Autonomous mobile genetic elements such as transposons or insertion sequences (IS) encode an enzyme, called transposase, required for excising and inserting the mobile element. The IS21 is among the largest of bacterial IS elements and encodes a transposase designated as istA (ORF1) as well as a second protein istB (ORF2) and represents the IS21/IS408/IS1162 family [E1,1]. The transposases of IS21-like IS contain a helix-turn-helix (HTH) motif in the N-terminal part that probably binds to DNA. An integrase catalytic domain (see <PDOC50994>) forms the central part of these IS21/IS408/IS1162 family transposases.

On the basis of sequence similarities, two types of HTH-domains can be found in IS21-like transposases.

The first, IS21 transposase-type HTH domain, occurs in transposases from the following elements:

• IS21 from Pseudomonas aeruginosa.
• IS1326 from Pseudomonas aeruginosa.
• IS640 from Shigella sonnei.
• IS5376 from Bacillus stearothermophilus.
• IS232 from Bacillus thuringiensis.
• IS21-like from Bacteroides fragilis.
• A potential insertion element from Chelatobacter heintzii.

The second is a IS408/IS1162 transposase-type HTH domain. Some proteins known to contain this domain:

• A putative transposase y4uI from Rhizobium sp. (strain NGR234).
• A putative transposase y4bL/y4kJ/y4tB from Rhizobium sp. (strain NGR234).
• Transposase from IS408 from Burkholderia cepacia.
• Transposase from IS1162 from Pseudomonas fluorescens.

The profiles we developed cover the entire IS21 transposase-type and IS408/IS1162 transposase-type HTH domains.