-
Notifications
You must be signed in to change notification settings - Fork 3
Compartments
John May edited this page May 2, 2013
·
14 revisions
This table details the current primary compartments that can be specified in Metingear. The code is a unique abbreviation that can be used when entering a reaction equations (see. Creating Metabolic Entities). The list is derived from the table of experimentall verified models from UCSD. Some synonyms are deliberately broad, such as, cell
which is resolved as cytoplasm
to ensure something can be assigned.
Name | Code | Synonyms | GO Term |
---|---|---|---|
cytoplasm | c | in, cytosol, internal species, cytoplasm matrix, cell | GO:0005737 |
periplasm | p | periplasmic space | GO:0042597 |
outer membrane-bounded periplasmic space | ombp | outer membrane-enclosed periplasmic space | GO:0030288 |
cell wall-bounded periplasmic space | cwbp | cell wall-enclosed periplasmic space | GO:0030287 |
extracellular | e | extracellular region, Out, Extra_Organism, External_Species, External | GO:0005576 |
golgi | g | golgi apparatus, golgi complex, golgi ribbon | GO:0005794 |
lysosome | l | GO:0005764 | |
glycosome | y | GO:0020015 | |
glyoxysome | w | GO:0009514 | |
peroxisome | x | peroxisomal, peroxisome vesicle | GO:0005777 |
mitochondrion | m | mitochondria, mitochondrium | GO:0005739 |
nucleus | n | cell nucleus | GO:0005634 |
endoplasmic reticulum | r | er | GO:0005783 |
chloroplast | h | GO:0009507 | |
apicoplast | a | GO:0020011 | |
glyoxysomes | o | ||
plastid | s | GO:0009536 | |
thylakoid | t | photosynthetic membrane | GO:0009579 |
vacuole | v | vacuolar carboxypeptidase Y | GO:0005773 |
flagellum | f | GO:0019861 | |
unknown | unk | empty string is considered unknown | |
golgi membrane | gm | GO:0000139 | |
mitochondrial membrane | mm | GO:0031966 | |
nuclear membrane | nm | GO:0031965 | |
plasma membrane | pm | plasmalemma, juxtamembrane, inner endospore membrane, cytoplasmic membrane, cell membrane, bacterial inner membrane, plasma membrane lipid bilayer | GO:0005886 |
endoplasmic reticulum membrane | rm | er Membrane | GO:0005789 |
vacuolar membrane | vm | GO:0005774 | |
peroxisomal membrane | xm | peroxisome membrane | GO:0005778 |