A number of ATP-binding proteins that are are thought to protect cells from extreme stress by controlling the aggregation of denaturation of vital cellular structures have been shown [1,2] to be evolutionary related. These proteins are listed below.

• Escherichia coli clpA, which acts as the regulatory subunit of the ATP- dependent protease clp.
• Rhodopseudomonas blastica clpA homolog.
• Escherichia coli heat shock protein clpB and homologs in other bacteria.
• Bacillus subtilis protein mecB.
• Yeast heat shock protein 104 (gene HSP104), which is vital for tolerance to heat, ethanol and other stresses.
• Neurospora heat shock protein hsp98.
• Yeast mitochondrial heat shock protein 78 (gene HSP78) [3].
• CD4A and CD4b, two highly related tomato proteins that seem to be located in the chloroplast.
• Trypanosoma brucei protein clp.
• Porphyra purpurea chloroplast encoded clpC.

The size of these proteins range from 84 Kd (clpA) to slightly more than 100 Kd (HSP104). They all share two conserved regions of about 200 amino acids that each contains an ATP-binding site. In addition to the ATP-binding A and B motifs there are many parts in these two domains that are also conserved. We have selected two of these regions as signature patterns. The first signature is located in the first domain, some ten residues to the C-terminal of the ATP-binding B motif. The second pattern is located in the second domain in-between the ATP-binding A and B motifs.