One way to retrieve proteins with similar domain architectures is to enter your query as a protein sequence, or as a set of conserved domains, directly into the CDART home page in any of the following formats:

• Protein sequence




You can submit a protein sequence as:

• a protein unique identifier (UID) - enter the Accession or GI number of any protein that is in the Entrez Protein database.




• protein sequence data - enter the sequence in FASTA format or as bare sequence data.




The CDART results will show the functional domains found in the query protein and will list proteins with a similar domain architecture. The similar proteins must include at least one of the conserved domain superfamilies in the query sequence. The similarity score of each domain architecture indicates the number of domain superfamilies in the architecture that match domain superfamilies in the query protein, and is used to rank the search results.

• Set of conserved domains (CDs)




As an alternative to submitting a protein sequence as a query, you can you can specify a query as a set of one or more conserved domains*, using any of the identifiers below to specify your domains of interest. They should be entered on a single line, separated by commas, and surrounded by square brackets [], as in the examples below:



• conserved domain superfamily cluster IDs - As explained in the Conserved Domain Database help document, 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.
  
  A superfamily ID (accession number) begins with the prefix "cl" for "cluster," and can be entered in CDART as the complete alphanumeric accession or as digits only (with or without the leading zeros). For example, a query to retrieve proteins with domain architectures that include superfamilies cl00075 (HATPase_c Superfamily) and cl02783 (TopoII_MutL_Trans Superfamily) can be entered in any of the following ways:
  
  [cl00075,cl02783]
  [00075,02783]
  [75,2783]
  [cl00075,2783]
  etc.
  




• Accession numbers or PSSM IDs for specific domain models - If you are interested in a specific conserved domain model, you can enter its conserved domain accession number or position specific scoring matrix ID (PSSM ID). If you enter a PSSM ID, be sure to include a leading "p" so it won't be interpreted as a cluster ID. Note: The PSSM ID is displayed in the "Statistics" box of a domain model's summary page in the Conserved Domain Database. For example, a query for the domain models pfam02518 (whose current PSSM ID is 190334) and cd03483 (whose current PSSM ID is 48471) can be entered as:
  
  [pfam02518,cd03483]
  or
  [p190334,p48471]
  
  




• mix of superfamily cluster IDs, conserved domain accessions, PSSM IDs - Use the same syntax rules as above. For example, a query to retrieve proteins with domain architectures that include superfamily cl00075 and domain model cd03483 (whose current PSSM ID is 48471) can be entered in any of the following ways:
  
  [cl00075,cd03483]
  [cl00075,p48471]
  [00075,p48471]
  [75,p48471]
  etc.
  

• Multiple queries




• You can enter multiple queries using any of the formats above (i.e., as protein sequences or sets of conserved domains) or a mix of those formats. Note that:



• Each protein Accession or GI number should be on a separate line



• FASTA formatted sequence data and bare sequences can occupy multiple lines. (The FASTA format definition line, however, should occupy a single line).



• If one of your queries is a set of conserved domains, they should be entered on a single line, separated by commas, and surrounded by square brackets [], as in the third line of the example below.



• If you include a bare sequence as one of the queries, use a blank line to separate it from the query that precedes it, as in the last part of the example below.




• Example: - The example below includes six queries, in the following order: (1) protein GI number; (2) protein accession number; (3) set of conserved domain superfamily cluster IDs; (4) protein sequence in FASTA format; (5) another protein sequence in FASTA format; (6) protein as bare sequence data:

     269849668
     EDV04934
     [75,2783]
     >gi|239592572|gb|EEQ75153.1| asparaginase [Ajellomyces dermatitidis SLH14081]
     MSPPIPQPRQRTRSQPLFKPAVILHGGAGNIQHSRLPPELYKQYRTSLLTYLRSTTALLNADIEEEEPSI
     NAKNDAVDDNMRISPASALNAAVHAVSLMEDNELFNCGRGSVFTSAGTIEMEASVMVASLLNDEDSVDDF
     NNSEVNCLASEKTPGSIKRGAGVMLVRNVRHPIQLAKEVLLRTGYASDGDGDGGNMHSQLSGEYVEGLAR
     DWGMEFCPDDWFWTKKRWDEHRRGLKKGKTRGRMTDGRNMGADVEVRGEGEADDGDGLYLSQGTVGCVCL
     DRWGNIAVATSTGGLTNKCPGRIGDTPTLGAGFWAEAWDVEGVEGLSNMSDSSNSVCASGRDRSKGCIQL
     KRDTMNYQTQDGRDNLLAYQASSSTTTTTSSYRMGSQWRSDFDSNSAFTLIRDCFSSSPPPPGYAALEPS
     KYPVEKFPLGKSTSSPHTDFNPHRYSQPQRRRILALSGTGNGDSFLRTAATRTAAAMVRFGSAQNSISLA
     QAVTAVAGPGGELQRSAGRRWGKTGEGEGGIIGIEAEVETDEQTLGEGKLRRGKVVFDFNSTGMFRAWME
     EKDGKDVERMMVFRDDYE
     >gi|336020358|ref|NP_001229488.1| mitogen-activated protein kinase kinase kinase kinase 4 isoform 4 [Homo sapiens]
     MANDSPAKSLVDIDLSSLRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQLAAIKVMDVTEDEEEEIKLEI
     NMLKKYSHHRNIATYYGAFIKKSPPGHDDQLWLVMEFCGAGSITDLVKNTKGNTLKEDWIAYISREILRG
     LAHLHIHHVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATY
     DYRSDLWSCGITAIEMAEGAPPLCDMHPMRALFLIPRNPPPRLKSKKWSKKFFSFIEGCLVKNYMQRPST
     EQLLKHPFIRDQPNERQVRIQLKDHIDRTRKKRGEKDETEYEYSGSEEEEEEVPEQEGEPSSIVNVPGES
     TLRRDFLRLQQENKERSEALRRQQLLQEQQLREQEEYKRQLLAERQKRIEQQKEQRRRLEEQQRREREAR
     RQQEREQRRREQEEKRRLEELERRRKEEEERRRAEEEKRRVEREQEYIRRQLEEEQRHLEVLQQQLLQEQ
     AMLLECRWREMEEHRQAERLQRQLQQEQAYLLSLQHDHRRPHPQHSQQPPPPQQERSKPSFHAPEPKAHY
     EPADRAREVEDRFRKTNHSSPEAQSKQTGRVLEPPVPSRSESFSNGNSESVHPALQRPAEPQVPVRTTSR
     SPVLSRRDSPLQGSGQQNSQAGQRNSTSIEPRLLWERVEKLVPRPGSGSSSGSSNSGSQPGSHPGSQSGS
     GERFRVRSSSKSEGSPSQRLENAVKKPEDKKEVFRPLKPADLTALAKELRAVEDVRPPHKVTDYSSSSEE
     SGTTDEEDDDVEQEGADESTSGPEDTRAASSLNLSNGETESVKTMIVHDDVESEPAMTPSKEGTLIVRQT
     QSASSTLQKHKSSSSFTPFIDPRLLQISPSSGTTVTSVVGFSCDGMRPEAIRQDPTRKGSVVNVNPTNTR
     PQSDTPEIRKYKKRFNSEILCAALWGVNLLVGTESGLMLLDRSGQGKVYPLINRRRFQQMDVLEGLNVLV
     TISGKKDKLRVYYLSWLRNKILHNDPEVEKKQGWTTVGDLEGCVHYKVVKYERIKFLVIALKSSVEVYAW
     APKPYHKFMAFKSFGELVHKPLLVDLTVEEGQRLKVIYGSCAGFHAVDVDSGSVYDIYLPTHIQCSIKPH
     AIIILPNTDGMELLVCYEDEGVYVNTYGRITKDVVLQWGEMPTSVAYIRSNQTMGWGEKAIEIRSVETGH
     LDGVFMHKRAQRLKFLCERNDKVFFASVRSGGSSQVYFMTLGRTSLLSW
  
     MEQDPKPPRLRLWALIPWLPRKQRPRISQTSLPVPGPGSGPQRDSDEGVLKEISITHHVKAGSEKADPSH
     FELLKVLGQGSFGKVFLVRKVTRPDSGHLYAMKVLKKATLKVRDRVRTKMERDILADVNHPFVVKLHYAF
     QTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALGLDHLHSLGIIYRDLKPENILLDEEGHI
     KLTDFGLSKEAIDHEKKAYSFCGTVEYMAPEVVNRQGHSHSADWWSYGVLMFEMLTGSLPFQGKDRKETM
     TLILKAKLGMPQFLSTEAQSLLRALFKRNPANRLGSGPDGAEEIKRHVFYSTIDWNKLYRREIKPPFKPA
     VAQPDDTFYFDTEFTSRTPKDSPGIPPSAGAHQLFRGFSFVATGLMEDDGKPRAPQAPLHSVVQQLHGKN
     LVFSDGYVVKETIGVGSYSECKRCVHKATNMEYAVKVIDKSKRDPSEEIEILLRYGQHPNIITLKDVYDD
     GKHVYLVTELMRGGELLDKILRQKFFSEREASFVLHTIGKTVEYLHSQGVVHRDLKPSNILYVDESGNPE
     CLRICDFGFAKQLRAENGLLMTPCYTANFVAPEVLKRQGYDEGCDIWSLGILLYTMLAGYTPFANGPSDT
     PEEILTRIGSGKFTLSGGNWNTVSETAKDLVSKMLHVDPHQRLTAKQVLQHPWVTQKDKLPQSQLSHQDL
     QLVKGAMAATYSALNSSKPTPQLKPIESSILAQRRVRKLPSTTL
     

A second way to access CDART is to start by retrieving a record of interest from the Entrez Protein database, then follow the "Domain Relatives" link in the right margin of the sequence record. That will open the precalculated CDART results for the protein.

Note that the "Domain Relatives" is one of four links available from a protein sequence record to conserved domain annotations, 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; 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; or as a list of proteins with similar domain architectures), 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:

Domain Relatives -- opens a graphical display of similar domain architectures, as determined by the CDART tool. A domain architecture is defined as the sequential order of conserved domains in a protein query sequence. The score for each CDART hit represents the number of domains that match those found in the query protein. (The CDART paper provides additional details. ) CDD Search Results -- opens a graphical display (illustrated example) of conserved domain model footprints on the query protein, ranked by their RPS-BLAST score and hit type. A model may appear more than once if it aligns to multiple regions of the query sequence. A concise display showing only the top-scoring hits is presented by default, and it can be changed to a full display of all hits if desired. (The CDD help document provides additional details.) Conserved Domains (Concise) -- opens a concise list of the conserved domain models that are the top-scoring RPS-BLAST hits to the query protein. Each domain model is listed only once, even if a model had a hit to more than one region on the query sequence. (The CDD help document provides additional details.) Conserved Domains (Full) -- opens a full list of all the conserved domain models that have a statistically significant RPS-BLAST hit to the query protein. Each domain model is listed only once, even if a model had a hit to more than one region on the query sequence. (The CDD help document provides additional details.)

• Query

  • The query you entered is displayed in a yellow background at the top of the CDART search results.

    • If your query was a protein sequence, the graphic shows the length of the protein in amino acids and the footprints of the highest scoring conserved domain superfamily(ies) found in the query sequence by RPS-BLAST. On the left side of the graphic is the description of the query and the total number of domain architectures found in the Entrez Protein database that contain at least one superfamily from the query. If you used any search result filters, a second number will show the number of remaining architectures after applying the filter. The two numbers may be the same.

    
    

    • If your query was a set of conserved domains rather than a protein sequence, the domains will be shown in the same order in which they were input, without a scale showing length. The "total architectures" statistic will indicate the number of domain architectures found in the Entrez Protein database that contain all of the domain superfamilies in your query.

    
    
  
  

  • The Download button to the right of the query graph lets you download all the similar architectures found for this query (after applying the filters, if specified). Click on the button will result in a Save as dialog to let you save the result in a text file.

  
  



• List of similar domain architectures

  • A domain architecture is defined as the sequential order of conserved domains in protein queries. Each domain architecture displayed by CDART therefore represents a unique set and order of conserved domain superfamilies found among sequences in the Entrez Protein database.
    
    

  • The CDART results list the proteins with a similar domain architecture to your query. The similar proteins must include at least one of the conserved domain superfamilies in the query sequence. The similarity score of each domain architecture indicates the number of domain superfamilies in the architecture that match domain superfamilies in the query protein, and is used to rank the search results. The results are paginated at 10 architectures per page, users can nagivate to any pages using the page selector or back/forward arrows at the bottom row of the table.
    
    

  • Architectures are displayed as graphs. Different Superfamilies are displayed as different shape/color combinations. Mouse over a superfamily footprint to open a pop-up that shows the superfamily accession number (cluster ID), title, and description. Click on a footprint to open the Conserved Domain Database summary page for that superfamily, which lists the individual conserved domain models that belong to the superfamily.
    
    

  • Protein sequences that share the same domain architecture are grouped together, and only one from each group is shown. To see all proteins in the group, follow the Lookup sequences in Entrez link to the right of the architecture graph.
    
    




• Filter your results

  • The "Filter your results" bar at the top of a CDART search results page allow you to refine the results by including/excluding architectures that contain specific domain superfamily(ies). The contents of the "Filter your results" dialog box are generated dynamically and represent the domain superfamilies that were found in your CDART search results. Select the desired superfamilies from the lists provided in the dialog box to include or exclude superfamilies from your CDART search results display.

    
    
    

  • As an alternative to selecting domain superfamilies from the lists and then using the "Include" or "Exclude" buttons, you can type the desired parameters directly into the "Filter your results" text box, in a format such as:
    
    

    • INCLSFAM[xxx,yyy,zzz]
      Include only sequences that contain the conserved domain superfamilies with cluster IDs xxx AND yyy AND zzz.
    
    
    • EXCLSFAM[xxx,yyy,zzz]
      Exclude sequences that contain the conserved domain superfamilies with cluster IDs xxx AND yyy AND zzz.
      
      

      The above operations can be combined using the logical operators NOT, AND and OR, as well as parentheses. For example:
      
      INCLSFAM[aaa,bbb] AND NOT INCLSFAM[xxx]
      
      will filter your search results so they include only superfamilies aaa AND bbb, but not xxx.
      
      The logical operators are executed with the following precedence:
      
      () > NOT > AND > OR

      
      
    
    



• Information provided for each domain architecture

  • Title - The title of the representative protein sequence that contains this domain architecture.
    
    

  • Taxonomy span - The highest taxonomic node common to all sequences with this domain architecture.
    
    

  • Similarity score - The number of conserved domain superfamilies in this domain architecture that match superfamilies in the query sequence. The score does not count repeats of superfamilies within a domain architecture; rather, it counts each superfamily only once, regardless of how many times that superfamily appears in a protein sequence.
    
    The domain architectures shown on a CDART search results page are ranked/sorted by score. If two or more architectures have the same score, they are ranked by the number of non-redundant protein sequences that contain the architecture (so hits that may be spurious hits are at the bottom).
    
    

  • Total nr (non-redundant) sequences -

    • Protein sequences that share the same domain architecture are grouped together.
    
    
    • If two or more of the proteins are identical in length and composition, they are placed in the same identical protein group ("IPG"). CDART displays one representative sequence from each IPG in order to produce a non-redundant (nr) list of sequences that contain a specific domain architecture. To find all sequences in this group, follow the Lookup sequences in Entrez link
    
    
    • The "total nr sequences" statistic represents the total number of IPGs with the domain architecture.
    
    

  • Lookup sequences in Entrez - Retrieves the non-redundant set of sequence records that contain the domain architecture. The link will leave the search result page, so it is recommended to right-click on it and select to open link in a new window.
    
    




• Navigate multiple queries

  
  

  The graphical interface can only navigate results of one query at a time. If multiple queries have been specified, some extra controls will appear.

  
  
  
  

  The View Query selector can be used to select to view results from a particular query. The Apply to all button can be used to apply a filter to results of all queries. The Download All button let the user download similar architectures from all queries at once.