The rpiR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 75-80 amino acids present in prokaryotic regulators of transcription. The domain is named after Escherichia coli rpiR, also known as alsR, a repressor of the rpiB gene and the als operon, which encode proteins involved in sugar metabolism. The DNA-binding rpiR-type HTH domain occurs usually in the N-terminal part; the C-terminal part can contain a phosphosugar-binding SIS domain. Most rpiR-type HTH regulators are involved in sugar metabolism as transcription repressors, but some are activators [1,2,3].

Some proteins known to contain a rpiR-type HTH domain:

• Escherichia coli rpiR, a transcription repressor of ripB, a ribose-phosphate isomerase, and of the als operon, involved in transport and metabolism of allose.
• Pseudomonas aeruginosa hexR, a transcription repressor of the hex regulon, involved in sugar metabolism.
• Bacillus subtilis glvR, a transcription activator of the glv operon, involved in transport and metabolism of maltose [3].

The profile we developed spans the entire rpiR-type HTH DNA-binding domain.