Updating the sequence based classification of glycosyl hydrolases
The host provides heat, moisture, and food, while the microorganisms contribute protein as microbial biomass and by-products of digestion such as volatile fatty acids that the animal uses (Madigan, Martinko, and Parker 1997 ).
Anatomically, the most complex specialization is found among the ruminants, such as cattle or sheep, with elaborate, multicompartmentalized stomachs specialized for a herbivorous diet.
Table 1 shows a list of gene names, characteristics of the products (which include the glucoside hydrolase family, if any), EMBL accession numbers of the sequenced DNAs, and the numbers of base pairs for the coding regions.
In terms of molecular evolution, rumen is a complex ecosystem in which natural gene transfer and traffic of genetic material could well occur.
Rumen organisms produce a wide range of highly active GHs that work synergistically (Flint 1997 ).
This xylanase contains a noncatalytic 455-residue linker sequence comprising 57 repeats of an octapeptide rich in amino acids G, S, K, and N (Black et al. When the relative synonymous codon usage (RSCU) values were used to construct this figure, the mean value, while its distances from the GH and non-GH groups are much higher (0.73 and 0.62, respectively).
To investigate the possible horizontal transfer of GH from rumen fungi, we aligned the catalytic domains of 54 endoglucanases of GH family 5 to a total length of 475 aa.
Search for updating the sequence based classification of glycosyl hydrolases:
The strong similarity between different glycosyl hydrolases of rumen fungi and bacteria suggests that most, if not all, of the glycosyl hydrolases of rumen fungi that play an important role in the degradation of cellulose and other plant polysaccharides were acquired by horizontal gene transfer events.