The KOG Browser
EuKaryotic Orthologous Groups (KOG) is a eukaryote-specific version of the Clusters of Orthologous Groups (COG) tool for identifying ortholog and paralog proteins. Where a KOG tool is provided for a JGI-sequenced organism, it provides a way to find JGI-predicted genes by KOG classification or ID.
KOG provides four functional groups, each of which is divided into KOG classifications identified by letters of the alphabet. Within each classification, groups of orthologous or paralogous proteins ("KOGs") are assigned a KOG ID.
With the KOG tool, you can:
The entry page to the KOG tool shows the full list of KOG classifications, ordered by KOG group and letter. Each classification can be expanded to reveal all the KOGs associated with that function. Only one classification can be expanded at a time.
For each classification, the number of JGI-predicted genes (gene models) related to that classification in the genome of interest is shown. When you expand a classification, you see the number of gene models related to each KOG. For each KOG group, a total gene count is given as well. The gene counts for classifications and KOGs are links.
From the KOG entry page, you can begin an advanced search to find genes, transcripts, or proteins by KOG ID or description.
To view the results shown in this picture, from the Search by KOG ID:
You can view a list of predicted genes (gene models) in a KOG or KOG classification by clicking the corresponding number of gene models on the KOG entry page.
The name of the KOG group appears as the page heading for the list of gene models. Below it is the name of the KOG classification.
To see the Protein page for a specific gene model, click Prot Id.
To see the Annotation page for a specific gene model, click Curated?
At the bottom of the list are buttons for retrieving FASTA sequences or ClustalW alignments.
To retrieve sequence in FASTA format,
To retrieve a ClustalW alignment,
To clear your selections, click Uncheck all.