The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases (EC 3.2.1.4), cellobiohydrolases (EC 3.2.1.91) (exoglucanases), or xylanases (EC 3.2.1.8) [1,2]. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family G [3] or as the glycosyl hydrolases family 11 (GH11) [4,E1,E2]. Family 11 is monospecific, only consisting of xylanases. The enzymes which are currently known to belong to this family are listed below.

• Aspergillus awamori xylanase C (xynC).
• Bacillus circulans, pumilus, stearothermophilus and subtilis xylanase (xynA).
• Clostridium acetobutylicum xylanase (xynB).
• Clostridium stercorarium xylanase A (xynA).
• Fibrobacter succinogenes xylanase C (xynC) which consist of two catalytic domains that both belong to family 10.
• Neocallimastix patriciarum xylanase A (xynA).
• Ruminococcus flavefaciens bifunctional xylanase XYLA (xynA). This protein consists of three domains: a N-terminal xylanase catalytic domain that belongs to family 11 of glycosyl hydrolases; a central domain composed of short repeats of Gln, Asn an Trp, and a C-terminal xylanase catalytic domain that belongs to family 10 of glycosyl hydrolases.
• Schizophyllum commune xylanase A.
• Streptomyces lividans xylanases B (xlnB) and C (xlnC).
• Trichoderma reesei xylanases I and II.

The GH11 domain folds into a jelly-roll shape likened to a partially closed right hand (see <PDB:4HK8>). Several anti-parallel β-strands bend almost 90° to produce a substrate-binding groove characteristic of the GH11 domain active sites. Two catalytic Glu residues face each other from opposite sides of the groove. The hydrolysis reaction is believed to follow a double-displacement mechanism, with one Glu residue acting as a general acid/base catalyst and the other as a nucleophile.

Two of the conserved regions in these enzymes are centered on glutamic acid residues which have both been shown [5], in Bacillus pumilis xylanase, to be necessary for catalytic activity. We have used both regions as signature patterns. We have also developed a profile that covers the entire GH11 domain.