Description:

Retrieves all proteins of a given genome with the given Pfam A motif or domain. If no genome is provided, all proteins with that particular Pfam A annotation are retrieved. Please be patient, as this can increase the response time of the query considerably.

Runtime:

Takes less than 1 minute to retrieve all proteins of a given genome with the given Pfam annotation. Retrieving all proteins with a particular annotation can take up to 2-3 minutes (if no genome is given).

Input:

Details

Genome	Name of the genome of interest. A list of all avaible genomes can be retrieved using the "Existing values..." feature.
Pfam A Annotation	Identifier or Acc number of the Pfam motif or domain of interest. To retrieve a list of all available Pfam A annotations, the "Existing values..." feature can be used. The beginning or end of the description of a Pfam motif can also be provided to retrieve proteins with a particular type of domain, for example, kinase.

Examples

Genome	Pfam A Annotation
Rhizopus oryzae	PF00187
Magnaporthe grisea	Mak10
Encephalitozoon cuniculi	kinase

Output:

Description

Returns information on the proteins with their associated Pfam motifs and domains along with the MCL and OrthoMCL clusters they have been placed into.

Details

Protein ID	Identifier of the protein.
Symbol	Symbol of the protein.
Genome	Genome the protein belongs to.
Pfam Acc	Acc number of the Pfam A motif or domain.
Version	Version number of the motif or domain.
Pfam ID	Identifier of the Pfam motif or domain.
E Value	E value associated with the Pfam motif identification.
Bit Score	Bit score associated with the identification of the Pfam motif in the protein.
MCL Cluster ID	Identifier of the MCL cluster the protein has been placed in, if any.
OrthoMCL Cluster ID	Identifier of the OrthoMCL cluster the protein has been placed in, if any.