SPARCLE (Subfamily Protein Architecture Labeling Engine)

• SPARCLE (Subfamily Protein Architecture Labeling Engine) is a resource for the functional characterization and labeling of protein sequences that have been grouped by their characteristic conserved domain architecture.


• A domain architecture is defined as the sequential order of conserved domains in a protein sequence.

To use SPARCLE, you can either:

• Enter query protein sequence into CD-Search. The search results will include a "Protein Classification" section if the query protein has a hit to a curated domain architecture in the SPARCLE database.
  
  
  • As an example, view the "Protein Classification" section on the CD-Search results for NP_387887, DNA gyrase subunit B, then follow the link for the domain architecture to open the corresponding SPARCLE record. This example is also provided as an illustration on the About SPARCLE page.
  
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• Search the SPARCLE database by keyword to retrieve domain architectures that contain the term(s) of interest in their descriptions.


• As an example, view the results of a search that looks for the words "chloride" and "channel" and limits the results to curated domain architecture records by adding curated[ReviewLevel] to the search.

With either approach, the corresponding SPARCLE record(s) will display the name and functional label of the architecture, supporting evidence, and links to other proteins with the same architecture.

Example and additional notes:

• DNA gyrase B (NP_387887), an antibiotic target, has a conserved domain architecture of a histidine kinase-like ATPase domain, a transducer domain, a topoisomerase-primase domain, followed by a type II topoisomerase carboxy domain (labeled as a DNA gyrase B domain by Pfam).
  
  
  • Note: the default graphical summary that appears when you click on the "conserved domain architecture" link above depicts the full length protein model; click on the display option to "View: Full Results" link in the upper right hand corner of the display to see the individual conserved domains that compose the full length protein model. (The CD-Search help document provides additional information about the features and options on the search results display.)
  
  
  • Regardless of which display option you use, the "Protein Classification" section that appears above the graphical summary includes a "domain architecture ID xxxxxx" link that opens the corresponding SPARCLE record.
  
  
  • The SPARCLE record (illustrated example), also referred to as the conserved domain architecture's "summary page," shows the architecture's name and functional label (description) of the domain architecture, the supporting evidence that was used to name the architecture, as well as links to other protein sequences with the same architecture and to the individual conserved domains that are in the architecture.
  
  
• Topoisomerase IV (Q45066), an enzyme of similar function, has a different domain architecture, as can be seen in the:


• CD-Search results for Q45066. The domain architecture of this enzyme is different than the architecture of DNA gyrase, despite the similarity in enzyme function. Note that the CD-Search results do not yet include a "Protein Classification" section above the graphical summary of conserved domains. This is because a curated SPARCLE record does not yet exist for this domain architecture. When a SPARCLE record becomes available, the CD-Search results display will include a Protein Classification" section and a link to the corresponding domain architecture.