The PAS region [1,2] is an approximately 300 amino-acid conserved region who was first isolated in the Drosophila protein period clock (PER), the Ah receptor nuclear translocator (ARNT) and the Drosophila single-minded (SIM). It is composed of two or more imperfect repeats. Within the bHLH/PAS proteins the PAS region is involved in protein dimerization with another protein of the same family. It has also been associated with light reception, light regulation and circadian rhythm regulators (clock). In bacteria, the PAS repeat is usually associated with the input domain of a histidine kinase, or a sensor protein that regulates a histidine kinase.

The PAS repeat is often associated with a PAC motif (PAS-associated C-terminal motif), a conserved region of 40-45 amino acids situated carboxy-terminal to any PAS repeat and which can contribute to the PAS structural domain.

The PAS family can be divided into two groups. The first group contains the PAS domain followed by a PAC motif:

• Proteins of the bHLH/PAS superfamily which are transcriptional activators. In mammals, the Per orthologs (Per1/rigui and Per2), AH receptor nuclear translocator (ARNT) [3], single-minded orthologs (SIM1 and SIM2), Hypoxia- inducible factor 1 α (HIF1A), AH receptor (AHR), Neuronal Pas domain proteins (NPAS1 and NPAS2) [5], Endothelial Pas domain protein 1 (EPAS1) [6], mouse ARNT2, and human BMAL1. In Drosophila, single-minded (SIM), AH receptor nuclear translocator (dARNT) [4], similar protein (SIMA) and trachealess protein (TRH).
• Neurospora crassa light regulation proteins Wc1 and Wc2.
• Azotobacter nitrogen fixation regulatory element nifL.
• Bacillus subtilis sporulation kinase C (kinC).

The second group contains a PAS domain alone:

• Clock proteins such as Drosophila period clock proteins (PER) and mammalian clock proteins.
• Plant phytochromes A and B. Regulatory photoreceptors which exist in two forms that are reversibly interconvertible by light: the pr form that absorbs maximally in the red region of the spectrum and the pFR form that absorbs maximally in the far-red region. photoconversion of pr in pfr induces an array of morphogenic responses.

We developed two profiles, one that spans a single PAS repeat and one that covers the whole PAC domain.