of Researchers Level III. His central research area is associated with bioinformatics of bacteria and archaea.

Alejandro Huerta-Saquero
Alejandro Huerta obtained his B.S. in Biology at the Faculty of Sciences of the National Autonomous University of Mexico (UNAM), and his Ph.D. in Biomedical Sciences at the Biomedical Research Institute of the UNAM. His dissertation focus on the regulation of the glutamine metabolism in Rhizobium etli. He had 4-year of postdoctoral experience at the Biotechnology Institute of the UNAM, where he studied the transcriptional regulation of enteropathogenic E. coli pathogenicity islands. Currently, he is a Professor at the Nanoscience and Nanotechnology Center of the UNAM in Ensenada, Baja California, Mexico, where he works on understanding the genetic and metabolic responses of Vibrio cholerae and other bacteria against antimicrobial nanomaterials. Alex is passionate about the sea, Baja craft beer and wine from the Guadalupe Valley.

Nancy Rivera Gómez
Nancy Rivera-Gomez got her Bachelor’s degree in biological sciences and Master's degree in Biotechnology by the Universidad Autonoma del Estado de Morelos. She got her doctorate by Universidad Nacional Autonoma de México, under direction by Dr. Perez-Rueda E., her research focused in bioinformatics analysis of the structure of transcription factors in bacterial and archaeal genomes. She worked as a manual curator of databases of enzymes in three different groups more. Currently, she works as a Catedra-CONACyT Fellow on studies of exomes of children's with autisms and intellectual disability on Institute National of Public Health in Mexico. She is passionate about microorganisms and their regulation, as well as in bioinformatics analysis of proteins and DNA.

Alba Romero
Alba obtained her Ph.D. at the Autonomous National University of México (UNAM), where she studied the transcriptional regulation of secondary metabolism in Streptomyces. During that time, she felt the necessity of a reliable database of well-annotated DNA-binding transcription factors in bacteria; because of that, she became involved in the ENTRAF project. Currently, she is a postdoctoral researcher at Andrés Bello University. Alba is studying the regulation and assembly of C. difficile spore's coat and exosporium. Besides transcriptional regulation, she is interested in the study of connections between protein's sequence, structure, and function with an emphasis in spore former bacteria.

Jose Antonio Ibarra
Jose Antonio is a chemical bacteriologist and parasitologist, and holds a M. Sc. in Microbiology by the National Polythechnic Institute (IPN) of Mexico. He holds a Ph.D. in Biochemistry by the Autonomous National University of México (UNAM). His research interests are: - Regulation of bacterial virulence genes - Biochemical characterization of transcriptional regulators - Use of recombinant proteins in basic and applied science - Search and characterization of antibiotic and antivirulence compounds "I am passionate about working for the Entraf project, to have a gloden knowledgebase of the transcription factors and the experimental evidences that have been found for them in a single website."

Emanuel Flores Bautista
Emanuel Flores is a bioengineer from the Autonomous University of Yucatán (UADY). During his bachelors thesis he worked on predicting the function of hypothetical transcription factors of E. coli under the supervision of Prof. Ernesto Pérez Rueda. He is currently a Biochemistry and Molecular Biophysics Ph.D. student at Caltech, working in the Phillips Lab to characterize unkown promoters in E. coli .

Rafael Hernandez Guerrero
Rafael is graduate student from the Universidad Autonoma de Yucatan