What is a conserved domain?

In molecular evolution such domains may have been utilized as building blocks, and may have been recombined in different arrangements to modulate protein function. We define conserved domains as recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis.

Conserved domains contain conserved sequence patterns or motifs, which allow for their detection in polypeptide sequences. The distinction between domains and motifs is not sharp, however, especially in the case of short repetitive units. Functional motifs are also present outside the scope of structurally conserved domains. The CD database is not meant to systematically collect such motifs.

Click anywhere on the image to open the complete, interactive 3D record for this protein structure (1IGR) in Cn3D, a free helper application available for Windows, Macintosh, and Unix platforms. Note: Cn3D must be present on your computer, however, in order for the link to work. Cn3D installation takes only a couple of minutes and a tutorial describes the program's features and functions.

Open the 1IGR structure summary record in the Molecular Modeling Database (MMDB) to access more information about the protein, its conserved domains, and ligands (small molecules). On that page, follow the "show annotation" link to open an interactive graphic in which you can click on a conserved domain or ligand of interest to view its complete information in the Conserved Domain Database or PubChem, respectively. Click on the grey bar representing the overall protein, or on a colored bar representing an individual 3D domain of interest, to retrieve similar 3D structures, as identified by the Vector Alignment Search Tool (VAST).

View the CD-Search help document for more details about the program that was used to identify the conserved domains in the protein chain. The concise display of the conserved domains is shown here and includes specific hits, superfamilies, and multi-domains. (Open the current, interactive CD-Search results for this protein to view alignments of its sequence to a conserved domain's consensus sequence, and/or to access a full display of all domain models found.)

Multiple sequence alignments provide basis for conserved domain models

Specifically, conserved domain models are based on multiple sequence alignments of related proteins spanning a variety of organisms to reveal sequence regions containing the same, or similar, patterns of amino acids. The illustration below provides an example, showing the multiple sequence alignment for the Furin-like domain, which is present in the Type 1 Insulin-like Growth Factor Receptor (1IGR) protein. Click anywhere on the image to open the complete, interactive CDD record for that domain model, cd00064. A separate section of this help document provides additional information about multiple sequence alignment display options.

In the CDD database, protein sequences from three-dimensional structures are included in domain models whenever possible, as one goal of the NCBI conserved domain curation effort is to make multiple sequence alignments agree with what we can infer from three-dimensional structure and three-dimensional structure superposition, in order to understand sequence/structure/function relationships. The sequence-based domain models and corresponding 3D structures are also cross-referenced to each other through Entrez "Links" between CDD and structure records.

Separate sections of this CDD help document provide additional details about the source databases from which domain models are collected, the conserved domain assembly process, including the generation of a position-specific scoring matrix (PSSM) for each domain model, and multiple sequence alignment display options.

Source Databases:  Where does CDD content come from?

The source databases differ in their scope of coverage and the method by which they develop their models. Therefore, each source database may have its own model for a given conserved domain, in addition to some domain models found only in that database. To provide a non-redundant view of the data, CDD clusters similar domain models from various sources into superfamilies. The data sources include:

The goal of the curation project is to provide CDD 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. The presence of conserved features help to affirm family membership in search results with borderline significance, for example. NCBI CDD Curators provide feature annotation and associated evidence in a computer friendly way, so that the scientific community can build software tools for the automation of tasks like annotation transfer, for example.

The content of imported domain models is determined by the providers of the source database, with slight modifications made at NCBI to link a domain model's member sequences to corresponding, complete protein sequence and 3D structure records in Entrez databases, when possible. The method by which imported domain models are integrated into the CDD database is described in the CD assembly process section of this help document.

When searching CDD, it is possible to limit search results to domains from any given source database by using the Database Search Field.

CD Assembly Process:  How have CDs been assembled?

Domain models from external data sources are assembled by various methods, ranging from automated processing to manual curation, depending on the individual source database. Upon import into CDD, protein sequence alignments (illustration) from each of the source databases are processed in an automated way to provide links from each aligned sequence to the corresponding, complete record in the Entrez Protein database. 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 (passing a stringent sequence similarity threshold) that have direct links to three-dimensional structures in the Moleclular Modeling Database (MMDB).

A representative sequence is chosen for each domain model, 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 50% of all aligned sequences (weighted by diversity) to determine the extent of the consensus. The most frequently occurring residue in each column (after weighting to account for redundancy) is reported.

A position-specific scoring matrix (PSSM) is calculated for the extent of the consensus sequence. The PSSM profiles the various amino acids that were present in a given position of the multiple sequence alignment for a domain model and how frequently each one was observed. The consensus sequence does not contribute to the residue frequency statistics. Each PSSM receives a unique identifier (PSSM ID).

A PSSM ID is the unique identifier for a domain model's position-specific scoring matrix (PSSM). If a domain model's PSSM changes in any way as a result of updates to its multiple sequence alignment, it receives a new PSSM ID. This happens because a conserved domain model can evolve over time. For example, as new sequence data become available, the curators of a source database might add sequences to a multiple sequence alignment or update the sequences already present. As a result of such changes to the domain model, the PSSM and its ID can change. (Additional notes: Each superfamily record in the Conserved Domain Database also has a PSSM ID, which refers to the specific set of conserved domain PSSM IDs that comprise the superfamily, rather than to an actual position-specific scoring matrix for the overall superfamily. Obsolete PSSMs (e.g., 667) cannot be retrieved through the Entrez CDD search interface because they are no longer indexed. However, they can be retrieved from the archival copy of the database by using the "Direct Fetch via UID" option on the CDD Search Methods page.)

Search databases compiled of these PSSMs are available through the CD-Search service (see help document) 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, NCBI-curated domains use 3D-structure information to explicitly to define domain boundaries, aligned blocks, and amend alignment details.

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 interactively with the Cn3D structure viewing program. More information about viewing structures is provided in the section of this document on CD summary pages, and the illustration at the right provides an example of a protein structure that has been annotated by NCBI curators to highight the Cl- binding residues. (Click on the illustration to open the current, interactive record for the Voltage-Gated Chloride Channel domain model, cd00400, in the Conserved Domain Database (CDD). From there, you can open an interactive version of the 3D structure, with conserved feature annotations, in the free Cn3D structure viewing program.)

Conserved features/sites:   In addition to working on the alignment model (illustration), 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/sites summary box, and as hash marks (#) in the multiple sequence alignment displays), and with the Cn3D structure viewing program. An example is shown in the illustration at the right. (Click on the illustration to open the current, interactive record for the Voltage-Gated Chloride Channel domain model, cd00400, in the Conserved Domain Database (CDD). Note that the live web page may look different from the illustration shown here, because the Conserved Domain Database continues to evolve with the addition of new data; however, the concepts shown in the illustration remain stable.)

In addition, the CD-Search tool can be used to identify conserved features in a query protein sequence, designated by small triangles (illustrated example) in the search results graphical summary, when such features can be mapped from the conserved domain annotations to the query sequence.

Phylogenetic organization:   Based on evidence from sequence comparison, NCBI Conserved Domain Curators attempt to organize related domain models into phylogenetic family hierarchies (illustrated example). 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 NCBI Bookshelf that discuss the domain. These references are selected by curators and, whenever possible, include articles that provide evidence for the biological function of the domain and/or discuss the evolution and classification of a domain family.

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?

Some domain families have only a single node, while others have a hierarchy that is two or more levels deep, sometimes with numerous nodes ("subfamilies")at each level. Such hierarchies have generic "parent" models and more specific "children". The parent node contains a span of conserved residues that is also present in each of the children. Each of the child nodes can have additional conserved residues that extend beyond that span and help to further characterize the members of the child node.

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, with or without a query sequence embedded.

An illustrated example of a subfamily hierarchy is provided below.

What is a superfamily?

Superfamily members are clustered through an automated process that involves the following steps:

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:

If more than 50 percent of the conserved domain accessions from a previous version of a cluster are no longer present in the new build of that cluster, or if the cluster size more than doubles with a new build, then the superfamily cluster accession is retired and replaced by a new accession(s). If two previous clusters merge into a single new cluster, the superfamily cluster accession number of the larger component cluster is used for the new grouping.

A superfamily also has a PSSM ID, which refers to the specific set of PSSM IDs for the domain models that comprise the superfamily, rather than to an actual position-specific scoring matrix for the overall superfamily. The superfamily PSSM ID will change if there is any change to the set of member PSSM IDs relative to the previous version of the cluster (e.g., if a member conserved domain gets a new PSSM ID due to changes in its multiple sequence alignment, of if a new conserved domain model is added to the superfamily as the result of a CDD database update).

The CD summary page for a Superfamily record does not include a multiple sequence alignment display; rather, it provides the name and description of the superfamily and lists the domain models that belong to it. The multiple sequence alignment for any member domain model can be viewed by clicking on it to open its CD summary page.

Superfamilies that contain a single domain model ("singletons")

The concept of superfamilies was applied to CDD in order to cluster related conserved domain models together and provide a non-redundant view of the available domain models. After the superfamily clustering algorithm is applied to the domain models in CDD, all resulting clusters are referred to as superfamilies, regardless of how many domain models they contain. The non-redundant view of CDD therefore includes superfamilies with a single domain model ("singletons") as well as superfamilies containing two or more domain models.

In the user interface, however, superfamilies that contain only one model are not displayed in search results, or listed as links from the domain model, because they look very similar to the model itself.

In contrast, superfamilies that contain two or more models ("multi-model superfamilies") are displayed in search results, and are also accessible as links from their member domain models. The number of multi-model superfamilies is provided in the Database Statistics box on the "Conserved Domains and Protein Classification News" page, and they can be retrieved by clicking on that statistic.

Search Tips: How to find conserved domains

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. The colored bars that depict the domain footprints (shown in both the concise display and full display of CD-Search results) 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.

(The PubMed help document and Entrez help document provide additional, general information about using the Entrez search system.)

The "See more..." link a the bottom of the "Search Details" box opens a more detailed display:

mismatch repair eukaryotes

will retrieve biosystems with those terms anywhere in the record.

Some of the records might include aligned sequences from organisms other than eukaryotes because we did not limit that search term to the Organism search field. Because of this, we might also retrieve conserved domain records they happen to contain the term "eukaryotes" in a comment or some other field of the record.

Similarly, the term "mismatch repair" can appear anywhere in the record.

The terms entered in a basic search may or may not be adjacent to each other in the retrieved records, depending on how Entrez parsed the query (as shown in the Search Details for a given search). To force terms to be searched as a phrase, use quotes. To refine your search in other ways, use the Limits option or the Advanced Search methods described below.

Limits

Note that the Limit will remain in effect for all subsequent searches in the current database unless you change or remove that limit. In the illustrated example above, any search you do will be limited to the Titles of records, until you remove the limit.

On the Entrez CDD search page, click on the Limits link, select the Text Word, enter the following query:

"mismatch repair"

and press "GO". That will retrieve only records which contain those terms in the conserved domain's description. The quotes surrounding the terms force them to be searched as a phrase.

Search #3:

Open the Limits page again and clear your previous search. Change the search field selection to Organism, enter the following query:

eukaryotes

and press "GO". That will retrieve conserved domain models containing only eukaryotic sequences in their multiple sequence alignments (i.e., eukaryota will be the root taxonomic node of the sequences in a domain model's alignment).

If desired, you can then combine the searches on the Advanced Search page, either by using the Search Builder, as shown in sample Search #4, or by using the History section of that page, as shown in sample Search #5.

You can also manually edit the current query by clicking the "Edit" link beneath the grey text box. That will allow you to type terms/search numbers/etc. directly into the box, add parentheses for nesting if desired, change Boolean operators, etc.

In addition, the following types of advanced searches can be entered in the query box of any Entrez search page (i.e., in the query box of the database's Home page, Limits page, or Advanced Search page):

Search Builder

(2) Type a term(s) in the text box beside the search field menu. Or, use the "Show index list" link to see the index of the search field and select the desired term from the index. (tips on using the "Show Index List")

(3) Select the Boolean operator (AND, NOT, OR) that should precede the term when it is added to the active query at the top of the page.

Continue the above steps, as desired, to add more term/search field combinations to your query.

Press the Search button to display the records retrieved by your search (i.e., it displays the search results page).

Click on the "Add to history" link if you prefer to simply add the query to your search history and remain on the Advanced Search page, where you can continue building your query.

The number of records that contain the term will appear in parentheses. You can also browse the index to explore the variety of terms available (for example, select "All Fields", enter "Huntington", and click on the "Show Index" link to see additional spellings and/or related terms, such as Huntington disease, Huntington's, Huntington's disease).

To select multiple terms that do not fall within a continuous range from the index, use the Control key while selecting the terms of interest. Then use the AND, OR, or NOT buttons to add that group of terms to the active query.

Note: When multiple terms are selected from the index window, they are OR'ed together within parentheses and then appended to your query with whatever Boolean operator you have selected.

On the Entrez CDD search page, click on Advanced Search and build your search one step at a time:

(a) Using the first pull-down menu in Search Builder, select the Text Word search field and enter the following query:

"mismatch repair"

and select "AND" as the Boolean operator. That term/search field selection will automatically be displayed in the grey text box at the top of the page, which shows your current query.

(b) Using the second pull-down menu in Search Builder, select the Organism search field and enter the following query:

eukaryotes

and select "AND" as the Boolean operator. That newest term/search field selection will automatically be added to the grey text box at the top of the page.

(c) Your query will now appear as:

"mismatch repair"[Text Word] AND eukaryotes[Organism]

Press the Search button if you want to display the records retrieved by your search (i.e., it displays the search results page).

Or, click on the "Add to history" link if you prefer to just add the query to your search history and remain on the Advanced Search page, where you can continue building your query.

Note that this search will produce the same results as sample searches #5 and #6. It is simply executed in a different way. That is, you remain on a single query page (Advanced search) and can browse the index of any search field as you build your query one step at a time.

History

Use the search numbers shown in the "History section" of the advanced search page to combine previous searches (for example, searches #2 and #3 shown above).

To do that, you can either:

Click on the "Edit" link beneath the grey text box and type in a search statement such as:

#2 AND #3

Or, instead of typing the search statement, use the "Add" link beside any search number in the "History" section of the Advanced Search page to add that search number into the grey text box.

That will retrieve records containing "mismatch repair" in the Text Word field and "eukaryotes" in the Organism field. Compare the retrieval from this search with that of the sample basic search above.

(Note that your search numbers might be different from those shown here, if you did earlier searches in the Entrez system before trying these examples.)

    term[field] BOOLEAN term[field] BOOLEAN term[field] etc.

For example, to identify the records that were retrieved by Search #2 of your search history, and also by Search #3, you could enter the following query:

#2 AND #3

To identify the records that were retrieved by Search #2 but not by Search #3, you could enter the following query:

#2 NOT #3

Simply enter all search terms and search fields as a single statement into the query box:

"mismatch repair"[Text Word] AND eukaryotes[Organism]

Note that this search will produce the same results as sample searches #4 and #5, but it takes only a single step when entered directly into the search box as a Boolean query.

Search #7:

("chloride channel"[All] OR ClC[All]) AND (cdd[Database] OR pfam[Database])

This search will retrieve biosystem records that contain the phrase "chloride channel" or the abbreviation "ClC" in any field of the record, and that are from the NCBI-curated or PFAM source databases.

Be sure to select the appropriate database from the pull-down menu at the top of the page, then "Browse" to find the file of UIDs you'd like to upload, and press "Retrieve." Batch Entrez will then display a report summarizing the data it found in your input file, such as: (1) number of lines that were present in the file (there should be one UID per line); (2) rejected lines (indicating how many invalid UIDs were detected); (3) removed duplicates (indicating how many duplicate UIDs were detected/removed); (4) passed to Entrez (indicating how many of the UIDs from your list are valid and will therefore be acted upon). The latter may include obsolete UIDs that have been superceded by newer UIDs. The obsolete UIDs, as well as any invalid UIDs that were present in your file, are explicitly reported at the top of the Batch Entrez report.

The currently available fields include:

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.**

Note: An additional unique identifier, the PSSM ID, is assigned to the position specific scoring matrix that is derived from the conserved domain's multiple sequence alignment. Conserved domains can also be retrieved by entering their PSSM ID (without a search field specifier).

will retrieve the CDD record that contains the specified unique identifier in the accession number field.

will retrieve the pfam08617 record from CDD.

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.

Many attributes from the Filter field are provided in the "Links" menus that are present on an Entrez search results page, and in the "Links" box on an individual CD Summary page. A detailed explanation of each type of link is provided in the description of the "Links" box.

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.

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 "Search Builder" section of the "Advanced search" page, then use the "Show index" link to view the index of that search field and see available values.)

will retrieve the NCBI curated domain models that contain four sites (i.e., four conserved features).

will retrieve conserved domains found in eukaryotes.

As of January 2010, this ranges from zero to 70 protein sequences from structures. (To see the current range, select the "Structure Representative" search field on the "Search Builder" section of the "Advanced search" page, then use the "Show index" link to view the index of that search field and see available values.)

NCBI-curated domain models tend to have more structure representatives because the curation process includes incorporation of protein sequences from resolved structures. However, domain models from external data sources may also contain structure representatives. As noted in the section on data processing, sequences in PFAM, SMART, and COGs alignments are substituted, whenever possible, for closely related sequences that have direct links to three-dimensional structures in the Moleclular Modeling Database (MMDB).

will retrieve domain models that contain six protein sequences from 3D structures in their multiple sequence alignment.

An example of a title:subtitle combination is present in pfam00654:"Voltage_CLC: Voltage gated chloride channel"A search of the subtitle field for "chloride channel" will retrieve that record and others.

Note: Not all conserved domain models have subtitles, and search of the Text Word field may therefore retrieve more comprehensive results.

will retrieve the CDD records that have the phrase "chloride channel" as part of their subtitle.

The quotes surrounding the search terms ensure they are searched as a phrase.**

Example:  "Voltage gated ClC" is the short title of the NCBI-curated conserved domain model (cd00400) for the voltage gated chloride channel.

Note: A search of this field will also retrieve superfamily clusters (cl* accessions) that contain one or more domain models with the search term in their short title, even if the title of the superfamily cluster itself does not contain the search string.

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. (The asterisk (*) is a wild card that can be used to search for a word stem.)

Note: As mentioned in the section on CD Assembly Process, when domain models evolve as new sequence data becomes available, their PSSMs can change, and in such cases, they received new PSSM IDs. Obsolete PSSMs (e.g., 667) cannot be retrieved through the Entrez CDD search interface, even with direct searches of the UID field, because they are no longer indexed. However, those obsolete PSSMs can be retrieved from the archival copy of the database by using the "Direct Fetch via UID" option on the CDD Search Methods page.

will retrieve the conserved domain record cd00400, whose PSSM ID is 79359.

79359

will also retrieve that same conserved domain record, because the UID field is searched by default for queries that are only a string of digits.

** 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.

It is also possible to search for a word stem by using an asterisk (*) as a wild card; for example, chlori* will retrieve records with terms such as chloride, chlorin, chlorinate, chlorite. The Entrez Help document provides additional information about truncating search terms in this way.

Click on the accession number or thumbnail image of any record on the DocSum page to view its conserved domain (CD) summary page.

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.

Number of Sites - NCBI-curated domain models will appear at the top of search results (if "sort by number of sites (down)" order is selected) because conserved features, such as catalytic or binding sites, are annotated only on those domain models.

PSSM Length - the superfamily records will appear at the bottom (if "sort by PSSM length (down)" is selected) because they do not have an actual Position Specific Scoring Matrix (PSSM). Rather, each member of a superfamily has a PSSM and corresponding PSSM ID. A superfamily's PSSM ID refers to the specific set of conserved domain PSSM IDs that comprise the superfamily, rather than to an actual position-specific scoring matrix for the overall superfamily.

Structure Representatives - NCBI-curated domain models will tend to appear at the top of search results (if "sort by structure representatives (down)" order is selected) because the curation process includes incorporation of protein sequences from resolved structures. Domain models from external data sources may also contain structure representatives. As noted in the section on data processing, sequences in PFAM, SMART, and COGs alignments are substituted, whenever possible, for closely related sequences that have direct links to three-dimensional structures in the Moleclular Modeling Database (MMDB).

Click on the "Clipboard: XX items" link in the upper right corner of the page to view the items in any format for up to 8 hours after your last activity in the database.

The Clipboard will not add an item that is currently in the Clipboard; it will not create duplicate entries. You can remove items from the Clipboard, if desired.

Entrez uses cookies to add your selections to the Clipboard. For you to use this feature, your Web browser must be set to accept cookies.

Items in the Clipboard are represented by the search number #0, which may be used in Boolean search statements. For example, to limit the items you have collected in the Clipboard to those from human, use the following search: #0 AND human[organism]. This does not affect or replace the Clipboard contents.

The Clipboard's "Send to" menu offers you the same "File" and "Collections" options as offered on the original search results page. The latter option saves all items (default), or the subset of items selected with check boxes, indefinitely in the My NCBI Collections section of your My NCBI account.

The links for "NCBI-curated," "imported," "families" (individual conserved domain models), and "superfamilies" (clusters of evolutionarily related conserved domain models into which the individual conserved domain models fall) show the number of retrieved records that fall into each of those categories, and allow you to view those subsets of your search results, if desired.

The "Related information" box that appears in the right margin of the display for an individual record allows you to retrieve related data for that particular domain model. (For example, the "Related CDs/Superfamily Members" link for accession cd00400 will retrieve the other domain models in the Conserved Domain Database that appear to be evolutionarily related to or redundant with cd00400.)

A "Find Related Data" box (instead of an "Related information" box) will appear in the right margin of a CDD search results page if you retrieved two or more records. The "Find Related Data" box allows you to retrieve related data for all the models retrieved by your search (default), or for the domain models you have selected with checkboxes. (For example, the "Find Related Data" option for Related CDs/Superfamily Member Links will retrieve the other domain models in CDD that appear to be evolutionarily related to or redundant with the domains retrieved by your search, or with the domains you have selected with checkboxes.)

The links in either display can include the following, depending on the related data that are available for the domains you have retrieved:

Most links are accessible on both the search results page and on a CD summary page, although a few of the links are available in only one of those places (*), such as Representatives and Books links, which are available only on the CD summary page.

For example, 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.

Several different types of links are available, allowing you to choose: (a) the format in which you want to view the conserved domains (e.g., in graphical format as domain footprints aligned to the protein sequence, or as a list of records from the Conserved Domain Database, each of which includes a multiple sequence alignment of the proteins used to create the domain model), and (b) the level of redundancy in the list of conserved domain models (e.g., a concise list of the top scoring models or a full list of all models that have a statistically significant RPS-BLAST hit to the protein).

The number of conserved domain models retrieved, and the order in which they are sorted/presented, depends upon the view you select:

Conserved Domains (Concise) -- opens a concise list of the conserved domain models that are the top-scoring RPS-BLAST hits to the protein query sequence. Each domain model is listed only once, even if a model had a hit to more than one region on the query sequence. more...

Conserved Domains (Full) -- opens a full list of all the conserved domain models that have a statistically significant RPS-BLAST hit to the protein. Each domain model is listed only once, even if a model had a hit to more than one region on the query sequence. more...

Domain Relatives -- opens a graphical display of similar domain architectures, as determined by the CDART tool, with links to the proteins that have each similar architecture. more...

A concise display (depicted below and in a more detailed illustrated example), is shown by default and features only the top scoring models from various hit types. A toggle switch near the upper right corner of the display allows you to see the full display (illustrated example), if desired, which shows all domain models that meet or exceed the RPS-BLAST threshold for statistical significance, i.e., the E-value cutoff. (Open the protein sequence record GI 157830769, featured in the illustration below, and follow the "CDD Search Results" link to try it yourself.)

In both the concise and full views, small triangles indicate the amino acids involved in conserved feaures/sites, such as catalytic and binding sites, when such annotations are available in a domain model.

In these graphical views, the domain hits are ordered not only by E-value, but also by classification (specific hits, non-specific hits, superfamilies, multidomains) and model origin (with priority given to NCBI-curated domains if they meet or exceed a domain-specific threshhold score).

If a domain model aligns to more than one region of the query sequence, it will be listed multiple times in the list of domain hits. This is true because the alignment coordinates and score of the domain model vary among different regions of the query sequence, and each hit is reported separately. (The list of domain hits is not shown in the illustration above but is visible beneath the graphical summary on an actual CD-Search results page.)

This list of domains corresponds to those shown in the concise graphical display of CD-Search results. The same domains will appear in both views, but the order in which they are presented might vary between the displays because the graphical display sorts hits by RPS-BLAST score and hit type, and the list display does not. Also, if a superfamily on the "CDD Search Results" graphical display contains only one domain model, the "Conserved Domains (Concise)" link will retrieve the record for that sole domain model, rather than retrieving the superfamily record.

For example, compare the concise set of top-scoring conserved domains on protein sequence GI 157830769, Cyclodextrin Glucanotransferase, in list vs. graphical format. Note that each link will open in a new window:

This list of domains corresponds to those shown in the full graphical display of CD-Search results. The same domains will appear in both views, but the order in which they are presented might vary between the displays because the graphical display sorts hits by RPS-BLAST score and hit type, and the list display does not. Also, if a superfamily on the "CDD Search Results" graphical display contains only one domain model, the "Conserved Domains (Full)" link will retrieve the record for that sole domain model, rather than retrieving the superfamily record.

For example, compare the full set of top-scoring conserved domains on protein sequence GI 157830769, Cyclodextrin Glucanotransferase, in list vs. graphical format. Note that each link will open in a new window:

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.

More information about CDART is available in the overview, help document, and corresponding publication.

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):

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. Whenever possible, the citations include articles that provide evidence for the biological function of a domain and/or discuss the evolution and classification of a domain family.

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.

Note that the BioSystems link can appear in two different places on a search results page:

Conversely, the "Gene," "HomoloGene," "LinkOut," "Family Structure," and "BioSystems" link currently appear only on the search results page.

(Note: Each superfamily record in the Conserved Domain Database also has a PSSM ID, which refers to the specific set of conserved domain PSSM IDs that comprise the superfamily, rather than to an actual position-specific scoring matrix for the overall superfamily.)

In addition to displaying an interactive view of the 3D structure(s), Cn3D will also display the multiple sequence alignment of those and other proteins used in the curation of the domain model. The Cn3D structure view and sequence view windows communicate with each other, so highlighting residues in one window will also highlight those residues in the other window.

As noted in the sections on the CD assembly process and unique features of curated domains, NCBI staff include protein sequences from resolved 3D structures (illustration) whenever possible in the multiple sequence alignment of a domain model.

In a multi-level domain hierarchy, the 3D structures might be present in the parent node (e.g., cd00400) if they are not present in an intermediate or terminal node (e.g., cd03683). In that case, click on the parent node to view structures that have been specially annotated to highlight the conserved feature.

You can click on any of the thumbnail structure images on a CD summary page to launch Cn3D. The thumbnail images in the conserved features summary box will launch a specially annotated view of the structure that highlights the particular feature of interest.

However, 3D structures are not always available. If a domain model does not include any structure-based protein sequences, the "Structure View" button will still open Cn3D, but only the sequence viewer window will be populated with data.

Controls in Cn3D will then allow you to manipulate the sequence alignment in various ways, if desired. For example, Cn3D offers column-specific coloring by sequence conservation when invoked with multiple alignment views. This is a convenient feature to study sequence conservation within a CD-alignment and to find out how well the aligned query fits the existing patterns of conservation and variability. The Cn3D tutorial provides more information on the controls available.

To examine the hierarchical classification more closely, you can download the CDTree program, which is used by the NCBI curators. CDTree enables you to interactively view the complete domain hierarchy, including a detailed display of the sequence cluster tree.

To embed your query in the hierarchy, simply check the box for Add Query Sequence before pressing the "Interactive Display" button. (The free CDTree program must be loaded onto your computer in order for that button to work.) When the CDTree program opens, your query sequence will be highlighted in red. If the sequence tree is large, you might need to de-select the View/Fit to Screen option in CDTree's Sequence Tree window in order see the tree, and the placement of your query sequence, in detail. The CDTree help document is packaged with the software and provides details on how to use the program.

Some hierarchies have only one node, while others have many nodes organized into two or more levels. If a hierarchy has multiple nodes, you can click on another node of interest to view the CD summary page for that domain.

Alternatively, you can download the CDTree program used by the NCBI curators in order to view the complete domain hierarchy interactively and in greater detail, with or without a query sequence embedded.

Note: 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.

In NCBI-curated domain models, protein sequences from resolved 3-D structures are generally listed first, so the "Top Listed Sequences" display option is useful for bringing these structure-based protein sequences to the top when viewing NCBI-curated domains. The remaining sequences in NCBI-curated domain models are listed in order of increasing GI number or some other non-biological criterion. (This is because the composition of the member sequences, not their order, is important in determining a domain model's position-specific scoring matrix, or PSSM. The other important factor is the degree of residue conservation in any given column of the alignment, which can be visualized with the Color Bits setting, described below.)

The biological relationships among the member sequences of an NCBI-curated domain model are displayed in the sequence cluster phylogenetic tree and the domain family hierarchy on the domain model's CD summary page. Both of these displays can also be viewed interactively using the CDTree program.

The color bit settings can be used to select a threshold for determining which columns are colored in red.

The score threshold that must be met in order for an alignment column to be displayed in red can be adjusted from a low of 0.5 to a high of 4.0. As the threshold increases, the number of columns shown in red will decrease.

Background: Each column in the multiple sequence alignment display receives a score that indicates that column's "information content" -- its contribution to the overall alignment score -- indicating how important the column is as an "anchor" for the alignment. The higher the score, the more important that column is in the alignment.

We use a fairly standard definition of "information content" for an aligned column:

A column's score is calculated on the fly, based on the sequence rows currently shown in the display. As the number and type of sequence rows in the display change, the column's score, and therefore its color, can change.

Although multiple features may have been annotated, only one feature at a time is shown in the multiple sequence alignment display.

A conserved features/sites summary box (illustration) lists the features that have been annotated. Clicking on the tab for a feature of interest will show its details. It will also refresh the mutliple sequence alignment display to mark the residues involved in the currently viewed feature (as depicted in the bottom of the illustration).

How and when is CDD updated?

Where can I send comments or feedback about the data?