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dPUC: Domain Prediction Using Context

by Alejandro Ochoa García, Manuel Llinás, Mona Singh

Extend your Pfam predictions without loss of precision using domain context!

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Search our domain predictions on twelve organisms (six Plasmodium species [P. falciparum, P. vivax, P. knowlesi, P. chabaudi, P. berghei, P. yoelii], Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Saccaromyces cerevisiae, Escherichia coli, and Mycobacterium tuberculosis.), and view them graphically, organized by orthology. Search below by protein ID, domain names and accessions (Pfam, SMART, and Superfamily), or keywords.

All searches are case-insensitive, but exact otherwise (including general keywords).

Protein search

Search for your proteins using their unique IDs. In the case of the Plasmodium species, you must use the PlasmoDB IDs (i.e. PFE1390w). Otherwise (for Human, Fly, Worm, Yeast, E. coli and M. tuberculosis) use the Uniprot accessions (i.e. Q9V3C0, but not DDX41_DROME, which can be searched for as a keyword below).

Domain search

Search for proteins containing your domain of interest. Search is case-insensitive, but everything else has to be exact (i.e. "zf-CCHC" is correct, but not "zfCCHC" or "zf_CCHC"). Use the following database links to look for the exact names or accessions of your domains. You can search for Pfam names (i.e. Utp13) or accessions (i.e. PF08625), or Superfamily SCCSs (i.e. c.37.1) or accessions (i.e. SSF52540), or SMART names (i.e. HELICc) or accessions (i.e. SM00490). Standard Pfam (version 23) and dPUC Pfam domains are available for all organisms, but Superfamily and SMART domains are only available for Plasmodium species and were obtained from PlasmoDB 6.0.

Queries with multiple domains are possible, and the results with the most matches are always displayed first, which is useful if you're looking for domain architectures. However all results with at least one queried domain will be listed.

Note that all domain accessions are unique, while domain names might conflict between Pfam and SMART (and our database search mapping will arbitrarily choose one over the other), so stick to domain accessions to avoid these mistakes.

Keyword search

Search for proteins containing arbitrary keywords (excluding protein and domain IDs). The keywords we indexed came from either the protein descriptions (i.e. "RNA helicase-1", obtained from PlasmoDB or Uniprot), or the descriptions of the domains (i.e. "DEAD/DEAH box helicase" or "P-loop containing nucleoside triphosphate hydrolases", obtained from Pfam and Superfamily, not available for SMART). In the case of Uniprot proteins, the protein name (i.e. DDX41_DROME) can also be searched for as a keyword.

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