The forkhead-associated (FHA) domain [1] is a putative nuclear signalling domain found in a variety of otherwise unrelated proteins. The FHA domain comprise approximately 55 to 75 amino acids and contains three highly conserved blocks separated by divergent spacer regions. Currently it has been found in the following proteins:

• Four transcription factors that also contain a forkhead (FH) domain: mouse myocyte nuclear factor 1 (MNF1), yeast transcription factor FHL1, which probably controls pre-mRNA processing, and yeast FKH1 and FKH2. In those protein the FHA domain is located N-terminal of the DNA-binding FH domain.
• Kinase-associated protein phosphatase (KAPP) from Arabidopsis thaliana, a protein which specifically interacts with the receptor-type Ser/Thr-kinase RLK5. In KAPP, the FHA domain maps to a region that interacts with the receptor-type protein kinase RLK5 only if the kinase is phosphorylated on serine residues [2].
• Two protein kinases from yeast that are involved in mediating the nuclear response to DNA damage: DUN1 and SPK1/SAD1 [3]. The latter is the only known protein containing two copies of the FHA domain.
• Protein kinase cds1 from fission yeast contains a FHA domain and might be the ortholog of SPK1.
• Protein kinase MEK1 from yeast, which is involved in meiotic recombination.
• Human nuclear antigen Ki67 which is expressed only in proliferating cells.
• Yeast hypothetical protein YHR115c, which contains a RING-finger C-terminal of the FHA domain.
• Yeast hypothetical proteins L8083.1 and 9346.10, which contain an extensive coiled-coil region C-terminal of the FHA domain.
• Caenorhabditis elegans hypothetical protein ZK632.2.
• Caenorhabditis elegans hypothetical protein C01G6.5.
• FraH from the prokaryote Anabaena, which contains a zinc-finger motif N- terminal of the FHA domain.
• An ORF from the bacterium Streptomyces, which is on the opposite strand of the protein kinase pks1, overlapping the ORF of the kinase.

The profile we developed for the FHA domain covers the total domain.