Subsystem Variants

A variant is a particular combination of functional roles for a subsystem. A subsystem's variants are described by a variant code, which is usually a number.

subsystem spreadsheet showning variant codes

For each genome that uses the subsystem, there is a single variant code, displayed in the third column of the subsystem spreadsheet on the Genome Viewer Subsystem Page? , as shown in the screen fragment on the right.

The nature of each variant is described on the Notes tab of the subsystem page, as shown in the screen fragment to the left. In this subsystem (Tryptophan synthesis), there are three major variants, two minor variants, and two incomplete variants.

An incomplete variant is one that is not functional. Incomplete variants always have a variant code of 0 or -1. If the curator suspects that the subsystem no longer works in this particular genome, the variant code is -1. If the curator suspects that the subsystem works, but there are functional roles remaining to be identified (a work in progress), the code is 0.

A major variant is a relatively constant set of functional roles. The biggest one is given the variant code of 1 and the other variants are generally described in terms of how they differ from variant 1. A minor variant is a small change that can apply to one or more major variants. So, a variant code of 3 indicates that the trpC role (Phosphoribosylanthranilate isomerase) in variant 1 is instead performed by priA (Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase). A variant code of 3.1 indicates that in addition to the use of priA, the trpAa and trpAb roles are performed by a single gene (which is called a fusion).

Topic revision: r1 - 01 Jan 2009 - 22:51:55 - Bruce Parrello

Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.