Subsystems

Subsystems are a generalization of the concept of pathways, and they have two components.

Acetoin_butanediol_metabolism.gif
Subsystem diagram for Acetoin, butanediol metabolism,
an example of a subsystem based on a metabolic pathway.
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 by 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 FIG ID 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 Protein Encoding Gene, or peg. So, the FIG ID 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 Rapid Annotation Server (RAST) went online. The Rapid Annotation Server uses subsystems to automatically call and annotate new genomes.

To search for genomes in a subsystem or to view a subsystem in the Genome Viewer, go to the subsystem search page.

Topic revision: r11 - 08 Feb 2009 - 21:36:59 - TWiki Guest
 
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.