RESUMO
We have developed an entirely sequence-based method that identifies and integrates relevant features that can be used to assign proteins of unknown function to functional classes, and enzyme categories for enzymes. We show that strategies for the elucidation of protein function may benefit from a number of functional attributes that are more directly related to the linear sequence of amino acids, and hence easier to predict, than protein structure. These attributes include features associated with post-translational modifications and protein sorting, but also much simpler aspects such as the length, isoelectric point and composition of the polypeptide chain.
Assuntos
Biologia Computacional/métodos , Processamento de Proteína Pós-Traducional , Sinais Direcionadores de Proteínas , Proteínas/química , Proteínas/classificação , Bases de Dados de Proteínas , Enzimas/química , Enzimas/classificação , Enzimas/metabolismo , Genoma Humano , Glicosilação , Humanos , Ponto Isoelétrico , Linguística , Redes Neurais de Computação , Fosforilação , Mapeamento Físico do Cromossomo , Ligação Proteica , Transporte Proteico , Proteínas/metabolismo , SoftwareRESUMO
O-GLYCBASE is a database of glycoproteins with O-linked glycosylation sites. Entries with at least one experimentally verified O-glycosylation site have been compiled from protein sequence databases and literature. Each entry contains information about the glycan involved, the species, sequence, a literature reference and http-linked cross-references to other databases. Version 4.0 contains 179 protein entries, an approximate 15% increase over the last version. Sequence logos representing the acceptor specificity patterns for GalNAc, GlcNAc, mannosyl and xylosyl transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu.dk/databases/OGLYCBASE/
Assuntos
Bases de Dados Factuais , Glicoproteínas/química , Glicoproteínas/metabolismo , Acetilgalactosamina/metabolismo , Acetilglucosamina/metabolismo , Sequência de Aminoácidos , Aspergillus niger , Glicosilação , Armazenamento e Recuperação da Informação , Internet , Manose/metabolismo , Processamento de Proteína Pós-Traducional , Xilose/metabolismoRESUMO
O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compared to version 2.0 the number of entries has increased by 20%. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu. dk/databases/OGLYCBASE/
Assuntos
Bases de Dados Factuais , Glicoproteínas/química , Sequência de Aminoácidos , Animais , Sítios de Ligação , Redes de Comunicação de Computadores , Glicoproteínas/metabolismo , Glicosilação , Armazenamento e Recuperação da Informação , Mucinas/metabolismoRESUMO
O-GLYCBASE is an updated database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the SWISS-PROT database. Entries include information about species, sequence, glycosylation sites and glycan type. O-GLYCBASE is now fully cross-referenced to the SWISS-PROT, PIR, PROSITE, PDB, EMBL, HSSP, LISTA and MIM databases. Compared with version 1.0 the number of entries have increased by 34%. Revision of the O-glycan assignment was performed on 20% of the entries. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through WWW or by anonymous FTP.
