Subsystems are a generalization of the concept of pathways, and they have two components. First is a list of functional roles that are united by any common process or biologically meaningful organizing principle. These are often metabolic pathways, but subsystems may also describe complex structures or phenotypes. Second is a spreadsheet, called a populated subsystem, which is a two-dimensional integration of biological functions with genome sequences. In the populated subsystem, functional roles are represented in columns, genomes are represented in rows, and cells of the spreadsheet are populated by the genes responsible for each function.

The table below shows a portion of the spreadsheet for the Arginine Biosynthesis subsystem. The name and ID of each participating organism are shown in the first two columns. The third column shows the ''variant code'', and the remaining columns correspond to the functional roles used to perform the subsystem's metabolic action, which in this case is the manufacture of Arginine.

Genome ID	Organism	Variant Code	argA/J	argB	argC	argD	argE	argF/I	argG	argH	ArgJ	ArgR
64091.1	Halobacterium sp. NRC-1 [A]	0						2495	2066	2065
257309.1	Corynebacterium diphtheriae NCTC 13129 [B]	1	1116	1117	1115	1118		1119	1121	1122	1116	1120
196164.1	Corynebacterium efficiens YS-314 [B]	1	1527	1528	1526	1529		1530	1532	1533	1527	1531
196627.4	Corynebacterium glutamicum ATCC 13032 [B]	1	1585	1586	1584	1587		1588	1590	1591	1585	1589
83332.1	Mycobacterium tuberculosis H37Rv [B]	1	1655	1656	1654	1657		1658	1660	1661	1655	1659
247156.1	Nocardia farcinica IFM 10152 [B]	1	1942, 3756	1943	1941	1944		1945	1967	1968	1942	1946
266940.1	Kineococcus radiotolerans SRS30216 [B]	1	2472	2473	2471	2474	673	2475	4581	2477	2472	2476
281090.3	Leifsonia xyli subsp. xyli str. CTCB07 [B]	1	38	39	37	40		41	1774	42	38
100226.1	Streptomyces coelicolor A3(2) [B]	1	1546	1545	1547	1190, 1251	1544	5923	6971	960	1546	1543
206672.1	Bifidobacterium longum NCC2705 [B]	1	1002	1001	1003	1000		999	997	996	1002	998

Each subsystem can have one or more variants, each of which uses a slightly different subset of the roles. The variant code specifies which of these variants is used be the specified genome. A variant code of 0 indicates that many of the functional roles are missing. A variant code of -1 indicates that the subsystem is not functional for the specified genome. Arginine Biosynthesis has only one real variant, so all the variant codes in the example are either 1 or 0.

To save space, the role names are abbreviated and the individual genes are shown as ID numbers only. To construct a FigId from the ID number, you paste it to the genome ID using the indicated gene type? . A missing gene type means that the gene is a ProteinEncodingGene, or peg. So, the FigId for the argB gene of Streptomyces coelicolor A3(2) is fig|100226.1.peg.1545.

Each subsystem has one or more biologists assigned as curators. The curators use the subsystems to annotate new genes and to make the annotations of existing genes more consistent. This process has been going on since 2003. In 2007, the RapidAnnotationServer (RAST) went online. The RapidAnnotationServer uses subsystems to automatically call and annotate new genomes.