Conserved domain database

Conserved Domains and Protein Classification. HOW TO. Citing the Resources.

The Conserved Domain Database CDD is a database of well-annotated multiple sequence alignment models and derived database search models, for ancient domains and full-length proteins. These two classifications coincide rather often, as a matter of fact, and what is found as an independently folding unit of a polypeptide chain also carries specific function. Domains are often identified as recurring sequence or structure units, which may exist in various contexts. In molecular evolution such domains may have been utilized as building blocks, and may have been recombined in different arrangements to modulate protein function. CDD defines conserved domains as recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent.

Conserved domain database

Identify the putative function of a protein sequence. Identify a protein's classification based on domain architecture. Identify the amino acids in a protein sequence that are putatively involved in functions such as binding or catalysis, as mapped from conserved domain annotations to the query sequence. View a query protein sequence embedded within the multiple sequence alignment of a domain model. Interactively view the 3D structure of a conserved domain. Find other proteins with similar domain architecture. Interactively view the phylogenetic sequence tree for a conserved domain model of interest with or without a query sequence embedded. Conserved Domains and Protein Classification. HOW TO. CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins. How To. The results of CD-Search are presented as an annotation of protein domains on the user query sequence illustrated example , and can be visualized as domain multiple sequence alignments with embedded user queries.

InterPro in Select Format Select format. The table lists the root node of each hierarchy, the number of models in the hierarchy including the root node and intermediate nodes if presentconserved domain database, and the name of the protein domain super family.

Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Geer, Renata C. Hurwitz, Christopher J. Lanczycki, Fu Lu, Gabriele H. Marchler, James S. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD.

A domain architecture is defined as the sequential order of conserved domains in a protein sequence. Regardless of which method you use, the results will display a list of similar domain architectures , which are ranked by the number of domains they share in common with the query protein's domain architecture. The results display also provides links to the proteins that have a each architecture. Click on any frame of the image below to link to corresponding sections in the CDART help document, which provide additional details about the input options and output display. Click on any frame of the image above to link to subsequent sections in this help document, which provide additional details about the input options and output display.

Conserved domain database

Protein or Nucleotide Query Sequence. Batch of Protein Sequences. Find proteins with similar domain architectures. Conserved Domains and Protein Classification. HOW TO. Search Methods: Quick Start Guide. Text Term Search. Retrieve conserved domain records that contain a term s of interest e. See the help document for search tips , including a list of available search fields and examples of their use. Note: the "text term search" function also allows you to enter either unique identifiers UIDs , in the form of an accession e.

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Science and Mathematics. Individual residues that are parts of functional sites but not structural motifs are highlighted in bold font. If these different models belong to the same CDART superfamilies, the proteins will be sorted into the same domain architecture. Sign In or Create an Account. With either approach, the corresponding SPARCLE record s will display the name and functional label of the architecture, supporting evidence, and links to other proteins with the same architecture. Chanjuan Zheng. These are clustered into sequence-similar groups, and multiple sequence alignment models are created for clusters that contain either 1 sequences obtained from experimentally determined 3D structure, or 2 sequences associated with publications, unless these publications describe very large sequence sets such as complete genomes. Protein Sci. CDD curators record the location of functional motifs on protein domain models, so that these motifs can be mapped onto protein sequences and facilitate the interpretation of sequence conservation and variation, for example. Webb E. CD-Search will then evaluate alternative domain architectures that can be formed including all the original hits and one or more of the additional domain hits. Domain family hierarchies. Submit a comment.

Identify the putative function of a protein sequence. Identify a protein's classification based on domain architecture. Identify the amino acids in a protein sequence that are putatively involved in functions such as binding or catalysis, as mapped from conserved domain annotations to the query sequence.

Structured graphics Scientific and statistical data formats Images other. PMC Klimke W. Citing articles via Web of Science Issue Section:. Keyword s. Volume Christopher J. To provide a non-redundant view of the data, CDD clusters similar domain models from various sources into superfamilies. Data source. Aron Marchler-Bauer. At this time, about 60 million bacterial RefSeq proteins are named via SPARCLE out of million total bacterial proteins and million proteins with naming evidence provided. Figure 1.