PlnTFDB currently contains 28193 protein models, 26184 distinct protein sequences, arranged in 84 gene families. The assortment of genes in each of the families is based on the presence of one or more characteristic domains previously described in the literature (identified through statistical analyses, see rules for the classification of TF families).
To identify genes coding for transcription factors, previously constructed domain alignments (from the Pfam database version 23.0) or newly established alignments (PlnTFDB) were used to query the Plant proteome, using the hmmpfam programme of the HMMER suite, links to the domain alignments are provided.
Additionally, 1280 proteins were categorized as Orphans. These proteins contain one or more domain(s) whose presence, or combination, according to the literature, does not allow their classification into any of the defined families. Their role in the transcriptional regulation remains unclear.