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Source Databases: Where does CDD content come from?
|
| Accession starts with | Source Database |
|---|---|
| cd | Curated at NCBI |
| pfam | Pfam |
| smart | SMART |
| COG | COGs |
| KOG | KOGs (available as a separate search set via CD-Search (RPS-BLAST); not searchable by text term in Entrez) |
| PRK | PRotein K(c)lusters (Entrez database) |
| CHL | Chloroplast and organelle proteins; subset of the PRK database. |
| LOAD_ | Library of Ancient Domains (LOAD) data set. (available as a separate data set via FTP; not searchable by text term in Entrez) |
Accessions that start with "cl" are for superfamily cluster records and can contain domain models from one or more source databases.
When searching CDD, it is possible to limit search results to domains from any given source database by using the Database Search Field.
How have CDs been assembled? 
Protein sequence alignments from each of the source databases are processed to provide links from each sequence to the protein division of Entrez. Occasionally, sequences that cannot be identified in Entrez's databases are omitted or substituted for closely related matches. Whenever possible, sequences in PFAM, SMART, and COGs alignments are substituted for closely related sequences that have direct links to three-dimensional structures.
A representative sequence is chosen, preferably with a structure-link, for technical reasons. The representative sequence is generally shown as the first member of the multiple sequence alignment for a domain model. By default, this representative is the 3D structure shown when CD alignments are visualized with Cn3D.
A consensus sequence is computed from the imported alignments. Alignment columns have to be represented in at least (weighted) 50% of all aligned sequences to determine the extent of the consensus. The most frequently occurring residue in each column (after weighting to account for redundancy) is reported. For the extent of the consensus sequence, a position-specific scoring matrix (PSSM) is calculated; the consensus sequence does not contribute to the residue frequency statistics. Search databases compiled of these PSSMs are available through the CD-Search service and on the NCBI FTP site as collections of pre-computed RPS-BLAST databases that can be used for locally installed versions of that program.
What is unique about NCBI-curated domains?
As noted in the section on CDD data sources, the goal of the NCBI conserved domain curation project is to provide database users with insights into how patterns of residue conservation and divergence in a family relate to functional properties, and to provide useful links to more detailed information that may help to understand those sequence/structure/function relationships. To do this, CDD Curators include the following types of information in order to supplement and enrich the traditional multiple sequence alignments that form the foundation of domain models:
3-dimensional structures and conserved core motifs: NCBI Conserved Domain Curators have re-evaluated and modified multiple sequence alignments imported from outside sources, and made them agree with what we can infer from three-dimensional structure and three-dimensional structure superposition. Curated alignments contain aligned blocks spanning all rows (with no gaps allowed inside blocks) and unaligned regions between blocks. The blocks are meant to represent conserved structural core motifs of the corresponding domain family. The 3D structures can be viewed with the Cn3D structure viewing program.
Conserved features: In addition to working on the alignment model, NCBI curators also record, when possible, the location and nature of features conserved in the domain family. Typically these would describe catalytic residues, binding sites, or motifs commonly referred to in the literature. Features are added if they seem applicable to the family described in the CD's scope and if there is evidence linking the feature to a set of addresses on the alignment. Such evidence is recorded and available for inspection, it may be free-text comments, citations linked to PubMed, or "structure evidence" - exemplifying the existence of a site by highlighting an actual molecular complex, for example. Both features and evidence can be visualized on CD summary pages (in the conserved features summary box and as hash marks (#) in the multiple sequence alignment displays), and with the Cn3D structure viewing program.
Phylogenetic organization: Based on evidence from sequence comparison, NCBI Conserved Domain Curators attempt to organize related domain models into phylogenetic family hierarchies (A separate illustration and additional information are provided below.) The CDTree program used by NCBI curators can be downloaded in order to view NCBI-curated domains interactively and in greater detail.
Links to electronic literature resources: NCBI curated domains also provide links to citations in PubMed and to the NCBI Bookshelf.
NCBI-curated domains can be recognized in CDD search results by their "cd" accession number prefix. It is also possible to limit CDD search results to domain models from any given source database by using the Database Search Field.
What is a domain family hierarchy?
A domain family hierarchy is a set of related domains that share a common ancestor, a common set of conserved residues, and a common general function, but differ from each other in their specific phylogeny, specific functions, and additional spans of conserved residues. Domain hierarchies are present in NCBI-curated domains in order to provide insights into how patterns of residue conservation and divergence in a family relate to functional properties.
Hierarchies have generic "parent" models and more specific "children", and may be more than two layers deep. NCBI CDD Curators attempt to split "children" nodes where they see evidence for ancient gene duplications resulting in orthologous groups, often occurring together with functional divergence. The CDTree program used by NCBI curators can be downloaded in order to view NCBI-curated domains interactively and in greater detail.
Click anywhere on the image to open the complete, interactive record for this domain model (cd00400) in the Conserved Domain Database (CDD).
What is a superfamily?
A superfamily cluster is a set of conserved domain models that generate overlapping annotation on the same protein sequences. These models are assumed to represent evolutionarily related domains and may be redundant with each other.
Clustering methodology:
Superfamily members are clustered through an automated process that involves the following steps:
- identify domain models that have overlapping hits on Entrez protein sequences from at least two different sentinel taxonomic nodes (e.g., high level nodes such as flowering plants, conifers, mollusks, flatworms, roundworms, annelid worms, insects, amphibians, mammals, etc.).
- pull those domain models into the superfamily
- if any domain models are part of an NCBI-curated family hierarchy, pull in all members of the hierarchy
- repeat steps 1-3 for each newly added domain until no more new models are pulled in
NOTE: Multi-domain models that were computationally detected are not included in Superfamily clusters. These models are likely to contain multiple single domains and might falsely join superfamily clusters.
Rationale:
Superfamilies provide a method for organizing data within CDD in a non-redundant way. CDD contains conserved domains from a number of different source databases, each of which may have its own model for a given conserved domain. The models might share many similiarities in their reported residue conservation patterns, but differ in the specific protein sequences used in the multiple alignment, their footprint length [domain boundaries], and biological annotations. Because of the similarities, RPS-BLAST might find that multiple domain models align to the same general region of a query protein, but have different footprints and E-value scores relative to the query protein. If the footprints of two or more domain models overlap on the query, those models are clustered into the same superfamily, then the superfamily continues to be extended using the methodology described above.
Example:
One example of a superfamily is Cluster ID cl02915, which contains various domain models for the voltage-gated chloride channel. Superfamily members include the NCBI-curated domain cd00400 and all members of that family hierarchy plus domain models from external resources.
Selection of Superfamily Representative:
A superfamily can contain one to many domain models. As of spring 2008, approximately 70% of the ~9,000 superfamilies contain a single model and the rest contain multiple models. Single model superfamilies often represent proteins specific to certain organisms or taxonomic lineages (for example, viruses). The numbers of superfamilies containing single or multiple domain models will continue to evolve as new domains are imported and new NCBI-curated hierarchies are added.
In superfamilies contatining multiple domain models, one of the models is selected as the source of the superfamily name and description. The representative is one of the following, listed in priority order:
- the parent node of an NCBI-curated domain family hierarchy, if one is present in the superfamily cluster. In the few cases where a superfamily contains more than one NCBI-curated domain, the parent of the hierarchy with the largest number of sequence hits is chosen as the superfamily representative.
- the Pfam domain model that hits the largest number of Entrez protein sequences in an RPS-BLAST search
- the SMART, COG, PRK, or CHL model that hits the largest number of Entrez protein sequences in an RPS-BLAST search
- the sole member of a superfamily
Search Tips: How to find conserved domains
Protein Query Sequence (CD-Search):
Most users will explore conserved domains starting from CD-Search results for a protein of interest.
The query can be a protein sequence in FASTA format or the GI or Accession of a protein sequence that exists in the Entrez Protein database.
The search results will show the conserved domains found in the protein, and the colored bars that depict the domain footprints are active hotlinks that open the corresponding CD summary pages with your query sequence embedded in the multiple sequence alignment of proteins used to create the domain model.
The second half of this help document provides details on how to use the CD-Search service, including input required and output shown.
Search Entrez CDD directly:
Conserved domains can also be searched directly in the Entrez CDD database. The Entrez query interface allows searching for keywords, publication dates, and taxonomic span, and more. The PubMed help document and Entrez help document provide general information about using the Entrez search system. The information below pertains specifically to CDD.
For example, search the Entrez CDD database for strings like "Kinase" or "pfam023*" or "Tetratrico*" to see how it works:
Search Results: Document Summary (DocSum)
The initial search results provide a list (document summary, or "DocSum") of the conserved domain records that contain your search term, which can appear in any field of the record, unless a search field was specified in the query.
If desired, you can narrow your search by restricting the query to a search field of interest or adding more terms with a Boolean AND.
Alternatively, you can broaden your search by adding more terms (e.g., synonyms) to your query with a Boolean OR, or by following links to Superfamily Members.
"Display" menu options:
The "Display" menu on the DocSum (search results) page allows you to view output in the formats below. The "Display" menu options act upon all of the CDD records in the current window (default) or on the subset selected with checkboxes.The detailed view ("CD Summary page) for a conserved domain can only be viewed for one record at a time by following the link for that record's accession number.
Format Description Summary shows the conserved domain's: accession number thumbnail image indicating if the conserved domain includes a protein sequence from a 3D structure.
If a 3D structure is included, the thumbnail will be a still graphic of the actual domain structure.
If no 3D structure is available for the protein family from which the domain model was created, the thumbnail icon will show a schematic of a multiple sequence alignment.short name, which concisely defines the domain a text summary, which provides a synopsis of biological function and salient features of the domain PSSMid Brief shows the conserved domain's: accession number short name, which concisely defines the domain PSSMid UI List shows only the conserved domain's: PSSMid Additional options The other options in the Display menu are described in the section of this help document on Links to related data in Entrez
In addition to displaying CDD search results in various formats, the Display menu can also be used to retrieve related data in CDD and in other Entrez databases by selecting the "xxxxx Links" menu items. It therefore provides integrated access to data many different data types.
For example, the Superfamily Member Links option will retrieve the other domain models in CDD that appear to be evolutionarily related to or redundant with the domains listed/selected on the page. The Protein, Structure, Gene, PubMed, etc. links traverse to associated data in those Entrez databases.
"Links" pop-up menus:
The "Links" menu for an individual CDD record on the Docsum page page allows you to retrieve related data for that particular domain model. For example, if you select the Superfamily Members option from the "Links" menu of a CDD record (e.g., cd00400), you will retrieve the other domain models in CDD that appear to be evolutionarily related to or redundant with cd00400. In contrast, the "xxxxx Links" options in the "Display" menu near the top of the search results page act upon all of the CDD records in the current window (default) or on the subset selected with checkboxes.
The links are described in the help document section on "CDD Record: What information is displayed for each domain model on its CD Summary page?" : "Links to related data in Entrez". Most links are accessible from both the DocSum page and the detailed CDD records (also called "CD summary pages"), with the exception of two (Architecture and Books) that are available only from the CD summary pages.
Search Fields
By default, Entrez searches All Fields of the database unless a specific search field is indicated in the query. Search fields can be selected from pop-up menus on either the Limits and Preview/Index page, or can be typed directly in your query (surrounding field names with square brackets [], for example, [Organism] or [Orgn]).* The Index button on the Preview/Index page allows you to browse the index of each search field, where you can see the available terms, the number of records containing each term or phrase, as well as the syntax for entering values in search fields such as Modification Date or Publication Date.
The currently available fields include:
Field name Abbreviation* Description Sample Search All Fields [all] Searches the complete database record "chloride channel"[All]
will retrieve the CDD records that contain the phrase "chloride channel" in any field of the record.
The quotes surrounding the search terms ensure they are searched as a phrase.**Accession [accn] Searches only the accession number of the record, which is always an alphanumeric combination. The accession number prefix indicates the source database cd00400[All]
will retrieve the CDD records that contain the phrase "chloride channel" in any field of the record. (The quotes surrounding the search terms ensure they are searched as a phrase.)Alternative Accession [AltAccn] Native accession format from an external source database. For example, the PFAM database uses accessions with a format such as pf08617. When these are imported into CDD, the accessions are represented in a format such as pfam08617. Similarly, the SMART database uses a format such as sm00100, while records that have been imported into CDD have a format such as smart00100. This is primarily done to indicate that SMART and PFAM domain alignments may have been modified slightly by NCBI staff, for example by the substitution of a protein sequence that does not have 3D structure with a highly similar one that does (as explained in the help document section on the CD assembly process). pf08617[AltAccn]
will retrieve the pfam08617 record from CDD.Database [db] Use this field to limit your search to a particular source database. cdd[db]
will retrieve the NCBI curated domain models and superfamily records, which are also created at NCBI, from CDD.
pfam[db]
will retrieve the domain models that were imported from the PFAM database.Filter [filt] The "Filter" search field allows you to narrow your retrieval to records that have certain attributes, such as curated or uncurated, or records that have links to other Entrez databases of interest.
Many attributes from the Filter field are provided in the "Display" and "Links" menus of an Entrez search results page, and in the "Links" box on a CD Summary Page. A detailed explanation of each type of link is provided in the description of the CD Summary page "Links" box.cdd_gene[filt]
will retrieve the CDD records that have associated data in the Entrez Gene database.
On the CDD search results page, you can then open "Display" menu and select the Gene Links option to view the corresponding Entrez Gene records.Modification Date [mdat] Date of the most recent changes to the alignment model and/or descriptive information Number of Sites [ns] The number of conserved features, such as catalytic or binding sites, that have been annotated on a domain. Conserved features are available on NCBI-curated domains.
As of April 2008, this ranges from zero to 21 sites. (To see the current range, select the "Number of Sites" search field on the "Preview/Index" page, then use the "Index" button to view the index of that search field and see available values.)4[ns]
will retrieve the NCBI curated domain models that contain four sites (i.e., four conserved features).Organism [Orgn] The root taxonomy node of a conserved domain. This is the highest node in the NCBI Taxonomy database that encompasses all organisms whose protein sequences are in the multiple sequence alignment for a domain model. eukaryotes[orgn]
will retrieve conserved domains found in eukaryotes.PSSM Length [plen] Length of the PSSM or domain search model. This is the same as the length of the consensus sequence. Publication Date [pdat] date a CD was published [create date = date at which the seed (or de-novo) alignment was imported into CDD; what is publication date = date of release into public version of CDD?] Structure Representative [strp] The number of structures that have protein sequences in the multiple sequence alignment for a domain model.
As of April 2008, this ranges from zero to 72 protein sequences from structures. (To see the current range, select the "Structure Representative" search field on the "Preview/Index" page, then use the "Index" button to view the index of that search field and see available values.)6[strp]
will retrieve domain models that contain six protein sequences from 3D structures in their multiple sequence alignment.Text Word [word] The long description (text summary) of the conserved domain. The Description of Sites [sd] Brief descriptions of conserved features. Title [titl] The short name of a conserved domain, which concisely defines the domain.
Example: Voltage gated ClC (voltage gated chloride channel)voltage[titl]
will retrieve the CDD records that have the term "voltage" as part of their short name, such as cd00400: Voltage gated ClC and pfam00654: Voltage CLC, which represent NCBI-curated and externally imported domain models, respectively, for the voltage gated chloride channel.
* In a query, the field name may be typed as the full name or abbreviation, and may be in upper, lower, or mixed case. It must be surrounded by square brackets []. A space between the search term and the field specifier is optionl. If desired, surround a phrase with quotes to force an adjacency search. For example, the sample queries below will work equally:
"chloride channel" [WORD]
"chloride channel"[WORD]
"chloride channel" [word]
"chloride channel"[Text Word]
** The quotes surrounding the search terms in the All Fields example ensure the terms are searched as a phrase. If quotes are not used and the terms are not automatically recognized as a phrase by the Entrez system, Entrez will insert a Boolean AND between the terms and they may or may not appear adjacent to each other in the retrieved records. More search tips are provided in the PubMed help document and Entrez help document.
Entrez Protein links to Conserved Domains:All sequence records in the Entrez Protein database have been RPS-BLASTed against the Conserved Domain database. These pre-calculated search results are available as "Conserved Domains" links from protein sequence records, making protein functional information one click away from the sequence record.
Domain architecture: CDART:The Conserved Domain Architecture Retrieval Tool (CDART) program has been used to analyze the domain architecture of all sequence records in the Entrez Protein database, and to identify proteins with similar architecture. Those proteins are accessible by selecting "Domain Relatives" in the "Links" menu of a protein sequence record of interest.
Or, you can search CDART directly by entering a query protein sequence in FASTA format, or entering the GI or Accession number of a protein sequence that already exists in the Entrez Protein database. CDART will then retrieve proteins that contain one or more of the domains present in the query sequence.
CDD Record (CD Summary page): What information is displayed for each domain model?
A CD-summary page provides the following information for a domain model (example: cd00400: voltage-gated chloride channel):
Text Summary (synopsis of function):
- The synopsis of the domain's biological function, shown at the top of a CD summary page, and was written by curators at the source database. The text summary in an NCBI curated domain also describes the taxonomic extent of the domain, whether it is a monomer or dimer, and any salient features. The text summary in a superfamily record is derived from the representative domain.
Links to related data in Entrez:* The "architecture" and "books" links are found only on the CD summary page for a conserved domain. They are not present in the "Display" or "Links" menu on the Docsum page page that shows initial search results.
Link Name Description Family Members Members of the hierarchy to which the domain belongs. This link is only provided for NCBI-curated domain records. Superfamily This links to the record for the CDD superfamily to which this domain belongs. Superfamily Members This retrieves all the other domain models that belong to the superfamily. Architecture * Proteins found by CDART to contain one or more of the domains present in the proteins that are hit by domains found in the domain superfamily Protein Superset of all protein sequences found by RPS BLAST to contain the domain (with an E-value equal to or better than the default cutoff of 0.01). Therefore, this superset includes CD-Search hit types: specific hits and non-specific hits. Protein Specific Hits Subset of protein sequences found by RPS BLAST to contain the domain (with an e-value that is equal to or lower than a domain-specific Threshold E-value). More about specific hits... Structure All of the protein sequences from 3D structure records that were hit by RPS BLAST by this domain model's PSSM Gene Links from the RPS BLAST concise display hits to the protein sequences listed in Entrez Gene records.
Details: Each protein listed in an Entrez Gene record has been RPS BLASTed against the domain models in CDD. Links are then created between specific regions of those protein sequences and top-scoring domain models which align to them. Top-scoring domain models are shown either as specific-hits, or as the superfamily to which the highest-ranking non-specific hit belongs.HomoloGene Links from the RPS BLAST concise display hits to the protein sequences listed in HomoloGene records. (The details provided for Gene links, above, also apply to HomoloGene links.) PubMed PubMed citations annotated on the domain. All references have been identified by curators, either by NCBI staff for the NCBI-curated domains, or by the staff of the external databases represented in CDD. For NCBI-curated domains, the PubMed link leads to the citations that have been annotated on that particular node of a domain family hierarchy, not for all nodes in the tree. Free in PMC The subset of PubMed links that are available as free full text in PubMed Central. Books * Full text information in the Entrez Books database that further clarifies or elucidates the domain's function, the protein's role in metabolic pathways, and other broad overview information, including diagrams and illustrations. Taxonomy The highest node in the NCBI Taxonomy database that encompasses all organisms whose protein sequences are in the multiple sequence alignment for a domain model. The taxonomy link for a superfamily retrieves the highest taxonomic node for all of its constituent domain models.
Statistics:
Item Description PSSM-ID the unique identifier for the position-specific scoring matrix (PSSM) generated by RPS-BLAST for a given multiple sequence alignment. If the sequence alignment changes in any way, for example, if new sequences are added to the alignment, a new PSSM will be generated and will receive a new PSSM-ID. View PSSM Opens a separate window with a graphical view of the domain model's PSSM, showing the relative frequencies of various residues at each position of the domain model. This viewer was prepared as part of an NCBI course on Exploring 3D Molecular Structures. Aligned lists the number of rows in the sequence alignment (including the consensus seuqence). In general, each row comes from a different sequence record. However, sometimes two or more rows can be from the same GI number (i.e., same sequence record), if the sequence contains multiple instances of the domain. Status information about the CD's curation status. Curated models have been realigned by NCBI with consideration of 3D structure. Alignments imported from outside sources have not been changed (except for the import process detailed above) Created date at which the seed (or de-novo) alignment was imported into CDD Updated date of the most recent changes to the alignment model and/or descriptive information