TABLE 1.

Name, description, bibliographic reference, and web link to some of the most important TF databases. The description information was directly taken from the website.

Databases
Name and description	References
P2TF (Predicted Prokaryotic Transcription Factors): an integrated and comprehensive database of TF proteins, which contains a compilation of the TF genes within completely sequenced genomes and metagenomes	Ortet et al. (2012)
JASPAR: an open-access database of curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups	Castro-Mondragon et al. (2022)
TF2DNA: database provides comprehensive information about transcription factor binding motifs and their regulated genes for five model organisms and humans	Pujato et al. (2014)
GRASSIUS: Divided in GrassTFDB which provides a comprehensive collection of transcription factors from maize, sugarcane, sorghum and rice and GrassCoRegDB which provides a collection of proteins that are transcriptional regulatory factors but do not bind DNA in a sequence specific fashion	Yilmaz et al. (2009)
RegulonDB: the primary database on transcriptional regulation in Escherichia coli K-12	Santos-Zavaleta et al. (2019)
SM-TF database: collects available 3D structures of small molecule-transcription factor complexes from Protein Data Bank (PDB)	Xu et al. (2016)
CollecTF: a database of transcription factor binding sites (TFBS) in the Bacteria domain	Kılıç et al. (2014)
AnimalTFDB3: a comprehensive database including classification and annotation of genome-wide transcription factors (TFs), and transcription cofactors in 97 animal genomes	Hu et al. (2019)
PlantTFDB: Plant Transcription Factor Database	Jin et al. (2017)
RegPrecise: a database for capturing, visualisation and analysis of transcription factor regulons that were reconstructed by the comparative genomic approach in a wide variety of prokaryotic genomes	Novichkov et al. (2013)
SigMol: a repertoire of Quorum Sensing Signalling Molecules in Prokaryotes	Rajput et al. (2016)
Bionemo: stores manually curated information about proteins and genes directly implicated in the Biodegradation metabolism	Carbajosa et al. (2009)
PRODORIC: a comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites	Dudek and Jahn (2022)
Tools
footprintDB: predicts transcription factors which bind a specific DNA site or motif and DNA motifs or sites likely to be recognized by a specific DNA-binding protein	Sebastian and Contreras-Moreira (2014)
CiiDER: a user-friendly tool for predicting and analysing transcription factor binding sites, designed with biologists in mind	Gearing et al. (2019)
BART (Binding Analysis for Regulation of Transcription): a bioinformatics tool for predicting functional transcriptional regulators (TRs)	Wang et al. (2018)
PROMO: a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest	Messeguer et al. (2002)
DeepTFactor: a deep learning-based tool for the prediction of transcription factors	Kim et al. (2021)