tailieunhanh - Báo cáo khoa học: Classification of the short-chain dehydrogenase ⁄reductase superfamily using hidden Markov models

The short-chain dehydrogenase⁄reductase (SDR) superfamily now has over 47 000 members, most of which are distantly related, with typically 20– 30% residue identity in pairwise comparisons, making it difficult to obtain an overview of this superfamily. | ỊFEBS Journal Classification of the short-chain dehydrogenase reductase superfamily using hidden Markov models Yvonne Kallberg1 2 Udo Oppermann3 and Bengt Persson1 2 4 1 IFM Bioinformatics Linkoping University Sweden 2 Department of Celland Molecular Biology CMB Karolinska Institutet Stockholm Sweden 3 StructuralGenomics Consortium The Botnar Research Centre NIHR BiomedicalResearch Unit University of Oxford UK 4 NationalSupercomputer Centre NSC and Swedish E-science Research Centre SERC Linkoping University Sweden Keywords bioinformatics classification genomes hidden Markov model short-chain dehydrogenases reductase Correspondence B. Persson IFM Bioinformatics Linkoping University S-581 83 Linkoping Sweden Fax 46 13 137 568 Tel. 46 13 282 983 E-mail bpn@ Received 23 August 2009 revised 12 February 2010 accepted 16 March 2010 doi The short-chain dehydrogenase7 reductase SDR superfamily now has over 47 000 members most of which are distantly related with typically 2030 residue identity in pairwise comparisons making it difficult to obtain an overview of this superfamily. We have therefore developed a family classification system based upon hidden Markov models HMMs . To this end we have identified 314 SDR families encompassing about 31 900 members. In addition about 9700 SDR forms belong to families with too few members at present to establish valid HMMs. In the human genome we find 47 SDR families corresponding to 82 genes. Thirteen families are present in all three domains Eukaryota Bacteria and Archaea and are hence expected to catalyze fundamental metabolic processes. The majority of these enzymes are of the extended type in agreement with earlier findings. About half of the SDR families are only found among bacteria where the classical SDR type is most prominent. The HMM-based classification is used as a basis for a sustainable and expandable nomenclature system. Introduction The short-chain dehydrogenase reductase SDR