When you first browse through your genome after it has been run through the ERGO automated annotation pipeline, you will notice that a number of metabolic and non-metabolic pathways have been "asserted" to be present in that organism. (You can tell a pathway has been asserted if you are looking at the pathway in the context of a particular organism and in the "Curate Pathway" box you see "Asserted". If you are browsing the functional overview tree, pathway assertion is indicated by the presence of a red circle next to the pathway name). How does Integrated Genomics decide to assert pathways?

There are two primary mechanisms by which a pathway is automatically asserted:

1) If all the non-optional steps present in a pathway can be connected to proteins in a given genome that can perform those steps, then the pathway is automatically asserted.

2) There are a collection of pathways for each domain of organisms (Archaeal, Bacterial and Eukaryote) that we believe are components of every organism in that domain, regardless of whether all the steps in the pathway have proteins matching that function. Sometimes these pathways reflect collections of genes where most but not all will be present in most organisms. Sometimes these are pathways where there is biochemical evidence that a functionality exists, but, as of yet, no one has isolated the protein that performs that function.

A box will be completely filled if at least one of its underlying pathways is asserted. Conversely, a box will be half-filled only if all the underlying pathways are unasserted. I tested this by unasserting all the pathways in an overview, and the box becomes half filled.

Under the current ERGO scheme, there are only two options for boxes: half-filled or completely filled. Even if all the genes in a pathway are missing, the box remains half-filled, not completely empty.