Description:

Retrieve annotation for all the proteins of a given genome that are in the same OrthoMCL cluster as the protein with a Pfam A annotation of interest. If no genome is provided, all proteins in the corresponding clusters are retrieved. This can increase the response time of the query considerably, please be patient.

Runtime:

Can take about 1-2 minutes to retrieve proteins of a given genome that are in the same cluster as proteins with a given Pfam A annotation and about 2-3 to retrieve all proteins if no genome is specified.

Input:

Details

Genome	Name of the genome of interest; to retrieve a list of genomes from the database, the button "Existing Values..." can be used.
Pfam A annotation	Identifier or Acc number of the Pfam A annotation of interest. Using the "Existing values..." feature provides a list of Pfam A annotations to chose from.

Examples

Genome	Pfam A annotation
Phytophthora sojae	PF00006
Saccharomyces paradoxus	Sec7
Gibberella zeae	Zip

Output:

Description

Annotation for all proteins in OrthoMCL clusters containing proteins with the Pfam A annotation of interest. Annotation includes GO and Enzyme annotation, KEGG pathways the proteins are known to be involved in, identified Pfam motifs, results of Wolf-PSort, PSort and SignalP predictions.

Details

Protein ID	Identifier of the protein.
Symbol	Symbol of the protein.
Genome	Genome that the protein belongs to.
Gene ID	Identifier of the gene.
Locus Tag	Locus Tag of the gene.
Chr	Chromosome on which the gene is located.
Start	Start position of the gene (in bp).
MCL cluster ID	Identifier of the MCL cluster in which the protein can be found.
OrthoMCL cluster ID	Identifier of the OrthoMCL cluster in which the protein can be found.
PSort Prediction	Sub-cellular localisation of the protein as predicted by PSort.
Wolf-PSort Prediction	Sub-cellular localisation of the protein as predicted by Wolf-PSort.
SignalP Prediction	Information whether the protein has been predicted to be a secretory or non-secretory protein (prediction done using SignalP).
GO Annotations	List of all the GO annotations assigned to the protein.
Pfam A Annotations	List of all the Pfam A domains that have been identified for the protein.
Enzymes	List of all the Enzyme annotations assigned to the protein.
Pathways	List of all the KEGG pathways which the protein is part of.
Protein Sequence	Sequence of the protein.