scholarly journals New families in the classification of glycosyl hydrolases based on amino acid sequence similarities

1993 ◽  
Vol 293 (3) ◽  
pp. 781-788 ◽  
Author(s):  
B Henrissat ◽  
A Bairoch
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Protein Sequence ◽  
Sequence Data ◽  
Data Bank ◽  
The Other ◽  
Glycosyl Hydrolases ◽  
Protein Sequence Data ◽  
Sequence Similarities

301 glycosyl hydrolases and related enzymes corresponding to 39 EC entries of the I.U.B. classification system have been classified into 35 families on the basis of amino-acid-sequence similarities [Henrissat (1991) Biochem. J. 280, 309-316]. Approximately half of the families were found to be monospecific (containing only one EC number), whereas the other half were found to be polyspecific (containing at least two EC numbers). A > 60% increase in sequence data for glycosyl hydrolases (181 additional enzymes or enzyme domains sequences have since become available) allowed us to update the classification not only by the addition of more members to already identified families, but also by the finding of ten new families. On the basis of a comparison of 482 sequences corresponding to 52 EC entries, 45 families, out of which 22 are polyspecific, can now be defined. This classification has been implemented in the SWISS-PROT protein sequence data bank.

scholarly journals A classification of glycosyl hydrolases based on amino acid sequence similarities

1991 ◽  
Vol 280 (2) ◽  
pp. 309-316 ◽  
Author(s):  
B Henrissat
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Mechanism Of Action ◽  
Classification System ◽  
Structural Data ◽  
Amino Acid Sequences ◽  
Steady Increase ◽  
Glycosyl Hydrolases ◽  
Sequence Similarities

The amino acid sequences of 301 glycosyl hydrolases and related enzymes have been compared. A total of 291 sequences corresponding to 39 EC entries could be classified into 35 families. Only ten sequences (less than 5% of the sample) could not be assigned to any family. With the sequences available for this analysis, 18 families were found to be monospecific (containing only one EC number) and 17 were found to be polyspecific (containing at least two EC numbers). Implications on the folding characteristics and mechanism of action of these enzymes and on the evolution of carbohydrate metabolism are discussed. With the steady increase in sequence and structural data, it is suggested that the enzyme classification system should perhaps be revised.

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

scholarly journals A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities

1998 ◽  
Vol 329 (3) ◽  
pp. 719-719 ◽  
Author(s):  
J. A. CAMPBELL ◽  
G. J. DAVIES ◽  
V. BULONE ◽  
B. HENRISSAT
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Similarities

scholarly journals Towards a classification of glycosyltransferases based on amino acid sequence similarities: prokaryotic α-mannosyltransferases

1996 ◽  
Vol 318 (1) ◽  
pp. 133-138 ◽  
Author(s):  
Roberto A GEREMIA ◽  
E Alejandro PETRONI ◽  
Luis IELPI ◽  
Bernard HENRISSAT
Keyword(s):  
Amino Acid ◽  
Sequence Similarity ◽  
Amino Acid Residues ◽  
Glycosyl Hydrolases ◽  
Hydrophobic Cluster Analysis ◽  
Alignment Algorithms ◽  
Automatic Alignment ◽  
Genes Encoding ◽  
Sequence Similarities

A number of genes encoding bacterial glycosyltransferases have been sequenced during the last few years, but their low sequence similarity has prevented a straightforward grouping of these enzymes into families. The sequences of several bacterial α-mannosyltransferases have been compared using current alignment algorithms as well as hydrophobic cluster analysis (HCA). These sequences show a similarity which is significant but too low to be reliably aligned using automatic alignment methods. However, a region spanning approx. 270 residues in these proteins could be aligned by HCA, and several invariant amino acid residues were identified. These features were also found in several other glycosyltransferases, as well as in proteins of unknown function present in sequence databases. This similarity most probably reflects the existence of a family of proteins with conserved structural and mechanistic features. It is argued that the present IUBMB classification of glycosyltransferases could be complemented by a classification of these enzymes based on sequence similarities analogous to that which we proposed for glycosyl hydrolases [Henrissat, B. (1991) Biochem. J. 280, 309–316].

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