The nearly ubiquitous polyamines (putrescine, spermidine and spermine) are polycationic mediators of cell proliferation and differentiation whose functions likely provide both stability and neutralization for nucleic acids. The following polyamine biosynthetic enzymes are evolutionary related and contain a polyamine biosynthesis (PABS) domain [1]:

• Spermidine synthase (EC 2.5.1.16) (putrescine aminopropyltransferase). It catalyzes the last step in the biosynthesis of spermidine from arginine and methionine; the conversion of putrescine to spermidine using decarboxylated S-adenosylmethionine as the cofactor.
• Spermine synthase (EC 2.5.1.22) (spermidine aminopropyltransferase). It converts spermidine into spermine using decarboxylated S-adenosylmethionine as the cofactor.
• Putrescine N-methyltransferase (EC 2.1.1.53). It catalyzes a step in the biosynthesis of nicotine in plants; the methylation of putrescine to N- methylputrescine using S-adenosylmethionine as the cofactor.

The PABS domain consists of two subdomains: an N-terminal subdomain composed of six β-strands, and a Rossmann-like C-terminal subdomain (see <PDB:1INL>). The larger C-terminal catalytic core subdomain consists of a seven-stranded β-sheet flanked by nine α helices. This subdomain resembles a topology observed in a number of nucleotide and dinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases (MTases) [2].

As a signature pattern, we selected a glycine-rich conserved region. We also developed a profile that spans both the N-terminal and the C-terminal catalytic subdomains.