List of SWISS-PROT keywords with strong correlation to sub-cellular locaisation
KEYWORD	LOCALIZATION	SWISS-PROT DESCRIPTION
Activator	NUCLEAR	Protein that positively regulates either the transcription of one or more genes, or the translation of mRNA.
Amphibian skin	EXTRACELLULAR	Protein specifically found in the skin of animals belonging to the vertebrate class amphibia, that includes frogs, toads, newts, salamanders and worm-like apoda.
Basement membrane	EXTRACELLULAR	Protein which is a component of the basement membrane, an extracellular matrix found under epithelial cells and around smooth and striated muscle cells. This matrix contains intrinsic macromolecular components such as collagen, laminin, and sulfated proteoglycans.
Blood coagulation	EXTRACELLULAR	Protein involved in blood clotting, a complex enzymatic cascade, in which the activated form of one factor catalyzes the activation of the next factor.
Calvin cycle	CHLOROPLAST	Protein involved in the cycle of biochemical reactions responsible for photosynthetic CO(2) fixation in many photosynthetic bacteria and in the stroma of plant chloroplasts.
Cell wall	EXTRACELLULAR	Protein which is part of the cell wall or which is involved in the formation and maintenance of it. The cell wall is an extracellular layer outside the plasma membrane which protects the cell against mechanical damage, osmotic strength and which determines the cell shape.
Centromere	NUCLEAR	Protein which binds centromeres or which is required for the assembly and movement of centromeres. Centromeres are the regions of replicated eukaryotic chromosomes where the two chromatids are joined together.
Chlorophyll biosynthesis	CHLOROPLAST	Protein involved in the synthesis of chlorophylls. These photosynthetic pigments are magnesium-porphyrin complexes with a long hydrophobic terpenoid side chain (the alcohol phytol).
Chloroplast	CHLOROPLAST	Protein encoded by or localized in the chloroplast, a photosynthetic organelle of eukaryotic green cells, in which light-harvesting and ATP synthesis occurs.
Chromatin regulator	NUCLEAR	Protein controlling the opening or closing of chromatin.
Chromosomal protein	NUCLEAR	Protein which is associated with chromosomal DNA, including histones, protamines and high mobility group proteins. Entries in SWISS-PROT:
Chylomicron	EXTRACELLULAR	Protein component of the chylomicrons or involved in their catabolism. Chylomicrons are the largest lipoprotein complexes with the lowest protein-to-lipid ratio. They are present in the blood or lymph and transport exogenous (dietary) cholesterol, triacylglycerols and other lipids from the intestine to the liver or to the adipose tissue.
Collagen	EXTRACELLULAR	Protein which contains one or more collagen-like domain. Collagen is a fibrous protein found in vertebrates, the major element of skin, bone, tendon, cartilage, blood vessels and teeth.
Complement pathway	EXTRACELLULAR	Pathway which activates the proteins of the complement system, a group of blood proteins of the globulin class involved in the lysis of foreign cells after they have been coated with antibody, and which also promote the removal of antibody-coated foreign particles by phagocytic cells.
Connective tissue	EXTRACELLULAR	Protein component of any mesodermally derived tissues including bone, cartilage, adipose tissue and fibrous tissues which support and connect internal organs.
Digestion	EXTRACELLULAR	Protein involved in the process whereby nutrients are rendered soluble and capable of being absorbed by the organism or cell, by action of various hydrolytic enzymes that break down proteins, carbohydrates, fats, etc.
DNA-binding	NUCLEAR	Protein which binds to DNA, typically to pack or modify the DNA, or to regulate gene expression. Among those proteins that recognize specific DNA sequences, there are a number of characteristic conserved motifs believed to be essential for specificity.
DNA condensation	NUCLEAR	Protein involved in DNA condensation. In most eukaryotes, the chromosomal packing involves the wrapping of DNA around a core of histones to form nucleosomes. Adjacent nucleosomes are packaged together via Histone 1 and nucleosomes are organised into a 30nm chromatin fibre. DNA condensation takes place as cells enter mitosis or when germ cells enter meiosis.
DNA-directed RNA polymerase	NUCLEAR	Enzymes which catalyze RNA synthesis the by addition of ribonucleotide units to a RNA chain using DNA as a template. They can initiate a chain de novo.
DNA repair	NUCLEAR	Protein involved in the repair of DNA, the various biochemical processes by which damaged DNA can be restored.
Endoplasmic reticulum	ENDOPLASMIC RETICULUM	Protein whose subcellular location is the endoplasmic reticulum, a membrane system continuous with the outer nuclear membrane. It consists of flattened, single-membrane vesicles whose inner compartments, the cisternae, interconnect to form channels throughout the cytoplasm.
Exonuclease	NUCLEAR	Enzyme that degrades DNA or RNA by progressively splitting off single nucleotides from one end of the chain.
Extracellular matrix	EXTRACELLULAR	Protein found in the extracellular matrix. The extracellular matrix consists of any material produced by cells and secreted into the surrounding medium, but this term generally applies to the non- cellular components of animal tissues.
Eye lens protein	CYTOPLASMIC	Protein found in the lens, a transparent body at the front of the vertebrate eye.
Gamma-carboxyglutamic acid	EXTRACELLULAR	Protein which possesses at least one gamma-carboxyglutamic acid, a posttranslationally modified glutamate residue found in blood coagulation proteins and in the proteins of calcified tissues. Gamma- carboxyglutamyl residues are good chelators of calcium ions.
Gaseous exchange	EXTRACELLULAR	Protein involved in the exchange of gases.
Glutamate biosynthesis	CYTOPLASMIC	Protein involved in the synthesis of the acidic amino acid glutamate. Glutamate is a component of proteins and can also act as a neurotransmitter in the central nervous system.
GMP biosynthesis	CYTOPLASMIC	Protein involved in the synthesis of GMP. GMP is the abbreviation for the nucleotide guanosine 5'-monophosphate.
Golgi stack	GOLGI	Protein found in the Golgi apparatus, an organelle present in eukaryotic cells that appears as a stack of 6-8 plate-like membranous compartments and associated vesicles and vacuoles, often located near the centrosome.
HDL	EXTRACELLULAR	Protein or apolipoprotein associated with High-Density Lipoproteins (HDL), a class of lipoproteins involved in lipid (cholesterol, phospholipids and triacylglycerol) metabolism in the body fluids.
Helicase	NUCLEAR	Protein with an helicase activity. Helicases are ATPases that act on DNA or RNA. Entries in SWISS-PROT:
Hemolysis	EXTRACELLULAR	Protein involved in hemolysis, the disruption of the integrity of the red cell membrane, thus causing the release of hemoglobin.
Homeobox	NUCLEAR	Protein which contains at least one homeobox, a conserved sequence originally detected, on the nucleotide level, in many of the genes which give rise to homeotic and segmentation mutants in Drosophila. The homeobox, also termed homeodomain, consists of about 60 amino acids and is involved in DNA-binding.
Inflammatory response	EXTRACELLULAR	Protein involved in the localized protective response to tissue damage, microbial infection, or the presence of foreign matter. It is characterized by swelling, redness, heat and pain and involves a complex series of events including vascular changes and accumulation of blood cells, such as neutrophil leucocytes and mononuclear phagocytes, at the site of injury.
Insulin family	EXTRACELLULAR	Protein that belongs to the insulin family. This family groups a number of hormones and growth factors.
Laminin EGF-like domain	EXTRACELLULAR	Protein containing at least one laminin EGF-like domain. Laminins are the major noncollagenous components of basement membranes. Their subunits contain consecutive repeats of about 60 amino acids, which include 8 conserved cysteines that form disulfide bonds (C1-C3, C2-C4, C5-C6, C7-C8).
Lignin degradation	EXTRACELLULAR	Protein involved in the breakdown of lignin, a polymer of phenylpropanoid subunits found in the walls of plant cells such as xylem and sclerenchyma fibres. It imparts strength to the wall and protects against degradation by microorganisms.
Lipid transport	EXTRACELLULAR	Protein involved in the transport of lipids, a diverse class of compounds which are insoluble in water but soluble in organic solvents. They include fats, oils, triacylglycerols, fatty acids, glycolipids, phospholipids and steroids.
Lipoyl	MITOCHONDRIAL	Protein which contains at least one lipoyl-binding domain. Lipoic acid is an essential cofactor for E2 acyltransferases and some other proteins.
Lysosome	LYSOSOME	Protein found in the lysosome, a membrane-limited organelle present in all eukaryotic cells, which contains a large number of hydrolytic enzymes that are used for the intracellular degradation of macromolecules.
MHC I	EXTRACELLULAR	Protein of the major histocompatibility complex (MHC) class I which is involved in the induction of strong immune reaction. MHC I is involved in immune responses against virus-infected cells and rejection of transplanted tissue.
Milk	EXTRACELLULAR	Protein found in milk, a fluid secreted by female mammals to provide food for their offspring. It consists of water, proteins, soluble carbohydrates, electrolytes, lipids and vitamins.
Mitochondrion	MITOCHONDRIA	Protein encoded by or localized in the mitochondrion, a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, eukaryotes.
Mitogen	EXTRACELLULAR	Protein which can induce mitosis of certain eukaryotic cells, i.e. it stimulates cellular proliferation.
mRNA splicing	NUCLEAR	Protein involved in the process by which nonsense sequences or intervening sequences (introns) are removed from pre-mRNA to generate a functional mRNA (messenger RNA) that contains only exons. This process occurs in the nucleus before the fuctional mRNA is sent to the cytoplasm.
Myogenesis	NUCLEAR	Protein involved in the differentiation and development of the muscle. Myogenesis is controlled by myogenic factors, a family of muscle- specific transcription factors that contain a conserved helix-loop- helix domain which is homologous to the myc family of proteins.
Neurotoxin	EXTRACELLULAR	Proteins, often exquisitely toxic, that inhibit neuronal function. Neurotoxins act typically against sodium channels or block or enhance synaptic transmission. Most venoms contain neurotoxic substances.
Nuclear protein	NUCLEAR	Protein located in the nucleus of a cell.
Nucleosome core	NUCLEAR	Protein characteristic of the nucleosome, a repeating structural unit in chromatin that packages DNA to give the chromatin a 'beads-on-a- string' appearance.
Paired box	NUCLEAR	Protein which contains a paired box domain, a conserved domain of about 120 amino acids, which is generally located in the N-terminal section of various proteins.
Pair-rule protein	NUCLEAR	A protein encoded by a pair-rule gene. These are developmental genes in Drosophila involved in delimiting segments in the early embryos. Mutations in pair rule genes affect every alternate segment.
Pancreas	EXTRACELLULAR	Protein characteristic of or secreted by the pancreas, a gland associated with gut in most vertebrates, which secretes hormones, insulin and glucagon from endocrine glands and digestive enzymes from exocrine glands.
Peroxisome	PEROXISOME	Protein found in the peroxisome or involved in its biosynthesis. The peroxisome is a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions.
Photorespiration	CHLOROPLAST	Oxygen consumption taking place in plants during the light period: in the presence of O(2) the enzyme rubisco catalyzes the oxidative fragmentation of ribulose 1,5-biphosphate to 3-phospho-D-glycerate and 2-phospho- glycolate in the chloroplast. 2-phosphoglycolate can then be transported to peroxisomes where it is reoxidized to glyoxylate and H(2)O.
Photosynthesis	CHLOROPLAST	Protein involved in photosynthesis, the process in which light energy is absorbed by photosynthetic pigments (e.g. chlorophyll) and converted to chemical energy (usually ATP and NADPH, =light reaction). This energy is subsequently used as an energy source for the reduction of carbon dioxide to carbohydrate (=Calvin cycle).
Photosystem I	CHLOROPLAST	Protein involved in photosystem I (PSI), a complex that uses light energy to mediate electron flow in the chloroplast thylakoid membrane of plants and in cyanobacteria.
Photosystem II	CHLOROPLAST	Protein involved in photosystem II (PSII), a complex that uses light energy to mediate electron flows in the chloroplast thylakoid membrane of plants and in cyanobacteria. PSII splits water, releasing hydrogen ions and molecular oxygen.
Pituitary	EXTRACELLULAR	Protein characteristic of the pituitary gland (hypophysis), an endocrine gland at the base of the hypothalamus, which secretes a number of hormones (pituitary hormones), such as vasopressin (antidiuretic hormone), oxytocin, adrenocorticotropin (ACTH), somatotropin (growth hormone, GH), prolactin and gonadotropin.
Plasma	EXTRACELLULAR	Protein secreted in the plasma, an acellular fluid in which blood cells are suspended. A variety of proteins are present in the blood plasma, including serum albumin, immunoglobulins, fibrinogens and other blood coagulation factors, protease inhibitors and complement components.
Plasminogen activation	EXTRACELLULAR	Protein involved in the plasminogen activation which occurs when an heterogeneous group of proteolytic enzymes convert plasminogen to plasmin.
Proline biosynthesis	CYTOPLASMIC	Protein involved in the biosynthesis of the cyclic amino acid proline. The structure of proline differs from the structure of other amino acids in that its side chain is bonded to the nitrogen of the amino group as well as to the carbon atom. This makes the amino group a secondary amine, and because of this, proline is also described as an imino acid. The presence of proline residues strongly influences the secondary structure of proteins.
Purine salvage	CYTOPLASMIC	Protein involved in the biosynthesis of purine nucleotides from free purines salvaged from their catabolism. This process is less expensive energetically and exerts feedback control on the de novo synthesis.
Pyridoxine biosynthesis	CYTOPLASMIC	Protein involved in the biosynthesis of pyridoxine, a precursor to the coenzyme pyridoxal phosphate.
Ribosome biogenesis	NUCLEAR	Protein involved in the synthesis of ribosomes.
Serine biosynthesis	CYTOPLASMIC	Protein involved in the synthesis of the amino acid serine, a constituent of proteins and precursor of several metabolites, including cysteine, glycine and choline. Serine is mostly formed from 3-phosphoglycerate in a 3-step reaction pathway.
Sexual differentiation	NUCLEAR	Protein involved in both the determination of cells to become sexual tissue in embryonic development and in the process by which male and female tissue becomes structurally and functionally specialized during embryonic development.
Sodium channel inhibitor	EXTRACELLULAR	Protein which interferes with the function of sodium channels which are membrane proteins forming a channel in a biological membrane selectively permeable to sodium ions. They are found in various venoms from snakes, scorpions and spiders.
SOS response	CYTOPLASMIC	Synthesis of DNA repair enzymes as an emergency response to severe DNA damage in bacteria. DNA damage in the cell is recognised as a block to DNA replication.
Spliceosome	NUCLEAR	Protein of the spliceosome, a very large complex of small nuclear RNA/protein particles (snRNPs) which assemble with pre-mRNA to achieve RNA splicing.
Surface film	EXTRACELLULAR	Protein found in the film of pulmonary surfactants which cover the alveolar surface of the mammalian lung. These surfactants are composed of 90 % phospholipids and 10 % proteins.
Sushi	EXTRACELLULAR	Protein which contains at least one sushi domain, a motif of approximately 60 amino acids characterized by a framework of four conserved half-cystine residues (1-3 and 2-4 disulfide-bonded) and several other highly conserved residues including proline, tryptophan, tyrosine/phenylalanine and cysteine.
Thrombophilia	EXTRACELLULAR	Protein which, if defective, causes thrombophilia, a disorder of the hemopoietic system in which the individuals are prone to serious spontaneous thrombosis.
Trans-acting factor	NUCLEAR	Protein which regulates transcription by binding to the DNA sequences, in the vicinity of the structural portion of a gene, which are required for gene expression. These DNA sequences, e.g. promoter sequences or operators are called cis-acting elements.
Transcription	NUCLEAR	Protein involved in the transfer of genetic information from DNA to messenger RNA (mRNA) by DNA-directed RNA polymerase. Entries in SWISS-PROT:
Transcription regulation	NUCLEAR	Protein involved in the regulation of the transcription process.
Venom	EXTRACELLULAR	Protein found in venom, a toxic secretion in animals that is actively delivered to the target animals, either to paralyze or incapacitate or else to cause pain as a defense mechanism.
Vitamin K	EXTRACELLULAR	Protein which which undergoes vitamin-K dependent carboxylation of glutamate. There are two natural forms, which are phylloquinone (vitamin K1 or phytylmenaquinone) in green vegetables and menaquinone (vitamin K2 or menaquinone-n, depending of the number of isoprene units of the side-chain or MK-n) in intestinal bacteria, as well as one synthetic provitamin form, menadione (vitamin K3).
VLDL	EXTRACELLULAR	Protein present in particles of Very Low-Density Lipoproteins or protein which interacts with them. VLDL are composed of 50% triacylglycerols, 12% cholesteryl esters, 7% free cholesterol, 18% phospholipids, and 10% proteins including apoB-100, apoC-I, apoC-II, apoC-III and apoE. Excess fatty acids or carbohydrate in the diet can be converted into triacylglycerols in the liver and packaged into VLDL.