A number of eukaryotic DNA-binding proteins contain a domain of about 170 to 190 amino acids known as the T-box domain [1,2,3] and which probably binds DNA. The T-box has first been found in the mice T locus (Brachyury) protein, a transcription factor involved in mesoderm differentiation. It has since been found in the following proteins:

• Vertebrate and invertebrate homologs of the T protein.
• Mammalian proteins TBX1 to TBX20.
• Mammalian protein TBR1 which is expressed specifically in brain.
• Mammalian and Xenopus laevis eomesodermin (eomes or TBR2).
• Xenopus laevis Vegt (or Antipodean), a transcription factor that activates the expression of wnt-8, eomes and Brachyury.
• Chicken TbxT.
• Drosophila protein optomotor-blind (omb).
• Drosophila protein brachyenteron (byn) (also known as Trg), which is required for the specification of the hindgut and anal pads.
• Drosophila protein H15.
• Caenorhabditis elegans proteins tbx-1 to tbx-40.

As signature patterns for the T-domain, we selected two conserved regions. The first region corresponds to the N-terminal of the domain and the second one to the central part. A profile that spans the complete domain was also developed.