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PROSITE documentation PDOC00027 [for PROSITE entry PS00027]

'Homeobox' domain signature and profile


The 'homeobox' is a protein domain of 60 amino acids [1,2,3,4,5] first identified in a number of Drosophila homeotic and segmentation proteins. It has since been found to be extremely well conserved in many other animals, including vertebrates. This domain binds DNA through a helix-turn-helix type of structure. Some of the proteins which contain a homeobox domain play an important role in development. Most of these proteins are known to be sequence specific DNA-binding transcription factors. The homeobox domain has also been found to be very similar to a region of the yeast mating type proteins. These are sequence-specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion.

A schematic representation of the homeobox domain is shown below. The helix-turn-helix region is shown by the symbols 'H' (for helix), and 't' (for turn).

        |        |         |         |         |         |         |
        1       10        20        30        40        50        60

The pattern we developed to detect homeobox sequences is 24 residues long and spans positions 34 to 57 of the homeobox domain.


Proteins which contain a homeobox domain can be classified, on the basis of their sequence characteristics, into various subfamilies. We have developed specific patterns for conserved elements of the antennapedia, engrailed and paired families.

Expert(s) to contact by email:

Buerglin T.R.

Last update:

April 2006 / Pattern revised.

Technical section

PROSITE methods (with tools and information) covered by this documentation:

HOMEOBOX_1, PS00027; 'Homeobox' domain signature  (PATTERN)

HOMEOBOX_2, PS50071; 'Homeobox' domain profile  (MATRIX)


1AuthorsGehring W.J.
Source(In) Guidebook to the homebox genes, Duboule D., Ed., pp1-10, Oxford University Press, Oxford, (1994).

2AuthorsBuerglin T.R.
Source(In) Guidebook to the homebox genes, Duboule D., Ed., pp25-72, Oxford University Press, Oxford, (1994).

3AuthorsGehring W.J.
SourceTrends Biochem. Sci. 17:277-280(1992).

4AuthorsGehring W.J. Hiromi Y.
TitleHomeotic genes and the homeobox.
SourceAnnu. Rev. Genet. 20:147-173(1986).
PubMed ID2880555

5AuthorsSchofield P.N.
SourceTrends Neurosci. 10:3-6(1987).

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