Compartments

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