2Fe-2S
type: Concept
alternative label: [2Fe-2S] cluster
alternative label: [Fe2S2] cluster
alternative label: 2 iron, 2 sulfur cluster binding
alternative label: Di-mu-sulfido-diiron
alternative label: Fe2/S2 (inorganic) cluster
alternative label: Fe2S2
comment: Protein which contains at least one 2Fe-2S iron-sulfur cluster: 2 iron atoms complexed to 2 inorganic sulfides and 4 sulfur atoms of cysteines from the protein.
subclass of: Iron-sulfur
subclass of: Metal-binding
category: Ligand

2 iron, 2 sulfur cluster binding
type: Class
database: go

3D-structure
type: Concept
comment: Protein, or part of a protein, whose three-dimensional structure has been resolved experimentally (for example by X-ray crystallography or NMR spectroscopy) and whose coordinates are available in the PDB database. Can also be used for theoretical models.
subclass of: Technical term
category: Technical term

3Fe-4S
type: Concept
comment: Protein which contains at least one 3Fe-4S iron-sulfur cluster: 3 iron atoms complexed to 4 inorganic sulfides and 3 sulfur atoms of cysteines from the protein. In a number of iron-sulfur proteins, the 4Fe-4S cluster can be reversibly converted by oxidation and loss of one iron ion to a 3Fe-4S cluster.
subclass of: Iron-sulfur
subclass of: Metal-binding
category: Ligand

3 iron, 4 sulfur cluster binding
type: Class
database: go

4Fe-4S
type: Concept
comment: Protein which contains at least one 4Fe-4S iron-sulfur cluster: 4 iron atoms complexed to 4 inorganic sulfides and 4 sulfur atoms of cysteines from the protein. In a number of iron-sulfur proteins, the 4Fe-4S cluster can be reversibly converted by oxidation and loss of one iron ion to a 3Fe-4S cluster.
subclass of: Iron-sulfur
subclass of: Metal-binding
category: Ligand

4 iron, 4 sulfur cluster binding
type: Class
database: go

Abscisic acid biosynthesis
type: Concept
alternative label: ABA anabolism
alternative label: ABA biosynthesis
alternative label: ABA formation
alternative label: ABA synthesis
alternative label: Abscisic acid anabolism
alternative label: Abscisic acid biosynthetic process
alternative label: Abscisic acid formation
alternative label: Abscisic acid synthesis
comment: Protein involved in the synthesis of abscisic acid (ABA) (5-(1-hydroxy-2,6,6,trimethyl-4-oxocyclohex-2-en-1-y1)-3-methylpenta-2,4-dienoic acid). ABA is a plant hormone which play a role in many aspects of plant growth, development and cellular signaling (e.g. seed dormancy, seed maturation, vegetative growth and responses to various environmental stimuli such as stomatal closure during drought). This phytohormone can be synthesized from farnesyl diphosphate (direct C15 pathway) or from 9-cis-violaxanthine (indirect C40 pathway).
subclass of: Biological process
category: Biological process

abscisic acid biosynthetic process
type: Class
database: go

Abscisic acid signaling pathway
type: Concept
alternative label: ABA mediated signaling
alternative label: ABA signaling pathway
alternative label: Abscisic acid mediated signaling
comment: Protein involved in the abscisic acid (ABA) (5-(1-hydroxy-2,6,6,trimethyl-4-oxocyclohex-2-en-1-y1)-3-methylpenta-2,4-dienoic acid) signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth, development and cellular signaling (e.g. seed dormancy, seed maturation, vegetative growth and responses to various environmental stimuli such as stomatal closure during drought). This phytohormone can be synthesized from farnesyl diphosphate (direct C15 pathway) or from 9-cis-violaxanthine (indirect C40 pathway).
subclass of: Biological process
category: Biological process

abscisic acid-activated signaling pathway
type: Class
database: go

Acetoin biosynthesis
type: Concept
alternative label: 3-hydroxy-2-butanone anabolism
alternative label: 3-hydroxy-2-butanone biosynthesis
alternative label: 3-hydroxy-2-butanone biosynthetic process
alternative label: 3-hydroxy-2-butanone formation
alternative label: 3-hydroxy-2-butanone synthesis
alternative label: Acetoin anabolism
alternative label: Acetoin biosynthetic process
alternative label: Acetoin formation
alternative label: Acetoin synthesis
comment: Protein involved in the synthesis of acetoin (3-hydroxy-2-butanone). Acetoin is a component of the butanediol cycle (butanediol fermentation) in microorganisms.
subclass of: Biological process
category: Biological process

acetoin biosynthetic process
type: Class
database: go

Acetoin catabolism
type: Concept
alternative label: 3-hydroxy-2-butanone breakdown
alternative label: 3-hydroxy-2-butanone catabolic process
alternative label: 3-hydroxy-2-butanone catabolism
alternative label: 3-hydroxy-2-butanone degradation
alternative label: Acetoin breakdown
alternative label: Acetoin catabolic process
alternative label: Acetoin degradation
comment: Protein involved in the degradation of acetoin (3-hydroxy-2-butanone). Acetoin is a component of the butanediol cycle (butanediol fermentation) in microorganisms.
subclass of: Biological process
category: Biological process

acetoin catabolic process
type: Class
database: go

Acetylation
type: Concept
alternative label: Acetylated
alternative label: N-acetylated
comment: Protein which is posttranslationally modified by the attachment of at least one acetyl group; generally at the N-terminus.
subclass of: PTM
category: PTM

Acetylcholine receptor inhibiting toxin
type: Concept
alternative label: nAChR inhibitor
alternative label: Nicotinic AChR inhibitor
comment: Toxin which interferes with the function of the nicotinic acetylcholine receptor (nAChR). The nAChR is a postsynaptic membrane protein that undergoes an extensive conformational change upon binding to acetylcholine, leading to opening of an ion-conducting channel across the plasma membrane. These toxins are mostly found in snake and cone snail venoms.
subclass of: Postsynaptic neurotoxin
category: Molecular function

acetylcholine receptor inhibitor activity
type: Class
database: go

Actin capping
type: Concept
alternative label: Actin filament capping
alternative label: F-actin capping
comment: Protein that binds to the free end of the actin filament and thereby blocks further addition of subunits.
subclass of: Molecular function
category: Molecular function

actin filament capping
type: Class
database: go

Actin-binding
type: Concept
alternative label: Actin filament binding
comment: Protein which binds to actin, and thereby can modulate the properties and/or functions of the actin filament.
subclass of: Molecular function
category: Molecular function

actin binding
type: Class
database: go

Actin-dependent inwards viral transport
type: Concept
comment: Viral protein that allows the active transport of viral material along actin filaments toward the intracellular replication sites during virus entry. This transport probably involves motor proteins like myosins or polymerization/depolymerization reactions as a driving force. Viruses such as poliovirus may utilize this type of intracellular transport.
subclass of: Cytoplasmic inwards viral transport
category: Biological process

actin-dependent intracellular transport of virus towards nucleus
type: Class
database: go

Activation of host autophagy by virus
type: Concept
comment: Viral protein involved in the activation of host autophagy. Autophagy is a major intracellular pathway in the delivery of cytoplasmic material to lysosomes for degradation. It is also essential for the removal of pathogenic protein aggregates from the cell during infection. Although autophagy is clearly important for antiviral immune response, it can also be activated by viruses and serves as platform for viral replication. Some viruses such as poliovirus, use the autophagic pathway as a nonlytic mechanism for viral release.
subclass of: Host-virus interaction
category: Biological process

induction by virus of host autophagy
type: Class
database: go

Activation of host caspases by virus
type: Concept
comment: Viral protein involved in the activation of host cell apoptosis by acting on host caspases. While many viruses encode protein that inhibit apoptosis, viruses can also use apoptosis to their advantage to suppress immune response or to disseminate. Therefore, some viral proteins are able to cleave or activate caspases in order to promote apoptosis.
subclass of: Modulation of host cell apoptosis by virus
category: Biological process

induction by virus of host apoptotic process
type: Class
database: go

Activation of host NF-kappa-B by virus
type: Concept
comment: Viral protein involved in the activation of host NF-kappa-B. This protein is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processed such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. Several viruses have developed strategies to activate the NF-kappa-B pathway in order to promote viral replication and prevent virus-induced apoptosis.
subclass of: Host-virus interaction
category: Biological process

induction by virus of host NF-kappaB cascade
type: Class
database: go

Activator
type: Concept
alternative label: Positive activator
comment: Protein that positively regulates either the transcription of one or more genes, or the translation of mRNA.
subclass of: Molecular function
category: Molecular function

Acute phase
type: Concept
alternative label: Acute-phase reaction
alternative label: Acute-phase response
comment: Protein involved in acute phase, a response of the vertebrate body to insults, infections, immunological reactions or inflammatory processes; characterised by redness (rubor), heat (calor), swelling (tumor), pain (dolor) and sometimes loss of function.
subclass of: Biological process
category: Biological process

acute-phase response
type: Class
database: go

Acyltransferase
type: Concept
comment: Enzyme catalyzing the transfer of acyl- (RCO-) groups.
subclass of: Transferase
category: Molecular function

acyltransferase activity
type: Class
database: go

Adaptive immunity
type: Concept
alternative label: Acquired immunity
comment: Protein involved in adaptive immunity. Vertebrates can develop a broad and almost infinite repertoire of antigen-specific receptors, which allows vertebrates to recognize almost any potential pathogen or toxin and to mount antigen-specific responses to it. Two types of adaptive immunity systems have evolved in vertebrates in order to generate immune receptor diversity. The jawed vertebrates strategy uses the V(D)JC recombination to achieve combinatorial diversity of immunoglobulin-based B cell receptors and T cell receptors. The jawless vertebrate strategy uses the somatic rearrangements of variable leucine-rich cassettes in the variable lymphocyte receptors (VLRs). The hallmarks of an adaptive immune system is the production of antigen-specific recognition receptor by somatic gene rearrangement. The long life of some antigen-primed cytotoxic lymphocytes and plasma cells provide protective memory to prevent reinvasion.
subclass of: Immunity
narrower: MHC II
narrower: T cell receptor
narrower: Immunoglobulin
category: Biological process

adaptive immune response
type: Class
database: go

ADP-ribosylation
type: Concept
alternative label: Adenosinediphospho-ribosylation
alternative label: ADP-ribosylated
comment: Protein which is posttranslationally modified by the attachment of at least one ADP-ribosyl group.
subclass of: PTM
category: PTM

Age-related macular degeneration
type: Concept
alternative label: ARMD
comment: Protein which, if defective, causes age-related macular degeneration (ARMD), the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid (known as drusen) that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch's membrane. ARMD is likely to be a mechanistically heterogeneous group of disorders, and the specific disease mechanisms that underlie the vast majority of cases are currently unknown. However, a number of studies have suggested that both genetic and environmental factors are likely to play a role.
subclass of: Disease
category: Disease

Aicardi-Goutieres syndrome
type: Concept
alternative label: AGS
alternative label: Cree encephalitis
alternative label: Pseudo-torch syndrome
alternative label: Pseudotoxoplasmosis syndrome
comment: Protein which, if defective, causes Aicardi-Goutieres syndrome, a genetic disorder that is phenotypically similar to in utero viral infection. The disease is characterized by severe neurological dysfunction in infancy, leading to progressive microcephaly, spasticity, dystonic posturing, profound psychomotor retardation and often death in early childhood.
subclass of: Disease
category: Disease

AIDS
type: Concept
alternative label: Acquired immunodeficiency syndrome
comment: Protein encoded by the human immunodeficiency viruses HIV-1 or HIV-2, which are the cause of acquired immunodeficiency syndrome (AIDS). This disease is characterized by a severe defect of cell-mediated immunity which is often accompanied by cancers such as Kaposi's sarcoma, as well as secondary infections such as tuberculosis.
subclass of: Disease
category: Disease

Albinism
type: Concept
comment: Protein which, if defective, causes albinism, a genetically determined or environmentally induced absence of pigmentation in animals normally pigmented. This can lead for example to lack of pigmentation in hair, skin and eyes.
subclass of: Disease
narrower: Hermansky-Pudlak syndrome
category: Disease

Alginate biosynthesis
type: Concept
alternative label: Alginate anabolism
alternative label: Alginate formation
alternative label: Alginate synthesis
alternative label: Alginic acid anabolism
alternative label: Alginic acid biosynthesis
alternative label: Alginic acid formation
alternative label: Alginic acid synthesis
comment: Protein involved in the synthesis of alginate. Alginate is an exopolysaccharide in the cell walls of brown algae and in the capsular material of certain strains of Pseudomonas and Azotobacter, in which it provides a protective barrier against host immune defenses and antibiotics.
subclass of: Biological process
category: Biological process

alginic acid biosynthetic process
type: Class
database: go

Alkaloid metabolism
type: Concept
alternative label: Alkaloid metabolic process
comment: Protein involved in a biochemical reaction with alkaloids, a group of nitrogenous organic molecules (mostly heterocyclic) usually found in plants. Various alkaloids have toxic or medical properties, such as caffeine, morphine and nicotine.
subclass of: Biological process
category: Biological process

alkaloid metabolic process
type: Class
database: go

Alkylphosphonate uptake
type: Concept
comment: Protein involved in alkylphosphonate uptake. Certain bacteria such as Escherichia coli can use alkylphosphonates as a phosphorus source.
subclass of: Biological process
category: Biological process

organic phosphonate transport
type: Class
database: go

Allergen
type: Concept
comment: Protein that stimulates the production of, and reacts with, antibodies (IgE) thus creating an allergic reaction (immediate-type hypersensitivity). Examples are pollen allergens from plants, venom allergens from insects, dust-mite allergens, and animal hair allergens.
subclass of: Disease
category: Disease

Allosteric enzyme
type: Concept
comment: Enzyme whose activity is modified by the noncovalent binding of an allosteric effector at a site other than the active site. This binding mediates conformational changes, altering its catalytic or binding properties.
subclass of: Molecular function
category: Molecular function

catalytic activity
type: Class
database: go

metabolic process
type: Class
database: go

Alpha-amylase inhibitor
type: Concept
comment: Protein that inhibits alpha-amylase, an enzyme that catalyzes the endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
subclass of: Molecular function
category: Molecular function

alpha-amylase inhibitor activity
type: Class
database: go

Alport syndrome
type: Concept
comment: Protein which, if defective, causes Alport syndrome, an hereditary disorder characterized by a progressive glomerulonephritis leading to end-stage renal disease, often associated with sensorineural hearing loss and ocular abnormalities.
subclass of: Disease
category: Disease

Alternative initiation
type: Concept
comment: Protein for which at least two isoforms exist due to the usage of alternative initiation codons in the same mRNA (the resulting isoforms differ in their N-terminus if they are in frame).
subclass of: Coding sequence diversity
category: Coding sequence diversity

Alternative promoter usage
type: Concept
comment: Protein for which at least two isoforms exist due to the alternative usage of promoters.
subclass of: Coding sequence diversity
category: Coding sequence diversity

Alternative splicing
type: Concept
comment: Protein for which at least two isoforms exist due to distinct pre-mRNA splicing events.
subclass of: Coding sequence diversity
category: Coding sequence diversity

Alzheimer disease
type: Concept
alternative label: Alzheimer's disease
comment: Protein which, if defective, causes Alzheimer disease, a neurodegenerative disorder characterized by progressive dementia and global loss of cognitive abilities. The condition primarily occurs after age 60, and is marked pathologically by severe cortical atrophy, senile plaques, neurofibrillary tangles, and neuropil threads. Early-onset forms also occurr.
subclass of: Disease
category: Disease

Amelogenesis imperfecta
type: Concept
comment: Protein which, if defective, causes amelogenesis imperfecta, a clinically and genetically heterogeneous group of disorders affecting the dental enamel. The enamel may be hypoplastic, hypomineralized or both, and affected teeth may be discoloured, sensitive or prone to disintegration either pre-eruption or post-eruption. In the hypoplastic type of amelogenesis imperfecta, the enamel is of normal hardness but does not develop to normal thickness. In the hypomineralized type, the enamel is of normal thickness but opaque or yellowish white without lustre on newly erupted teeth; it is so soft that it is lost soon after eruption. Amelogenesis imperfecta occasionally occurs in conjunction with other dental, oral and extra-oral features.
subclass of: Disease
category: Disease

Amidation
type: Concept
alternative label: Amidated
comment: Peptide which is posttranslationally modified by C-terminal amidation. The amino acid to be modified is almost always followed by a glycine, which provides the amide group. In a first reaction step the glycine is oxidized to form alpha-hydroxy-glycine. The oxidized glycine cleaves into the C-terminally amidated peptide and an N-glyoxylated peptide. C-terminal amidation is essential to the biological activity of many neuropeptides and hormones. In a few cases alpha-oxidative cleavage of an amino acid other than glycine has been observed. All such cases are additionally annotated with the word "atypical" in the feature description.
subclass of: PTM
category: PTM

Amino-acid biosynthesis
type: Concept
alternative label: Amino-acid anabolism
alternative label: Amino-acid formation
alternative label: Amino-acid synthesis
comment: Protein involved in the synthesis of naturally-occuring amino acids. In addition to their use for protein biosynthesis, they are the precursors of many molecules such as purines, pyrimidines, histamines, adrenaline and melanin.
subclass of: Biological process
narrower: Arginine biosynthesis
narrower: Aromatic amino acid biosynthesis
narrower: Asparagine biosynthesis
narrower: Branched-chain amino acid biosynthesis
narrower: Cysteine biosynthesis
narrower: Glutamate biosynthesis
narrower: Histidine biosynthesis
narrower: Lysine biosynthesis
narrower: Methionine biosynthesis
narrower: Proline biosynthesis
narrower: Serine biosynthesis
narrower: Threonine biosynthesis
category: Biological process

amino acid biosynthetic process
type: Class
database: go

Amino-acid transport
type: Concept
alternative label: Amino acid transport
comment: Protein involved in the transport of amino acids.
subclass of: Transport
category: Biological process

amino acid transport
type: Class
database: go

Aminoacyl-tRNA synthetase
type: Concept
alternative label: Amino acid translase
alternative label: Aminoacyl-tRNA ligase
alternative label: Aminoacyl-tRNA synthase
comment: Enzyme that activates an amino acid for translation by forming an aminoacyladenylate intermediate and then links this activated amino acid to the corresponding tRNA molecule (amino acid-tRNA, aminoacyl-tRNA). In general, a specific aminoacyl-tRNA synthase is available for each amino acid.
subclass of: Ligase
category: Molecular function

aminoacyl-tRNA ligase activity
type: Class
database: go

Aminopeptidase
type: Concept
comment: Enzyme that catalyzes the removal of amino acids from the N-terminus of peptides and proteins.
subclass of: Protease
category: Molecular function

aminopeptidase activity
type: Class
database: go

Aminotransferase
type: Concept
alternative label: Transaminase
comment: Enzyme that catalyzes the transfer of an alpha-amino group from an amino acid to an alpha-keto acid. The amino group is usually covalently bound by the prosthetic group pyridoxal phosphate.
subclass of: Transferase
category: Molecular function

transaminase activity
type: Class
database: go

Ammonia transport
type: Concept
alternative label: Ammonium transport
comment: Protein involved in the transport of ammonia/ammonium. Ammonia is an excellent nitrogen source for many bacteria, fungi, and plants, but it can be cytotoxic, especially for animal cells at high concentration. Its transport across cellular membranes is thus of high biological relevance. Ammonia (NH3) is a weak base and exists predominantly as the ammonium ion (NH4+) in biological fluids.
subclass of: Transport
category: Biological process

ammonium transmembrane transport
type: Class
database: go

Amphibian defense peptide
type: Concept
comment: Protein specifically found in the skin of animals belonging to the vertebrate class amphibia, that includes frogs, toads, newts, salamanders and worm-like apoda. The skins of anuran amphibians, in addition to mucous glands, contain highly specialized poison glands, which, in reaction to stress or attack, exude a complex noxious species-specific cocktail of biologically active molecules. These secretions often contain a plethora of peptides such as neuropeptides and hormones. The frog dermatous glands also synthesize and store an extraordinarily rich variety of wide-spectrum antimicrobial peptides that are released onto the outer layer of the skin to provide an effective and fast-acting defense against harmful microorganisms.
subclass of: Molecular function
category: Molecular function

defense response
type: Class
database: go

Amyloid
type: Concept
alternative label: Amyloid fibre-forming
alternative label: Amyloid fibril-forming
alternative label: Amyloid filament-forming
alternative label: Amyloid-forming
alternative label: Amyloid-like fibre-forming
alternative label: Amyloid-like fibril-forming
alternative label: Amyloid-like filament-forming
alternative label: Functional amyloid
comment: Proteins which may form wide, insoluble, unbranched filaments possessing a cross-beta sheet quaternary structure, where the beta sheets are oriented perpendicular to the fibre axis. Amyloid fibrils may be involved in abnormal protein depositions, or amyloidosis, such as Alzheimer's or Parkinson's diseases. Functional amyloids, found in a wide range of organism, from bacteria to mammals are involved in diverse functions such as biofilm formation, formation of aerial hyphae, long-term memory or regulation of melanin biosynthesis.
subclass of: Cellular component
narrower: Prion
category: Cellular component

Amyloidosis
type: Concept
comment: Protein which, if defective, causes amyloidosis, a vast group of diseases defined by the accumulation of amyloid in tissues. Amyloidoses are classified according to clinical signs, biochemical type of amyloid protein involved, and the extent of amyloid deposition (generalized or localized). Most amyloidoses are multisystemic diseases affecting several organs or systems. Mainly affected organs are the kidneys, heart, gastrointestinal tract, liver, skin, peripheral nerves and eyes, but any organ can be affected. The most frequent forms are primary amyloidosis, also known as light-chain immunoglobulin amyloidosis (AL), reactive or inflammatory amyloidosis, also known as acquired amyloidosis (AA), and transthyretin amyloidosis (ATTR). Localized amyloidosis affecting the brain is characteristic of Alzheimer's disease, trisomy 21, and prion diseases (transmissible spongiform encephalitis, Creutzfeldt-Jakob disease, Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia). In prion diseases the amyloid precursor is the prion protein.
subclass of: Disease
category: Disease

Amyloplast
type: Concept
comment: Protein found in the amyloplast, a colorless plant plastid that forms and stores starch. Amyloplasts are found in many tissues, particularly in storage tissues.
subclass of: Plastid
category: Cellular component

amyloplast
type: Class
database: go

Amyotrophic lateral sclerosis
type: Concept
alternative label: ALS
comment: Protein which, if defective, causes amyotrophic lateral sclerosis (ALS), a degenerative disorder of motor neurons in the cortex, brain stem and spinal cord. ALS is characterized by muscular weakness and atrophy.
subclass of: Neurodegeneration
category: Disease

Angiogenesis
type: Concept
alternative label: Vascularization
comment: Protein involved in angiogenesis, the sprouting or splitting of capillaries from pre-existing vasculature. Angiogenesis plays an important role for example during embryonic development, normal growth of tissues and maintenance of the normal vasculature, wound healing, tumor growth and metastasis.
subclass of: Biological process
category: Biological process

angiogenesis
type: Class
database: go

Anion exchange
type: Concept
alternative label: Anion exchanger activity
comment: Protein involved in the exchange of anions across a membrane. Anion exchange is a cellular transport function which contributes to the regulation of cell pH and volume by a functionally related anion exchanger protein family.
subclass of: Ion transport
category: Biological process

obsolete anion:anion antiporter activity
type: Class
database: go

ANK repeat
type: Concept
alternative label: ANK motif
alternative label: Ankyrin repeat
comment: Protein containing at least one ANK repeat, a conserved domain of approximately 33 amino acids, that was originally identified in ankyrin. It has been described as an L-shaped structure consisting of a beta-hairpin and two alpha-helices. Many ankyrin repeat regions are known to function as protein-protein interaction domains.
subclass of: Domain
category: Domain

Annexin
type: Concept
alternative label: Annexin repeat
comment: Protein containing at least one annexin repeat, a conserved domain of 61 residues, which is present in proteins of the annexin family in either four or eight copies. The annexin calcium binding sites are found within the repeated domains.
subclass of: Domain
category: Domain

Antenna complex
type: Concept
alternative label: Light-harvesting antenna
alternative label: Light-harvesting complex
comment: Component of an antenna complex or protein regulating the expression of such components. Antenna complexes are light-harvesting systems (LHC) which are protein-pigment complexes in or on photosynthetic membranes. LHCs receive radiant energy and transfer it to the reaction centers; an array of LHCs is often referred to as an "antenna". LHCs typically include one or more associated pigments (phycobilins, chlorophylls, bacteriochlorophylls and carotenoids).
subclass of: Cellular component
narrower: Phycobilisome
category: Cellular component

light-harvesting complex
type: Class
database: go

Antibiotic
type: Concept
alternative label: Antibacterial
alternative label: Bactericide
comment: Protein with antibacterial activity.
subclass of: Antimicrobial
narrower: Bacteriocin
category: Molecular function

defense response to bacterium
type: Class
database: go

Antibiotic biosynthesis
type: Concept
alternative label: Antibiotic anabolism
alternative label: Antibiotic formation
alternative label: Antibiotic synthesis
comment: Protein involved in the synthesis of antibiotics. Antibiotics are organic compounds produced by living organims that can selectively inhibit the growth of, or kill bacteria.
subclass of: Biological process
narrower: Streptomycin biosynthesis
narrower: Bacteriocin biosynthesis
category: Biological process

antibiotic biosynthetic process
type: Class
database: go

Antibiotic resistance
type: Concept
alternative label: Resistance to antibiotic
comment: Protein that confers, on bacteria, the ability to withstand antibiotics. The resistance is often due either to mutations that prevent antibiotic binding to the protein or to amplification of the gene encoding the protein.
subclass of: Biological process
narrower: Cycloheximide resistance
narrower: Trimethoprim resistance
category: Biological process

response to antibiotic
type: Class
database: go

Antifreeze protein
type: Concept
alternative label: AFP
alternative label: Ice structuring protein
alternative label: ISP
comment: Protein that lowers the freezing point of blood or other biological fluids by inhibiting the formation of water ice crystals.
subclass of: Molecular function
category: Molecular function

Antimicrobial
type: Concept
comment: Protein which has deleterious effects on any type of microbe. Microbe is a general term for microscopic unicellular organisms, such as bacteria, archaea, fungi and protista. While the term microbe is often also used for viruses, we do not apply the keyword antimicrobial to antiviral proteins.
subclass of: Molecular function
narrower: Antibiotic
narrower: Bacteriolytic enzyme
narrower: Defensin
narrower: Fungicide
category: Molecular function

Antioxidant
type: Concept
comment: Protein capable of counteracting the damaging effects of oxidation, e.g. by trapping free radicals generated during the metabolic burst and possibly inhibiting ageing. Scavengers of highly reactive and harmful oxygen species.
subclass of: Molecular function
category: Molecular function

antioxidant activity
type: Class
database: go

Antiport
type: Concept
alternative label: Antiporter
alternative label: Countertransporter
alternative label: Exchanger
alternative label: Exchange transporter
comment: Protein involved in the transport of a solute across a biological membrane coupled, directly, to the transport of a different solute in the opposite direction.
subclass of: Transport
category: Biological process

antiporter activity
type: Class
database: go

Antiviral defense
type: Concept
comment: Protein synthesized or activated in the cell in response to viral infection, or protein with specific antiviral activity within the cell. Eukaryotic cells have an innate immune mechanism to fight viral infection, which is activated through the interferon signaling pathway or through dsRNA detection in the cytoplasm. It leads to the establishment of an antiviral cell state, which prevents virus replication or induces apoptosis. Most viruses have developed specific proteins to prevent the establishment of an antiviral state. About half of all bacteria and most archaea have a CRISPR (clustered regularly interspersed short plaindromic repeats) system of adaptive immunity to exogenous DNA. CRISPRs clusters are tandem arrays of alternating repeats and spacers, where the spacers in some cases are homologous to sequences from virus and plasmid genomes. The CRISPR arrays are transcribed, processed and in some way aid in detection and resistance to foreign DNA. In at least a few bacteria (E.coli, S.epidermidis) it seems DNA is the target, whereas in Pyrococcus furiosis it seems the CRISPR system targets RNA.
subclass of: Biological process
category: Biological process

defense response to virus
type: Class
database: go

Antiviral protein
type: Concept
comment: Protein with antiviral activity. Often this activity is fortuitous (e.g. a bacterial protein displaying anti-HIV activity).
subclass of: Molecular function
category: Molecular function

regulation of defense response to virus
type: Class
database: go

Aortic aneurysm
type: Concept
comment: Protein which, if defective, causes aortic aneurysm. Aortic aneurysm is the dilation of the wall of the aorta. It forms a sac that is filled with fluid or clotted blood, often resulting in a pulsating tumor. Aortic aneurysms are classified by their location on the aorta.
subclass of: Disease
category: Disease

Apicoplast
type: Concept
alternative label: Golgi-adjunct organelle
alternative label: Thick-walled organelle
comment: Protein encoded by the apicoplast genome or protein located in the apicoplast, a plastid found in some apicomplexan parasites which is a non-photosynthetic plastid relict. This organelle contains ring-like DNA of about 35 Kb as a third type of cell genome. Apicoplasts do not contain thylakoids; it is not yet clear if they contain internal membranes.
subclass of: Plastid
category: Cellular component

apicoplast
type: Class
database: go

Apoplast
type: Concept
comment: Protein which is found in the part of the plant which is external to the living protoplast, ie the cell wall, the intercellular space and the lumina of dead cells such as xylem vessels and tracheids.
subclass of: Cellular component
category: Cellular component

apoplast
type: Class
database: go

Apoptosis
type: Concept
alternative label: Active cell death
alternative label: Apoptotic programmed cell death
alternative label: Type I programmed cell death
comment: Protein involved in apoptotic programmed cell death. Apoptosis is characterized by cell morphological changes, including blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation and chromosomal DNA fragmentation, and eventually death. Unlike necrosis, apoptosis produces cell fragments, called apoptotic bodies, that phagocytic cells are able to engulf and quickly remove before the contents of the cell can spill out onto surrounding cells and cause damage. In general, apoptosis confers advantages during an organism's life cycle.
subclass of: Biological process
category: Biological process

apoptotic process
type: Class
database: go

Arabinose catabolism
type: Concept
alternative label: Arabinose breakdown
alternative label: Arabinose catabolic process
alternative label: Arabinose degradation
comment: Protein involved in arabinose breakdown. Arabinose is a 5-carbon aldose sugar found in plant gums, pectins and bacterial cell wall polysaccharides.
subclass of: Carbohydrate metabolism
category: Biological process

arabinose catabolic process
type: Class
database: go

Archaeal flagellum
type: Concept
alternative label: Archaeal flagella
alternative label: Archaeal flagellar apparatus
alternative label: Archaellum
comment: The archaellum (archaeal flagellum) is the motility apparatus of archaea which propels the cell through liquid medium. The archaellum is the functional equivalent of the bacterial flagellum but its architecture, composition and mode of assembly is completely unrelated. The archaellum is thinner (10-15 nm) compared to the bacterial flagellum (18-24 nm). Its filament is assembled from archaellin subunits, which are N-glycosylated proteins. The archaellum is considered to be a type IV pilus-like structure and accordingly is assembled from the base into a 3-start helix. Archaellins have a type III signal sequence which is removed by the pre-archaellin peptidase. Core components of the assembly machinery are ArlI and ArlJ (previously FlaI, FlaJ) which are distantly related to PilB and PilC from type II secretion systems and type IV pills assembly systems. ArlI is a dual function ATPase which first assembles the filament and then rotates it by using the energy from ATP hydrolysis. Ion gradients are not used for archaellum rotation.
subclass of: Cellular component
category: Cellular component

archaeal-type flagellum
type: Class
database: go

Archaeal flagellum biogenesis
type: Concept
alternative label: Archaeal flagella biogenesis
alternative label: Archaeal flagellar apparatus biogenesis
comment: Protein which is involved in the formation, organization or maintenance of the archaellum (archaeal flagellum) the motility apparatus of archaea which propels the cell through liquid medium. The archaellum is the functional equivalent of the bacterial flagellum but its architecture, composition and mode of assembly is completely unrelated. The archaellum is thinner (10-15 nm) compared to the bacterial flagellum (18-24 nm). Its filament is assembled from archaellin subunits (archaeal flagellin), N-glycosylated proteins. The archaellum is considered to be a type IV pilus-like structure and accordingly is assembled from the base into a 3-start helix. Archaellins have a type III signal sequence which is removed by the pre-archaellin peptidase. Core components of the assembly machinery are ArlI and ArlJ (previously FlaI, FlaJ) which are distantly related to PilB and PilC from type II secretion systems and type IV pills assembly systems. ArlI is a dual function ATPase which first assembles the filament and then rotates it by using the energy from ATP hydrolysis.
subclass of: Biological process
category: Biological process

Arginine biosynthesis
type: Concept
alternative label: Arginine anabolism
alternative label: Arginine biosynthetic process
alternative label: Arginine formation
alternative label: Arginine synthesis
comment: Protein involved in the synthesis of the basic amino acid arginine (Arg).
subclass of: Amino-acid biosynthesis
category: Biological process

arginine biosynthetic process
type: Class
database: go

Arginine metabolism
type: Concept
alternative label: Arginine metabolic process
comment: Protein involved in biochemical reactions with the basic amino acid arginine (Arg).
subclass of: Biological process
category: Biological process

arginine metabolic process
type: Class
database: go

Aromatic amino acid biosynthesis
type: Concept
alternative label: Aromatic amino acid anabolism
alternative label: Aromatic amino acid family biosynthetic process
alternative label: Aromatic amino acid formation
alternative label: Aromatic amino acid synthesis
comment: Protein involved in the synthesis of an amino acid with an aromatic side-chain: phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp).
subclass of: Amino-acid biosynthesis
narrower: Phenylalanine biosynthesis
narrower: Tryptophan biosynthesis
narrower: Tyrosine biosynthesis
category: Biological process

aromatic amino acid family biosynthetic process
type: Class
database: go

Aromatic hydrocarbons catabolism
type: Concept
alternative label: Aromatic compound catabolic process
alternative label: Aromatic hydrocarbons breakdown
alternative label: Aromatic hydrocarbons degradation
comment: Protein involved in the breakdown of aromatic hydrocarbons. Aromatic hydrocarbons are compounds which only contain carbon and hydrogen, examples include the common pollutants benzene and naphthalene.
subclass of: Biological process
category: Biological process

aromatic compound catabolic process
type: Class
database: go

Arsenical resistance
type: Concept
alternative label: Arsenic resistance
alternative label: Resistance to arsenic
comment: Protein that confers, on bacteria and other microorganisms, the ability to withstand aromatic compounds of arsenic.
subclass of: Biological process
category: Biological process

response to arsenic-containing substance
type: Class
database: go

Ascorbate biosynthesis
type: Concept
alternative label: Ascorbate anabolism
alternative label: Ascorbate biosynthetic process
alternative label: Ascorbate formation
alternative label: Ascorbate synthesis
alternative label: Ascorbic acid anabolism
alternative label: Ascorbic acid biosynthesis
alternative label: Ascorbic acid biosynthetic process
alternative label: Ascorbic acid formation
alternative label: Ascorbic acid synthesis
alternative label: Vitamin C anabolism
alternative label: Vitamin C biosynthesis
alternative label: Vitamin C biosynthetic process
alternative label: Vitamin C formation
alternative label: Vitamin C synthesis
comment: Protein involved in the synthesis of ascorbate, the ionized form of ascorbic acid (vitamin C). Ascorbic acid is derived from glucose via the uronic acid pathway. This water-soluble vitamin is essential for the synthesis of bone, cartilage and dentine. It is required in the diet of primates and some other species that cannot synthesize L-ascorbic acid because of their deficiency in L-gulono-gamma-lactone oxidase, a key enzyme for the biosynthesis of this vitamin.
subclass of: Biological process
category: Biological process

L-ascorbic acid biosynthetic process
type: Class
database: go

Asparagine biosynthesis
type: Concept
alternative label: Asparagine anabolism
alternative label: Asparagine biosynthetic process
alternative label: Asparagine formation
alternative label: Asparagine synthesis
comment: Protein involved in the synthesis of the polar amino acid asparagine (Asn).
subclass of: Amino-acid biosynthesis
category: Biological process

asparagine biosynthetic process
type: Class
database: go

Aspartic protease inhibitor
type: Concept
alternative label: Aspartic proteinase inhibitor
alternative label: Aspartic-type endopeptidase inhibitor
alternative label: Aspartyl protease inhibitor
comment: Protein which inhibits the catalytic activity of an aspartyl protease, a class of proteases that contains an active site aspartate residue (Asp), e.g. pepsin, HIV retropepsin, renin, etc.
subclass of: Protease inhibitor
category: Molecular function

aspartic-type endopeptidase inhibitor activity
type: Class
database: go

Aspartyl esterase
type: Concept
comment: Enzyme which catalyzes the hydrolysis of esters and is characterized by a catalytically active aspartic acid residue in its active site.
subclass of: Hydrolase
category: Molecular function

aspartyl esterase activity
type: Class
database: go

Aspartyl protease
type: Concept
alternative label: Acid protease
alternative label: Aspartate protease
alternative label: Aspartic protease
alternative label: Aspartic proteinase
alternative label: Aspartic-type endopeptidase
alternative label: Aspartyl proteinase
comment: Proteolytic enzyme with an aspartate residue (Asp) in its active site. There are many families of aspartyl proteases. The most well known one is the pepsin family (A1 in MEROPS classification) which is known to exist in vertebrates, fungi, plants, retroviruses and some plant viruses.
subclass of: Protease
category: Molecular function

aspartic-type endopeptidase activity
type: Class
database: go

Asperger syndrome
type: Concept
comment: Protein which, if defective, is involved in Asperger syndrome, a complex, multifactorial disorder. It is characterized by clinically significant impairment of social interaction, and restricted repetitive and stereotyped patterns of behavior. Asperger syndrome is primarily distinguished from autism by the higher cognitive abilities and a more normal and timely development of language and communicative phrases.
subclass of: Autism spectrum disorder
category: Disease

Asthma
type: Concept
comment: Protein which, if defective, is associated with asthma, a bronchial disorder associated with airway inflammation, swelling and obstruction. It is marked by recurrent attacks of paroxysmal dyspnea, with wheezing due to spasmodic contraction of the bronchi.
subclass of: Disease
category: Disease

Atherosclerosis
type: Concept
alternative label: Arteriosclerosis
comment: Protein which, if defective, causes atherosclerosis, which is characterized by deposits of plaques (atheromas) in the blood vessels, thus narrowing the vessel lumen and restricting blood flow. Atheromas consist of lipids (cholesterol), carbohydrates, blood products, fibrous tissue and calcium deposits.
subclass of: Disease
category: Disease

ATP synthesis
type: Concept
alternative label: Adenosine 5'-triphosphate anabolism
alternative label: Adenosine 5'-triphosphate biosynthesis
alternative label: Adenosine 5'-triphosphate biosynthetic process
alternative label: Adenosine 5'-triphosphate formation
alternative label: Adenosine triphosphate anabolism
alternative label: Adenosine triphosphate biosynthesis
alternative label: Adenosine triphosphate biosynthetic process
alternative label: Adenosine triphosphate formation
alternative label: ATP anabolism
alternative label: ATP biosynthesis
alternative label: ATP biosynthetic process
alternative label: ATP formation
comment: Protein involved in the synthesis of adenosine 5'-triphosphate (ATP). ATP is a ribonucleotide adenosine (a purine base adenine linked to the sugar D-ribofuranose) which carries 3 phosphate groups esterified to the sugar moiety. It is the cell's source for energy and phosphate.
subclass of: Biological process
narrower: CF(1)
category: Biological process

ATP biosynthetic process
type: Class
database: go

ATP-binding
type: Concept
alternative label: Adenosine 5'-triphosphate binding
alternative label: Adenosine triphosphate binding
comment: Protein which binds adenosine 5'-triphosphate (ATP), a ribonucleotide adenosine (a purine base adenine linked to the sugar D-ribofuranose) that carries three phosphate groups esterified to the sugar moiety. It is the cell's source for energy and phosphate.
subclass of: Nucleotide-binding
narrower: Helicase
category: Ligand

ATP binding
type: Class
database: go

Atrial fibrillation
type: Concept
alternative label: AF
alternative label: ATFB
comment: Protein which, if defective, causes atrial fibrillation, a common cardiac arrhythmia marked by disorganized atrial electrical activity and rapid randomized contractions of small areas of the atrial myocardium, causing a totally irregular, and rapid, ventricular rate.
subclass of: Disease
category: Disease

Atrial septal defect
type: Concept
alternative label: Atrioseptal defect
comment: Protein which, if defective, causes atrial septal defect, a congenital cardiac anomaly characterized by persistent patency of the atrial septum that results in blood flow between the atria. It is due to failure of fusion between either the septum secundum or the septum primum and the endocardial cushions.
subclass of: Disease
category: Disease

Autism
type: Concept
alternative label: Autistic disorder
comment: Protein which, if defective, is involved in autism, a pervasive developmental disorder. It is a complex, multifactorial disease characterized by impairments in reciprocal social interaction and communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age. Most individuals with autism manifest moderate mental retardation.
subclass of: Autism spectrum disorder
category: Disease

Autism spectrum disorder
type: Concept
alternative label: ASD
comment: Protein which, if defective, is involved in autism spectrum disorder, a clinically heterogeneous group of disorders that share common features of impaired social relationships, impaired language and communication, repetitive behaviors, and a restricted range of interests. The spectrum includes diverse phenotypic manifestations, such as classic autism, Asperger syndrome, childhood disintegrative disorder, Rett syndrome, and pervasive developmental disorder not otherwise specified.
subclass of: Disease
narrower: Autism
narrower: Asperger syndrome
category: Disease

Autocatalytic cleavage
type: Concept
alternative label: Autocatalytic peptide cleavage
comment: Protein catalyzing its own cleavage.
subclass of: PTM
narrower: Protein splicing
category: PTM

Autoimmune encephalomyelitis
type: Concept
alternative label: Autoimmune encephalitis
comment: Protein which, if defective, causes autoimmune encephalomyelitis. This form of autoimmune inflammation of the brain and spinal cord causes demyelination.
subclass of: Disease
category: Disease

Autoimmune uveitis
type: Concept
comment: Protein which, if defective, causes autoimmune inflammation of the uvea, which is the vascular middle coat of the eye, comprising the iris, ciliary body and choroid.
subclass of: Vision
subclass of: Disease
category: Disease

Autoinducer synthesis
type: Concept
alternative label: Autoinducer anabolism
alternative label: Autoinducer biosynthesis
alternative label: Autoinducer biosynthetic process
alternative label: Autoinducer formation
comment: Protein involved in the synthesis of an autoinducer, a molecule which triggers the regulators of biosynthetic genes.
subclass of: Biological process
category: Biological process

Autophagy
type: Concept
comment: Protein participating in autophagy, a process of intracellular bulk degradation in which cytoplasmic components including organelles are sequestered within double-membrane vesicles that deliver the contents to the lysosome/vacuole for degradation. There are three primary forms of autophagy: chaperone-mediated autophagy, microautophagy and macroautophagy. During macroautophagy, the sequestering vesicles, termed autophagosomes, fuse with the lysosome or vacuole resulting in the delivery of an inner vesicle (autophagic body) into the lumen of the degradative compartment.
subclass of: Biological process
category: Biological process

autophagy
type: Class
database: go

Auxin biosynthesis
type: Concept
alternative label: Auxin anabolism
alternative label: Auxin biosynthetic process
alternative label: Auxin formation
alternative label: Auxin synthesis
comment: Protein involved in the synthesis of auxins. Auxins are plant hormones which play a role in many aspects of plant growth and development.
subclass of: Biological process
category: Biological process

auxin biosynthetic process
type: Class
database: go

Auxin signaling pathway
type: Concept
alternative label: Auxin mediated signaling pathway
comment: Protein involved in the auxin signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth and development (e.g. caulogenesis, rhizogenesis, tropisms, nodulation). The major form of this phytohormone is indole-3-acetic acid (IAA) that can be synthesized both from tryptophan (Trp) using Trp-dependent pathways and from an indolic Trp precursor via Trp-independent pathways. Plants can also obtain IAA by b-oxidation of indole-3-butyric acid (IBA), a second endogenous auxin, or by hydrolysing IAA conjugates, in which IAA is linked to amino acids, sugars or peptides.
subclass of: Biological process
category: Biological process

auxin-activated signaling pathway
type: Class
database: go

B-cell activation
type: Concept
comment: Protein involved in the activation and proliferation of B-cells. B-cells are activated by the binding of antigen to receptors on its cell surface which causes the cell to divide and proliferate. Some stimulated B-cells become plasma cells, which secrete antibodies. Others become long-lived memory B-cells which can be stimulated at a later time to differentiate into plasma cells.
subclass of: Biological process
category: Biological process

B cell activation
type: Class
database: go

Bacterial flagellum
type: Concept
alternative label: Bacterial flagella
alternative label: Bacterial flagellar apparatus
comment: Bacterial protein present in a flagellum, a long hair-like cell surface appendage. The flagellar apparatus consists of the flagellar filament made of polymerized flagellin, the hook-like structure near the cell surface and a system of rings embedded in the cell enveloppe (the basal body or flagellar motor). The basal body and the hook anchor the whip-like filament to the cell surface. The flagellum is a rotating structure with switches propels the cell through a liquid medium.
subclass of: Cellular component
category: Cellular component

bacterial-type flagellum
type: Class
database: go

Bacterial flagellum biogenesis
type: Concept
alternative label: Bacterial flagella biogenesis
alternative label: Bacterial flagellar apparatus biogenesis
comment: Protein which is involved in the formation, organization or maintenance of the bacterial flagellum, a long hair-like cell surface appendage. The flagellar apparatus consists of the flagellar filament made of polymerized flagellin, the hook-like structure near the cell surface and a system of rings embedded in the cell enveloppe (the basal body or flagellar motor). The basal body and the hook anchor the whip-like filament to the cell surface. The flagellum is a rotating structure whose switches propels the cell through a liquid medium.
subclass of: Biological process
category: Biological process

bacterial-type flagellum organization
type: Class
database: go

Bacterial flagellum protein export
type: Concept
alternative label: Bacterial flagella protein export
alternative label: Bacterial flagellar apparatus protein export
alternative label: Bacterial flagellar protein export
comment: Protein which is involved in the export of bacterial flagellar proteins. The bacterial flagellum export apparatus consists of six integral membrane proteins (FlhA, FlhB, FliO, FliP, FliQ and FliR) and three soluble proteins (FliH, FliI and FliJ), and is located at the base of the flagellum. This system is characterized by ATP hydrolysis and a lack of substrate signal peptide cleavage.
subclass of: Protein transport
category: Biological process

Bacterial host gene expression shutoff by virus
type: Concept
comment: Viral protein which prevents host gene expression by blocking host transcription or inducing the degradation of the bacterial chromosome. This gives viral transcripts a competitive edge to use the hijacked host translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response.
subclass of: Host gene expression shutoff by virus
narrower: Degradation of host chromosome by virus
narrower: Bacterial host transcription shutoff by virus
category: Biological process

Bacterial host transcription shutoff by virus
type: Concept
comment: Viral protein involved in inhibiting transcription of bacterial genes to ensure the shutoff of host proteins expression and give viral transcripts a competitive edge for access to the cellular translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response. Some bacterial viruses inhibit the host RNAP: bacteriophage SPO1 for example is known to shut off host RNA synthesis.
subclass of: Bacterial host gene expression shutoff by virus
category: Biological process

Bacterial microcompartment
type: Concept
comment: Protein located in or on a bacterial microcompartment (BMC), proteinaceous polyhedral shells that encapsulate enzymes. The selectively permeable organelles protect their contents from the cytoplasm and/or the cytoplasm from reactants in their interior. Examples of BMCs include carboxysomes, which enhance autotrophic CO(2) fixation by encapsulating RuBisCO and carbonic anhydrase, as well as BMCs involved in ethanolamine or propanediol degradation; both pathways make toxic intermediates. Artifical BMCs can be expressed and filled with cargo proteins for biotechnological uses. BMCs are found in many bacterial phyla; in most cases their cargo is unknown.
subclass of: Cellular component
narrower: Carboxysome
category: Cellular component

bacterial microcompartment
type: Class
database: go

Bacteriochlorophyll
type: Concept
comment: Protein interacting with bacteriochlorophyll, a photosynthetic pigment found in non-oxygenic photosynthetic bacteria. It is a magnesium-porphyrin complex esterified to a long hydrophobic terpenoid side chain (the alcohol phytol). It differs from chlorophyll of oxygenic organisms in the substituents around the tetrapyrrole nucleus of the molecule, and in the absorption spectra. Different bacteria have different species of bacteriochlorophyll.
subclass of: Chlorophyll
category: Ligand

bacteriochlorophyll binding
type: Class
database: go

Bacteriochlorophyll biosynthesis
type: Concept
alternative label: Bacteriochlorophyll anabolism
alternative label: Bacteriochlorophyll biosynthetic process
alternative label: Bacteriochlorophyll formation
alternative label: Bacteriochlorophyll synthesis
comment: Protein involved in the synthesis of bacteriochlorophylls. These photosynthetic pigments are magnesium-porphyrin complexes with a long hydrophobic terpenoid side chain (the alcohol phytol). Biosynthesis of bacteriochlorophyll is a light-independent reaction.
subclass of: Chlorophyll biosynthesis
category: Biological process

bacteriochlorophyll biosynthetic process
type: Class
database: go

Bacteriocin
type: Concept
comment: Peptidic antibiotic, often plasmid encoded, produced by specific strains of bacteria that is lethal against other strains of the same or related species. E.g. bacteriocin, colicin, lantibiotic.
subclass of: Antibiotic
narrower: Lantibiotic
category: Molecular function

killing of cells of another organism
type: Class
database: go

Bacteriocin biosynthesis
type: Concept
alternative label: Bacteriocin anabolism
alternative label: Bacteriocin biosynthetic process
alternative label: Bacteriocin formation
alternative label: Bacteriocin synthesis
comment: Protein involved in the synthesis of a bacteriocin.
subclass of: Antibiotic biosynthesis
category: Biological process

bacteriocin biosynthetic process
type: Class
database: go

Bacteriocin immunity
type: Concept
comment: Protein that confers to a bacteria immunity against a specific bacteriocin that it synthesizes.
subclass of: Biological process
category: Biological process

bacteriocin immunity
type: Class
database: go

Bacteriocin transport
type: Concept
comment: Protein involved in the export of a bacteriocin (bacterial antibiotic).
subclass of: Protein transport
category: Biological process

bacteriocin transport
type: Class
database: go

Bacteriolytic enzyme
type: Concept
comment: Enzyme, e.g. lysozyme or endopeptidase, essential for lysis of bacterial cell walls.
subclass of: Antimicrobial
category: Molecular function

Bait region
type: Concept
comment: Protein having a peptide stretch which contains specific cleavage sites for different proteinases, and which enables inhibition of all four classes of proteinases.
subclass of: Domain
category: Domain

negative regulation of peptidase activity
type: Class
database: go

peptidase inhibitor activity
type: Class
database: go

Bardet-Biedl syndrome
type: Concept
alternative label: BBS
comment: Protein which, if defective, causes Bardet-Biedl syndrome (BBS), a genetically heterogeneous, autosomal recessive disorder. It is characterized by pigmentary retinopathy, obesity, polydactyly, hypogenitalism, renal malformation and intellectual disability. Secondary features include diabetes mellitus, hypertension and congenital heart disease.
subclass of: Ciliopathy
category: Disease

Bartter syndrome
type: Concept
comment: Protein which, if defective, causes Bartter syndrome (BS). In general, Bartter syndrome refers to a group of autosomal recessive disorders characterized by often severe intravascular volume depletion due to renal salt-wasting associated with low blood pressure, hypokalemic alkalosis, hypercalciuria, and normal serum magnesium levels. Patients with Bartter syndrome are often critically ill from birth onwards, and their long-term clinical course may be complicated by nephrocalcinosis, leading to renal failure. Clinical disease results from defective renal reabsorption of sodium chloride in the thick ascending limb (TAL) of the Henle loop, where only 30% of filtered salt is normally reabsorbed.
subclass of: Disease
category: Disease

Basement membrane
type: Concept
comment: 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.
subclass of: Extracellular matrix
category: Cellular component

basement membrane
type: Class
database: go

Behavior
type: Concept
comment: Protein which affects the behavior, the action or reaction, of an organism to a stimulus or situation.
subclass of: Biological process
category: Biological process

behavior
type: Class
database: go

Bence-Jones protein
type: Concept
comment: Protein which is a dimer of immunoglobulin light chains synthesized in large amounts by patients who have myeloma or bone marrow tumor. Bence-Jones protein is sufficiently small to be excreted by the kidney into urine.
subclass of: Molecular function
category: Molecular function

Bernard Soulier syndrome
type: Concept
alternative label: BSS
comment: Protein which, if defective, causes Bernard Soulier syndrome (BSS), a familial coagulation disorder characterized by a prolonged bleeding time, unusually large platelets, and impaired prothrombin consumption. BSS is caused by a genetic deficiency in platelet membrane glycoprotein Ib alpha chain and platelet glycoprotein IX, where platelets aggregate normally but do not stick to collagen of the sub-endothelial membrane.
subclass of: Disease
category: Disease

Bile acid catabolism
type: Concept
alternative label: Bile acid breakdown
alternative label: Bile acid catabolic process
alternative label: Bile acid degradation
alternative label: Bile salt breakdown
alternative label: Bile salt catabolic process
alternative label: Bile salt catabolism
alternative label: Bile salt degradation
comment: Protein involved in degradation of bile acids. Bile acids, which exist mainly as bile salts, are a family of carboxylic acid derivatives of cholesterol which play an important role in the digestion and absorption of fat. They are made in the liver, stored in the gallblader, and secreted as needed into the intestines.
subclass of: Lipid degradation
subclass of: Steroid metabolism
category: Biological process

bile acid catabolic process
type: Class
database: go

Bile pigment
type: Concept
alternative label: Bilin chromophore
comment: Protein binding covalently at least one linear tetrapyrrole chromophore, e.g. bilirubin, biliverdin, bilifuscin, biliprasin, choleprasin, bilihumin, and bilicyanin. Bile pigments are produced by breaking down protoporphyrin IX derived from hemoglobin and other heme proteins.
subclass of: Chromophore
category: Ligand

Biological process
type: Concept
comment: Keywords assigned to proteins because they are involved in a particular biological process.
narrower: Acetoin biosynthesis
narrower: Acetoin catabolism
narrower: Acute phase
narrower: Alginate biosynthesis
narrower: Alkaloid metabolism
narrower: Alkylphosphonate uptake
narrower: Amino-acid biosynthesis
narrower: Angiogenesis
narrower: Antibiotic biosynthesis
narrower: Antibiotic resistance
narrower: Antiviral defense
narrower: Apoptosis
narrower: Arginine metabolism
narrower: Aromatic hydrocarbons catabolism
narrower: Arsenical resistance
narrower: Ascorbate biosynthesis
narrower: ATP synthesis
narrower: Autoinducer synthesis
narrower: Autophagy
narrower: Auxin biosynthesis
narrower: B-cell activation
narrower: Bacteriocin immunity
narrower: Behavior
narrower: Biological rhythms
narrower: Biomineralization
narrower: Biotin biosynthesis
narrower: Branched-chain amino acid catabolism
narrower: Cadmium resistance
narrower: Calvin cycle
narrower: cAMP biosynthesis
narrower: Carbohydrate metabolism
narrower: Carbon dioxide fixation
narrower: Carnitine biosynthesis
narrower: Carotenoid biosynthesis
narrower: Catecholamine biosynthesis
narrower: Catecholamine metabolism
narrower: Cell adhesion
narrower: Cell cycle
narrower: Cell shape
narrower: Cellulose biosynthesis
narrower: cGMP biosynthesis
narrower: Chemotaxis
narrower: Chlorophyll biosynthesis
narrower: Chromate resistance
narrower: Chromosome partition
narrower: Citrate utilization
narrower: Cobalamin biosynthesis
narrower: Coenzyme A biosynthesis
narrower: Coenzyme M biosynthesis
narrower: Collagen degradation
narrower: Competence
narrower: Conjugation
narrower: Cytadherence
narrower: Cytochrome c-type biogenesis
narrower: Cytokinin biosynthesis
narrower: Cytolysis
narrower: Cytosine metabolism
narrower: Deoxyribonucleotide synthesis
narrower: Detoxification
narrower: Diaminopimelate biosynthesis
narrower: Differentiation
narrower: Digestion
narrower: DNA condensation
narrower: DNA damage
narrower: DNA excision
narrower: DNA integration
narrower: DNA recombination
narrower: DNA replication
narrower: DNA synthesis
narrower: Endocytosis
narrower: Enterobactin biosynthesis
narrower: Erythrocyte maturation
narrower: Ethylene biosynthesis
narrower: Exocytosis
narrower: Exopolysaccharide synthesis
narrower: Fertilization
narrower: Flagellar rotation

Biological rhythms
type: Concept
alternative label: Rhythmic process
comment: Protein involved in the generation of rhythmic pattern of behaviors or activities, e.g. circadian rhythm which is a metabolic or behavioural rhythm within a cycle of 24 hours.
subclass of: Biological process
category: Biological process

rhythmic process
type: Class
database: go

Biomineralization
type: Concept
comment: Protein involved in the process by which mineral crystals are deposited in an organized fashion in the matrix (either cellular or extracellular) of living organisms. Such process give rise to inorganic-based structures such as bone, tooth, ivory, shells, cuticles, corals or bacterial magnetosomes.
subclass of: Biological process
category: Biological process

biomineral tissue development
type: Class
database: go

Biotin
type: Concept
alternative label: Biopeiderm
alternative label: Coenzyme R
alternative label: Vitamin B7
alternative label: Vitamin B8
alternative label: Vitamin H
comment: Protein which contains at least one biotin as prosthetic group or cofactor (e.g. some carboxylases and decarboxylases, and biotin carboxyl carrier protein) or which binds biotin, like avidin. Biotin is a water-soluble vitamin (member of the B complex vitamins) essential for fatty acid biosynthesis, catabolism, and it acts as a growth factor for many cells.
subclass of: Ligand
category: Ligand

Biotin biosynthesis
type: Concept
alternative label: Biopeiderm anabolism
alternative label: Biopeiderm biosynthesis
alternative label: Biopeiderm biosynthetic process
alternative label: Biopeiderm formation
alternative label: Biopeiderm synthesis
alternative label: Biotin anabolism
alternative label: Biotin biosynthetic process
alternative label: Biotin formation
alternative label: Biotin synthesis
alternative label: Coenzyme R anabolism
alternative label: Coenzyme R biosynthesis
alternative label: Coenzyme R biosynthetic process
alternative label: Coenzyme R formation
alternative label: Coenzyme R synthesis
alternative label: Vitamin B7 anabolism
alternative label: Vitamin B7 biosynthetic process
alternative label: Vitamin B7 formation
alternative label: Vitamin B7 synthesis
alternative label: Vitamin B8 anabolism
alternative label: Vitamin B8 biosynthetic process
alternative label: Vitamin B8 formation
alternative label: Vitamin B8 synthesis
alternative label: Vitamin H anabolism
alternative label: Vitamin H biosynthesis
alternative label: Vitamin H biosynthetic process
alternative label: Vitamin H formation
alternative label: Vitamin H synthesis
comment: Protein involved in the synthesis of biotin, a prosthetic group for some carboxylase and decarboxylase enzymes. This water-soluble vitamin is essential for fatty acid biosynthesis, catabolism, and it acts as a growth factor for many cells.
subclass of: Biological process
category: Biological process

biotin biosynthetic process
type: Class
database: go

Blood coagulation
type: Concept
comment: Protein involved in blood clotting, a complex enzymatic cascade, in which the activated form of one factor catalyzes the activation of the next factor. Both, the extrinsic clotting pathway, induced by a damaged surface, and the intrinsic pathway, induced by a trauma, converge in a final common pathway to form cross-linked fibrin clots.
subclass of: Hemostasis
narrower: Fibrinolysis
narrower: Hemophilia
narrower: Thrombophilia
narrower: von Willebrand disease
category: Biological process

blood coagulation
type: Class
database: go

Blood coagulation cascade activating toxin
type: Concept
comment: Toxin which activates the blood coagulation cascade, which leads to the production of fibrin clots. Blood coagulation activating toxins include a variety of snake venom proteases.
subclass of: Hemostasis impairing toxin
category: Molecular function

Blood coagulation cascade inhibiting toxin
type: Concept
comment: Toxin which inhibits the blood coagulation cascade, which leads to the production of fibrin clots. Blood coagulation inhibiting toxins include a variety of snake venom proteases.
subclass of: Hemostasis impairing toxin
category: Molecular function

Blood group antigen
type: Concept
alternative label: Agglutinogen
comment: Protein belonging to the set of cell surface antigens found chiefly, but not solely, on blood cells. More than fifteen different blood group systems are recognised in humans. In most cases the antigenic determinant resides in the carbohydrate chains of membrane glycoproteins or glycolipids.
subclass of: Molecular function
category: Molecular function

Bradykinin receptor impairing toxin
type: Concept
comment: Toxin which interferes with the function of the bradykinin receptor (BDKR). BDKRs are G-protein coupled receptors whose principal ligand is the 9-amino acid peptide bradykinin.
subclass of: G-protein coupled receptor impairing toxin
category: Molecular function

Bradyzoite
type: Concept
comment: Protein expressed in the bradyzoite stage, a latent, slowly growing and cyst-forming stage in the life cycle of coccidians (e.g. Toxoplasmy). Encysted bradyzoites promote chronic infection and widespread dissemination of the parasite.
subclass of: Developmental stage
category: Developmental stage

Branched-chain amino acid biosynthesis
type: Concept
alternative label: Branched-chain amino acid anabolism
alternative label: Branched-chain amino acid biosynthetic process
alternative label: Branched-chain amino acid formation
alternative label: Branched-chain amino acid synthesis
comment: Protein involved in the synthesis of the essential aliphatic branched-chain amino acids leucine (Leu), isoleucine (Ile) and valine (Val).
subclass of: Amino-acid biosynthesis
narrower: Isoleucine biosynthesis
narrower: Leucine biosynthesis
category: Biological process

branched-chain amino acid biosynthetic process
type: Class
database: go

Branched-chain amino acid catabolism
type: Concept
alternative label: Branched-chain amino acid breakdown
alternative label: Branched-chain amino acid catabolic process
alternative label: Branched-chain amino acid degradation
comment: Protein involved in the degradation of the branched-chain amino acids leucine (Leu), isoleucine (Ile) and valine (Val).
subclass of: Biological process
category: Biological process

branched-chain amino acid catabolic process
type: Class
database: go

Brassinosteroid biosynthesis
type: Concept
alternative label: Brassinosteroid anabolism
alternative label: Brassinosteroid biosynthetic process
alternative label: Brassinosteroid formation
alternative label: Brassinosteroid synthesis
comment: Protein involved in the synthesis of brassinosteroids, a class of steroid plant hormones. Brassinosteroids are involved in numerous plant processes, such as cell expansion and elongation (in association with auxin), vascular differentiation, pollen elongation and pollen tube formation and protection to plants during chilling and drought stress. Brassinolide is the first isolated brassinosteroid.
subclass of: Steroid biosynthesis
category: Biological process

brassinosteroid biosynthetic process
type: Class
database: go

Brassinosteroid signaling pathway
type: Concept
alternative label: BR signalling pathway
alternative label: BR-signalling pathway
comment: Protein involved in the brassinosteroid (BR) signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth and development including cell expansion and elongation (in association with auxin), vascular differentiation and pollen elongation and pollen tube formation. Also involved in plants protection during chilling and drought stress. BRs are polyhydroxysteroid phytohormones and over 70 BR compounds have been isolated in plants. Brassinolide was the first BR isolated from Brassica napus and remains one of the most active BR.
subclass of: Biological process
category: Biological process

brassinosteroid mediated signaling pathway
type: Class
database: go

Bromination
type: Concept
alternative label: Bromated
alternative label: Brominated
comment: Protein which is posttranslationally modified by the attachment of at least one bromine.
subclass of: PTM
category: PTM

Bromodomain
type: Concept
comment: Protein containing at least one bromodomain. The bromodomain is a conserved region, approximately 70 amino acids, characteristic for a class of regulatory proteins. It mediates interactions with proteins that are necessary for transcriptional activation.
subclass of: Domain
category: Domain

Brugada syndrome
type: Concept
alternative label: BRS
comment: Protein which, if defective, causes Brugada syndrome, a heart disease characterized by an electrocardiogram pattern showing ST segment elevation in right precordial leads (V1 to V3), incomplete or complete right bundle branch block, and ventricular tachyarrhythmia. In some cases, tachycardia does not terminate spontaneously and it may degenerate into ventricular fibrillation and lead to sudden death.
subclass of: Disease
category: Disease

c-di-GMP
type: Concept
alternative label: 3',5'-cyclic di-GMP
alternative label: 3'-5'-cyclic diguanylic acid
alternative label: Bis-(3'-5') cyclic diguanylic acid
alternative label: Bis-(3'-5')-cyclic dimeric guanosine monophosphate
alternative label: c-(Gpgp)
alternative label: cGpGp
alternative label: Cyclic-bis(3',5')diguanylic acid
alternative label: Cyclic diguanylate
alternative label: Cyclic diguanylic acid
alternative label: Cyclic dinucleotide di-GMP
alternative label: Guanosine 3',5'-cyclic monophosphate
comment: Protein whose function is c-di-GMP-dependent or which catalyzes its hydrolysis. c-di-GMP is the abbreviation for cyclic di-GMP, bis-(3'-5') cyclic diguanylic acid. It acts as a bacterial second messenger.
subclass of: Ligand
category: Ligand

Cadmium
type: Concept
alternative label: Cadmium ion
alternative label: Cd
comment: Protein which binds at least one cadmium atom, or protein whose function is cadmium-dependent. Cadmium is a heavy metal, chemical symbol Cd.
subclass of: Ligand
category: Ligand

Cadmium resistance
type: Concept
alternative label: Cadmium ion resistance
alternative label: Cd resistance
alternative label: Resistance to cadmium
alternative label: Resistance to cadmium ion
alternative label: Resistance to Cd
comment: Protein that confers, on bacteria and other microorganisms, the ability to withstand the transition metal cadmium (Cd).
subclass of: Biological process
category: Biological process

response to cadmium ion
type: Class
database: go

Calcium
type: Concept
alternative label: Ca
alternative label: Calcium ion
comment: Protein which binds at least one calcium atom, or protein whose function is calcium-dependent. Calcium is a metal, chemical symbol Ca. Calcium is essential for a variety of bodily functions, such as neurotransmission, muscle contraction and proper heart function.
subclass of: Ligand
narrower: Calcium channel
narrower: Calcium transport
narrower: Calcium/phospholipid-binding
category: Ligand

Calcium channel
type: Concept
alternative label: Ca channel
alternative label: Calcium ion channel
comment: Cell membrane glycoprotein forming a channel in a biological membrane selectively permeable to calcium ions. Calcium is essential for a variety of bodily functions, such as neurotransmission, muscle contraction and proper heart function.
subclass of: Calcium
subclass of: Calcium transport
subclass of: Ion channel
category: Molecular function

calcium channel activity
type: Class
database: go

calcium ion transmembrane transport
type: Class
database: go

Calcium channel impairing toxin
type: Concept
alternative label: Ca channel inhibitor
alternative label: Calcium ion channel inhibitor
comment: Protein which interferes with the function of calcium channels which are membrane proteins forming a channel in a biological membrane selectively permeable to calcium ions. They are found in various venoms from snakes, scorpions and spiders.
subclass of: Ion channel impairing toxin
narrower: Voltage-gated calcium channel impairing toxin
narrower: Ryanodine-sensitive calcium-release channel impairing toxin
category: Molecular function

calcium channel regulator activity
type: Class
database: go

Calcium transport
type: Concept
alternative label: Calcium ion transport
alternative label: Ca transport
comment: Protein involved in the transport of calcium ions. Calcium is essential for a variety of bodily functions, such as neurotransmission, muscle contraction and proper heart function.
subclass of: Calcium
subclass of: Ion transport
narrower: Calcium channel
category: Biological process

calcium ion transport
type: Class
database: go

Calcium-activated potassium channel impairing toxin
type: Concept
comment: Protein which interferes with the function of calcium-activated potassium channels (KCa) which are membrane proteins forming a channel in a biological membrane selectively permeable to potassium ions and gated by intracellular calcium. They are mostly found in snake and scorpion venoms.
subclass of: Potassium channel impairing toxin
category: Molecular function

Calcium/phospholipid-binding
type: Concept
alternative label: Calcium-dependent phospholipid binding
comment: Protein which contains at least one binding site for calcium and phospholipid. For example, proteins with annexin repeats, of which a pair may form one binding site for calcium and phospholipid, or some proteins with C2 domains.
subclass of: Calcium
category: Ligand

calcium-dependent phospholipid binding
type: Class
database: go

Calmodulin-binding
type: Concept
comment: Protein which binds at least one calmodulin, an ubiquitous small calcium-binding protein. Its binding to proteins may cause a conformational change which either activates or inactivates their function.
subclass of: Molecular function
category: Molecular function

calmodulin binding
type: Class
database: go

Calvin cycle
type: Concept
alternative label: Calvin-Benson cycle
alternative label: Reductive pentose phosphate cycle
comment: 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. The energy and reducing power for this reaction are provided by the ATP and NADPH produced during the light reactions of photosynthesis. The Calvin cycle is the only photosynthetic pathway in C3 plants. In C4 and CAM plants CO(2) is initially fixed into other organic acids that are subsequently decarboxylated to release CO(2) to the Calvin cycle. Non-photosynthetic organism (e.g. Rhizobium) also use the cycle to fix CO(2).
subclass of: Biological process
category: Biological process

reductive pentose-phosphate cycle
type: Class
database: go

cAMP
type: Concept
alternative label: 3',5'-cyclic AMP
alternative label: Adenosine-3',5'-cyclic-monophosphate
alternative label: Adenosine 3',5'-phosphate
alternative label: Cyclic adenylic acid
alternative label: Cyclic AMP
comment: Protein whose function is cAMP-dependent or which catalyzes its hydrolysis. cAMP is the abbreviation for cyclic AMP, adenosine 3',5'-cyclic monophosphate, the first second messenger hormone signaling system to be characterised. It is generated from ATP by the action of adenyl cyclase that is coupled to hormone receptors by G proteins. cAMP activates a specific protein kinase and is inactivated by phosphodiesterase action giving 5'AMP.
subclass of: Ligand
narrower: cAMP-binding
category: Ligand

cAMP biosynthesis
type: Concept
alternative label: 3',5'-cyclic AMP anabolism
alternative label: 3',5'-cyclic AMP biosynthesis
alternative label: 3',5'-cyclic AMP biosynthetic process
alternative label: 3',5'-cyclic AMP formation
alternative label: 3',5'-cyclic AMP synthesis
alternative label: Adenosine-3',5'-cyclic-monophosphate anabolism
alternative label: Adenosine-3',5'-cyclic-monophosphate biosynthesis
alternative label: Adenosine-3',5'-cyclic-monophosphate biosynthetic process
alternative label: Adenosine-3',5'-cyclic-monophosphate formation
alternative label: Adenosine-3',5'-cyclic-monophosphate synthesis
alternative label: Adenosine 3',5'-phosphate anabolism
alternative label: Adenosine 3',5'-phosphate biosynthesis
alternative label: Adenosine 3',5'-phosphate biosynthetic process
alternative label: Adenosine 3',5'-phosphate formation
alternative label: Adenosine 3',5'-phosphate synthesis
alternative label: cAMP anabolism
alternative label: cAMP biosynthetic process
alternative label: cAMP formation
alternative label: cAMP synthesis
alternative label: Cyclic adenylic acid anabolism
alternative label: Cyclic adenylic acid biosynthesis
alternative label: Cyclic adenylic acid biosynthetic process
alternative label: Cyclic adenylic acid formation
alternative label: Cyclic adenylic acid synthesis
alternative label: Cyclic AMP anabolism
alternative label: Cyclic AMP biosynthesis
alternative label: Cyclic AMP biosynthetic process
alternative label: Cyclic AMP formation
alternative label: Cyclic AMP synthesis
comment: Protein involved in the synthesis of cAMP. cAMP is the abbreviation for cyclic AMP, adenosine 3',5'-cyclic monophosphate.
subclass of: Biological process
category: Biological process

cAMP biosynthetic process
type: Class
database: go

cAMP-binding
type: Concept
alternative label: 3',5'-cyclic AMP-binding
alternative label: Adenosine-3',5'-cyclic-monophosphate-binding
alternative label: Adenosine 3',5'-phosphate-binding
alternative label: Cyclic adenylic acid-binding
alternative label: Cyclic AMP-binding
comment: Protein which binds at least one cAMP. cAMP is the abbreviation for cyclic AMP, adenosine 3',5'-cyclic monophosphate.
subclass of: cAMP
subclass of: Nucleotide-binding
category: Ligand

cAMP binding
type: Class
database: go

Cap snatching
type: Concept
comment: Protein involved in cap snatching, a process in which a cellular mRNA is cleaved few nucleotides after the 5'cap. The resulting 10- to 13-nucleotides long capped fragment serve as primer for the initiation of viral mRNA synthesis. Cap snatching is used by negative stranded RNA virus which do not encode a guanylyl transferase, like influenza or hantaviruses.
subclass of: Biological process
category: Biological process

cap snatching
type: Class
database: go

Capsid decoration protein
type: Concept
comment: Viral decoration protein attached to the capsid of some prokaryotic viruses. Decoration proteins are located on the outermost surface of the capsid and are involved in stabilizing the head structure.
subclass of: Capsid protein
category: Cellular component

viral capsid, decoration
type: Class
database: go

Capsid inner membrane protein
type: Concept
comment: Viral protein part of the inner membrane of the capsid, a lipid bilayer contained inside the virion capsid.
subclass of: Virion
category: Cellular component

viral inner membrane
type: Class
database: go

Capsid protein
type: Concept
alternative label: Coat protein
alternative label: Head protein
comment: Structural protein which is part of the complex forming the protective shell around the nucleic acids of the virus. In prokaryotic viruses, this closed shell is also referred to as the head.
subclass of: Virion
narrower: Helical capsid protein
narrower: T=1 icosahedral capsid protein
narrower: T=2 icosahedral capsid protein
narrower: T=3 icosahedral capsid protein
narrower: T=pseudo3 icosahedral capsid protein
narrower: T=4 icosahedral capsid protein
narrower: T=7 icosahedral capsid protein
narrower: T=13 icosahedral capsid protein
narrower: T=16 icosahedral capsid protein
narrower: T=25 icosahedral capsid protein
narrower: T=147 icosahedral capsid protein
narrower: T=169 icosahedral capsid protein
narrower: T=219 icosahedral capsid protein
narrower: Outer capsid protein
narrower: Inner capsid protein
narrower: Intermediate capsid protein
narrower: Capsid decoration protein
category: Cellular component

viral capsid
type: Class
database: go

Capsule
type: Concept
comment: Protein which is part of a capsule, the protective structure surrounding some bacteria or fungi. The bacterial capsule is a layer of material, usually polysaccharide, attached to the cell wall possibly via covalent attachments to either phospholipid or lipid-A molecules. It has several functions: promote bacterial adhesion to surfaces or interaction with other organisms; act as a permeability barrier, as a defense mechanism against phagocytosis and/or as a nutrient reserve. Among pathogens, capsule formation often correlates with pathogenicity. The fungal capsule is an extracellular layer which lies outside the cell wall and it is usually composed of polysaccharides. It protects the cell from different environmental dangers such as phagocytosis, dessication, etc.
subclass of: Secreted
category: Cellular component

capsule
type: Class
database: go

Capsule biogenesis/degradation
type: Concept
comment: Protein which is involved in the formation, organization, maintenance or degradation of the capsule. The capsule is a protective structure surrounding some bacteria or fungi. The bacterial capsule is a layer of material, usually polysaccharide, attached to the cell wall possibly via covalent attachments to either phospholipid or lipid-A molecules. The fungal capsule is an extracellular layer which lies outside the cell wall and it is usually composed of polysaccharides.
subclass of: Biological process
category: Biological process

Carbohydrate metabolism
type: Concept
alternative label: Carbohydrate metabolic process
alternative label: Sugar metabolic process
alternative label: Sugar metabolism
comment: Protein participating in biochemical reactions in which carbohydrates are involved. Carbohydrate is a general term for sugars and related compounds with the general formula Cn(H2O)n. The smallest are monosaccharides (e.g. glucose); polysaccharides (e.g. starch, cellulose, glycogen) can be large and vary in length.
subclass of: Biological process
narrower: Arabinose catabolism
narrower: Fucose metabolism
narrower: Galactose metabolism
narrower: Glucose metabolism
narrower: Glycogen metabolism
narrower: Polysaccharide degradation
narrower: Xylose metabolism
category: Biological process

carbohydrate metabolic process
type: Class
database: go

Carbon dioxide fixation
type: Concept
alternative label: Carbon utilization by fixation of carbon dioxide
alternative label: Carbon utilization by fixation of CO(2)
alternative label: Carbon utilization by fixation of CO2
alternative label: CO(2) fixation
alternative label: CO2 fixation
comment: Protein involved in the process of carbon dioxide fixation, e.g. incorporation of carbon dioxide into carbohydrates by photosynthetic organisms or formation of oxaloacetate from pyruvate.
subclass of: Biological process
category: Biological process

carbon fixation
type: Class
database: go

Carboxypeptidase
type: Concept
comment: Protein that hydrolyzes a C-terminal peptide bond in polypeptide chains.
subclass of: Protease
category: Molecular function

carboxypeptidase activity
type: Class
database: go

Carboxysome
type: Concept
comment: Protein located in or on the carboxysome, bacterial microcompartments in which ribulose bisphosphate carboxylase (RuBisCO)-mediated CO(2) fixation occurs. The cytoplasmic polyhedral inclusion bodies are surrounded by a thin protein coat. Found in cyanobacteria and some chemoautotrophs, they enhance autotrophic CO(2) fixation in air by increasing the CO(2) concentration around RuBisCO, thus reducing its reaction with O(2), a competing substrate. They contain carbonic anhydrase as part of the CO(2) concentration mechanism.
subclass of: Bacterial microcompartment
category: Cellular component

carboxysome
type: Class
database: go

Cardiomyopathy
type: Concept
comment: Protein which, if defective, causes cardiomyopathy, a chronic disorder which affects the heart muscle causing a reduced pumping function. It is a major cause of morbidity and mortality.
subclass of: Disease
category: Disease

Cardiotoxin
type: Concept
comment: Protein which has a poisonous or deleterious effect upon the heart or other parts of the cardiovascular system.
subclass of: Toxin
category: Molecular function

Carnitine biosynthesis
type: Concept
alternative label: 3-hydroxy-4-(trimethylammonio)butanoate anabolism
alternative label: 3-hydroxy-4-(trimethylammonio)butanoate biosynthesis
alternative label: 3-hydroxy-4-(trimethylammonio)butanoate biosynthetic process
alternative label: 3-hydroxy-4-(trimethylammonio)butanoate formation
alternative label: 3-hydroxy-4-(trimethylammonio)butanoate synthesis
alternative label: Carnitine anabolism
alternative label: Carnitine biosynthetic process
alternative label: Carnitine formation
alternative label: Carnitine synthesis
alternative label: Gamma-trimethyl-hydroxybutyrobetaine anabolism
alternative label: Gamma-trimethyl-hydroxybutyrobetaine biosynthesis
alternative label: Gamma-trimethyl-hydroxybutyrobetaine biosynthetic process
alternative label: Gamma-trimethyl-hydroxybutyrobetaine formation
alternative label: Gamma-trimethyl-hydroxybutyrobetaine synthesis
comment: Protein involved in the biosynthesis of carnitine (L-3-hydroxy-4, N,N,N-trimethylaminobutyrate), an essential metabolite with a number of indispensable roles in intermediary metabolism.
subclass of: Biological process
category: Biological process

carnitine biosynthetic process
type: Class
database: go

Carotenoid biosynthesis
type: Concept
alternative label: Carotenoid anabolism
alternative label: Carotenoid biosynthetic process
alternative label: Carotenoid formation
alternative label: Carotenoid synthesis
comment: Protein involved in the synthesis of carotenoids, a group of orange, yellow, red, purple or brown pigments in plants, bacteria and some fungi. Carotenoids, which comprise the carotenes and the xanthophylls, are long polyisoprenoid molecules having conjugated double bonds enabling light absorbtion.
subclass of: Biological process
category: Biological process

carotenoid biosynthetic process
type: Class
database: go

Cataract
type: Concept
comment: Protein which, if defective, causes cataract, a partial or complete ocular opacity that affects the crystalline lens or its capsule, leading to impaired vision or blindness. The many types of cataract are classified by their morphology (size, shape, location) or etiology (cause and time of occurrence). Cataracts may occur as an isolated anomaly, as part of generalized ocular developmental defects, or as a component of a multisystem disorder.
subclass of: Disease
category: Disease

Catecholamine biosynthesis
type: Concept
alternative label: Catecholamine anabolism
alternative label: Catecholamine biosynthetic process
alternative label: Catecholamine formation
alternative label: Catecholamine synthesis
comment: Protein involved in the synthesis of catecholamines, which are amine derivatives of catechol (2-hydroxyphenol). They are synthesized from the amino acid tyrosine (Tyr) in sympathetic-nerve terminals and in the adrenal gland. Catecholamines act as hormones or neuro-transmitters, e.g. adrenaline, noradrenaline and dopamine.
subclass of: Biological process
category: Biological process

catecholamine biosynthetic process
type: Class
database: go

Catecholamine metabolism
type: Concept
alternative label: Catecholamine metabolic process
comment: Protein participating the biochemical reactions in which catecholamines are involved. Catecholamines are amine derivatives of catechol (2-hydroxyphenol). They are synthesized from the amino acid tyrosine (Tyr) in sympathetic-nerve terminals and in the adrenal gland. Catecholamines act as hormones or neuro-transmitters, e.g. adrenaline, noradrenaline and dopamine.
subclass of: Biological process
category: Biological process

catecholamine metabolic process
type: Class
database: go

Caveolin-mediated endocytosis of virus by host
type: Concept
alternative label: Virion endocytosis by caveolin-coated vesicle
comment: Viral protein involved in virus internalization by the host cell via caveolae, which are specialized lipid rafts that form 50-70 nm flask-shaped invaginations of the cell membrane. Caveolins form the structural backbone of caveolae. Internalization via caveolae is not a constitutive process but only occurs upon cell stimulation.Endocytic caveolae deliver their viral content to early endosomes. Caveolae represent a low capacity but highly regulated pathway. This pathway is used by viruses including HPV-31, BK virus, NDV, RSV, Coxsackie B virus, SV40, murine polyomavirus, and Echovirus 1.
subclass of: Virus endocytosis by host
category: Biological process

caveolin-mediated endocytosis of virus by host cell
type: Class
database: go

CBS domain
type: Concept
comment: Protein containing at least one CBS domain, a conserved domain found in a wide range of proteins, which is named after cystathionine beta-synthase (CBS), an enzyme that contains 2 copies of this domain.
subclass of: Domain
category: Domain

Cell adhesion
type: Concept
comment: Protein involved in the adherence of cells to other cells or to a matrix. Cell adhesion is mediated by cell surface proteins.
subclass of: Biological process
category: Biological process

cell adhesion
type: Class
database: go

Cell adhesion impairing toxin
type: Concept
comment: Toxin which interferes with the adherence of cells to other cells or to a matrix. Cell adhesion impairing toxins are mostly found in venom of snakes.
subclass of: Toxin
category: Molecular function

Cell cycle
type: Concept
comment: Protein involved in the complex series of events by which the cell duplicates its contents and divides into two. The eukaryotic cell cycle can be divided in four phases termed G1 (first gap period), S (synthesis, phase during which the DNA is replicated), G2 (second gap period) and M (mitosis). The prokaryotic cell cycle typically involves a period of growth followed by DNA replication, partition of chromosomes, formation of septum and division into two similar or identical daughter cells.
subclass of: Biological process
narrower: Cell division
narrower: Growth arrest
category: Biological process

cell cycle
type: Class
database: go

Cell division
type: Concept
comment: Protein involved in the separation of one cell into two daughter cells. In eukaryotic cells, cell division includes the nuclear division (mitosis) and the subsequent cytoplasmic division (cytokinesis).
subclass of: Cell cycle
narrower: Mitosis
narrower: Septation
category: Biological process

cell division
type: Class
database: go

Cell inner membrane
type: Concept
alternative label: Inner membrane
comment: Protein found in or associated with the prokaryotic cell inner membrane, a selectively permeable membrane which separates the cytoplasm from the periplasm in prokaryotes with 2 membranes.
subclass of: Cell membrane
category: Cellular component

plasma membrane
type: Class
database: go

Cell junction
type: Concept
comment: Protein found in or associated with a cell junction, a cell-cell or cell-extracellular matrix contact within a tissue of a multicellular organism, especially abundant in epithelia. In vertebrates, there are three major types of cell junctions: anchoring junctions (e.g. adherens junctions), communicating junctions (e.g. gap junctions) and occluding junctions (e.g. tight junctions).
subclass of: Cellular component
narrower: Gap junction
narrower: Tight junction
category: Cellular component

anchoring junction
type: Class
database: go

Cell membrane
type: Concept
alternative label: Cytoplasmic membrane
alternative label: Plasmalemma
alternative label: Plasma membrane
comment: Protein found in or associated with the cytoplasmic membrane, a selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the cell inner membrane in prokaryotes with 2 membranes.
subclass of: Membrane
narrower: Cell inner membrane
category: Cellular component

Cell outer membrane
type: Concept
alternative label: Outer membrane
comment: Protein found in or associated with the prokaryotic cell outer membrane, a selectively permeable membrane which separates the prokaryotic periplasm from its surroundings. Traditionally only Gram-negative bacteria were thought of as having an outer membrane, but recent work has shown some Actinobacteria, including Mycobacterium tuberculosis, as well as at least 1 archaea (Ignicoccus hospitalis) have a cell outer membrane.
subclass of: Membrane
category: Cellular component

cell outer membrane
type: Class
database: go

Cell projection
type: Concept
alternative label: Cell protrusion
comment: Protein found in or associated with a cell protrusion such as pseudopodium, filopodium, lamellipodium, growth cone, flagellum, acrosome or axon, or bacterial comet tail. These membrane-cytoskeleton-coupled processes are involved in many biological functions, such as cell motility, cancer-cell invasion, endocytosis, phagocytosis, exocytosis, pathogen infection, neurite extension and cytokinesis.
subclass of: Cellular component
narrower: Cilium
category: Cellular component

cell projection
type: Class
database: go

Cell shape
type: Concept
comment: Protein involved in the formation and maintenance of the cell shape, the physical dimensions of a cell. In most plants, algae, bacteria and fungi the cell wall is responsible for the shape of the cells.
subclass of: Biological process
narrower: Peptidoglycan synthesis
category: Biological process

regulation of cell shape
type: Class
database: go

Cell wall
type: Concept
comment: Protein found in or associated with a complex and rigid layer surrounding the cell. Cell walls are found in bacteria, archaea, fungi, plants, and algae. The cell wall envelopes the inner or plasma membrane in all bacteria and is surrounded by the outer membrane in bacteria with 2 membranes (Gram-negative). Bacterial cell walls contain peptidoglycan whereas those of archaea do not. Some archaea may contain pseudopeptidoglycan, which is composed of N-acetyltalosaminuronic acid, instead of N-acetyl muramic acid in peptidoglycan. The plant cell wall is made of fibrils of cellulose embedded in a matrix of several other kinds of polymers such as pectin and lignin. Algal cell walls are usually composed of cellulose, glycoproteins, sporopollenin, calcium and various polysaccharides such as manosyl, xylanes, alginic acid. Diatom cell walls (or frustules) contain silica. The cell wall plays a role in cell shape, cell stability and development, and protection against environmental dangers.
subclass of: Secreted
narrower: S-layer
category: Cellular component

cell wall
type: Class
database: go

Cell wall biogenesis/degradation
type: Concept
comment: Protein which is involved in the formation, organization, maintenance or degradation of the cell wall. The cell wall is an extracellular layer outside the cell membrane which protects the cell against mechanical damage, osmotic strength and which determines the cell shape. It is prominent in most plants, algae, bacteria and fungi.
subclass of: Biological process
category: Biological process

cell wall organization
type: Class
database: go

Cellular component
type: Concept
comment: Keywords assigned to proteins because they are found in a specific cellular or extracellular component.
narrower: Amyloid
narrower: Antenna complex
narrower: Apoplast
narrower: Centromere
narrower: CF(0)
narrower: CF(1)
narrower: Chlorosome
narrower: Chromosome
narrower: Chylomicron
narrower: Nematocyst
narrower: Copulatory plug
narrower: Cuticle
narrower: DNA-directed RNA polymerase
narrower: Dynein
narrower: Endoplasmic reticulum
narrower: Exosome
narrower: Fimbrium
narrower: Gas vesicle
narrower: Glycosome
narrower: Glyoxysome
narrower: Golgi apparatus
narrower: HDL
narrower: Hydrogenosome
narrower: Intermediate filament
narrower: Keratin
narrower: LDL
narrower: Lysosome
narrower: Membrane
narrower: Membrane attack complex
narrower: MHC I
narrower: MHC II
narrower: Microtubule
narrower: Mitochondrion
narrower: Nucleus
narrower: Nucleomorph
narrower: Lipid droplet
narrower: Periplasm
narrower: Peroxisome
narrower: Photosystem I
narrower: Photosystem II
narrower: Primosome
narrower: Proteasome
narrower: Reaction center
narrower: Sarcoplasmic reticulum
narrower: Signal recognition particle
narrower: Signalosome
narrower: Spliceosome
narrower: Synapse
narrower: Thick filament
narrower: Thylakoid
narrower: Viral occlusion body
narrower: VLDL
narrower: Vacuole
narrower: Plastid
narrower: Virion
narrower: Cytoplasm
narrower: Secreted
narrower: Cell junction
narrower: Cell projection
narrower: Endosome
narrower: Cytoplasmic vesicle
narrower: Archaeal flagellum
narrower: Bacterial flagellum
narrower: Kinetochore
narrower: Mitosome
narrower: Host cell junction
narrower: Host cell projection
narrower: Host cytoplasm
narrower: Host cytoplasmic vesicle
narrower: Host endoplasmic reticulum
narrower: Host endosome
narrower: Host Golgi apparatus
narrower: Host lipid droplet
narrower: Host lysosome
narrower: Host mitochondrion
narrower: Host nucleus
narrower: Host periplasm

Cellulose biosynthesis
type: Concept
alternative label: Cellulose anabolism
alternative label: Cellulose biosynthetic process
alternative label: Cellulose formation
alternative label: Cellulose synthesis
comment: Protein involved in the synthesis of cellulose, a linear polymer of (1-4)-beta-linked D-glucose subunits. It is the most abundant cell-wall and structural polysaccharide in plants and it is also found in some lower invertebrates. Cellulose is the major component of wood and thus of paper. Cotton is the purest natural form of cellulose. As a raw material, it forms the basis for many derivatives used in chromatography, ion exchange materials, explosives manufacturing and pharmaceutical preparations.
subclass of: Biological process
category: Biological process

cellulose biosynthetic process
type: Class
database: go

Cellulose degradation
type: Concept
alternative label: Cellulose breakdown
alternative label: Cellulose catabolic process
alternative label: Cellulose catabolism
comment: Protein involved in the conversion of cellulose into D-glucose. Cellulose is the most abundant cell-wall and structural polysaccharide in plants and it is also found in some lower invertebrates. Cellulose is the major component of wood and thus of paper. Cotton is the purest natural form of cellulose. As a raw material, it forms the basis for many derivatives used in chromatography, ion exchange materials, explosives manufacturing and pharmaceutical preparations.
subclass of: Polysaccharide degradation
category: Biological process

cellulose catabolic process
type: Class
database: go

Centromere
type: Concept
alternative label: Chromosome pericentric region
comment: 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.
subclass of: Cellular component
category: Cellular component

chromosome, centromeric region
type: Class
database: go

CF(0)
type: Concept
alternative label: ATPase membrane proton channel
alternative label: Proton-transporting ATP synthase complex coupling factor F(0)
comment: Protein component of the F-type ATP synthase complex CF(0) or protein involved in its assembly. F-type ATPases consist of the two complex components CF(0), the membrane proton channel, and CF(1), the catalytic core.
subclass of: Hydrogen ion transport
subclass of: Cellular component
category: Cellular component

proton-transporting ATP synthase complex, coupling factor F(o)
type: Class
database: go

CF(1)
type: Concept
alternative label: ATPase catalytic core
alternative label: Proton-transporting ATP synthase complex catalytic core F(1)
comment: Protein component of the F-type ATP synthase complex CF(1) or protein involved in its assembly. F-type ATPases consist of the two complex components CF(0), the membrane proton channel, and CF(1), the catalytic core.
subclass of: ATP synthesis
subclass of: Cellular component
category: Cellular component

proton-transporting ATP synthase complex, catalytic core F(1)
type: Class
database: go

cGMP
type: Concept
alternative label: 3',5'-cyclic GMP
alternative label: Cyclic GMP
alternative label: Cyclic guanylic acid
alternative label: Guanosine 3',5'-cyclic monophosphate
alternative label: Guanosine 3',5'-phosphate
comment: Protein whose function is cGMP-dependent or which catalyzes its hydrolysis. cGMP is the abbreviation for cyclic GMP, guanosine 3',5'-cyclic monophosphate. It acts as a second messenger.
subclass of: Ligand
narrower: cGMP-binding
category: Ligand

cGMP biosynthesis
type: Concept
alternative label: 3',5'-cyclic GMP anabolism
alternative label: 3',5'-cyclic GMP biosynthesis
alternative label: 3',5'-cyclic GMP biosynthetic process
alternative label: 3',5'-cyclic GMP formation
alternative label: 3',5'-cyclic GMP synthesis
alternative label: cGMP anabolism
alternative label: cGMP biosynthetic process
alternative label: cGMP formation
alternative label: cGMP synthesis
alternative label: Cyclic GMP anabolism
alternative label: Cyclic GMP biosynthesis
alternative label: Cyclic GMP biosynthetic process
alternative label: Cyclic GMP formation
alternative label: Cyclic GMP synthesis
alternative label: Cyclic guanylic acid anabolism
alternative label: Cyclic guanylic acid biosynthesis
alternative label: Cyclic guanylic acid biosynthetic process
alternative label: Cyclic guanylic acid formation
alternative label: Cyclic guanylic acid synthesis
alternative label: Guanosine-3',5'-cyclic-monophosphate anabolism
alternative label: Guanosine-3',5'-cyclic-monophosphate biosynthesis
alternative label: Guanosine-3',5'-cyclic-monophosphate biosynthetic process
alternative label: Guanosine-3',5'-cyclic-monophosphate formation
alternative label: Guanosine-3',5'-cyclic-monophosphate synthesis
alternative label: Guanosine 3',5'-phosphate anabolism
alternative label: Guanosine 3',5'-phosphate biosynthesis
alternative label: Guanosine 3',5'-phosphate biosynthetic process
alternative label: Guanosine 3',5'-phosphate formation
alternative label: Guanosine 3',5'-phosphate synthesis
comment: Protein involved in the synthesis of cGMP. cGMP is the abbreviation for cyclic GMP, guanosine 3',5'-cyclic monophosphate.
subclass of: Biological process
category: Biological process

cGMP biosynthetic process
type: Class
database: go

cGMP-binding
type: Concept
alternative label: 3',5'-cyclic GMP-binding
alternative label: Cyclic GMP-binding
alternative label: Cyclic guanylic acid-binding
alternative label: Guanosine 3',5'-cyclic monophosphate-binding
alternative label: Guanosine 3',5'-phosphate-binding
comment: Protein which binds at least one cGMP. cGMP is the abbreviation for cyclic GMP, guanosine 3',5'-cyclic monophosphate.
subclass of: cGMP
subclass of: Nucleotide-binding
category: Ligand

cGMP binding
type: Class
database: go

Chaperone
type: Concept
comment: Protein which is transiently involved in the noncovalent folding, assembly and/or disassembly of other polypeptides or RNA molecules, including any transport and oligomerisation processes they may undergo, and the refolding and reassembly of protein and RNA molecules denatured by stress. Though involved in these processes, chaperones are not an integral part of these functioning molecules. Also used for metallochaperones, which function to provide a metal directly to target proteins while protecting this metal from scavengers.
subclass of: Molecular function
category: Molecular function

Charcot-Marie-Tooth disease
type: Concept
comment: Protein which, if defective, causes Charcot-Marie-Tooth disease (CMT), a heterogeneous group of hereditary motor and sensory neuropathies (HMSN) characterized by distal muscular atrophy and weakness, hollow feet, absent or diminished deep-tendon reflexes and impaired sensation. CMT is classified into two major classes. CMT type 1 includes demyelinating neuropathies that are characterized by nerve conductance velocities (NCVs) less than 38m/s and segmental demyelination and remyelination; CMT type 2 includes axonal neuropathies that are characterized by normal or mildly reduced NCVs and chronic axonal degeneration and regeneration.
subclass of: Neuropathy
category: Disease

Chemotaxis
type: Concept
comment: Protein involved in the movement of a cell, or organism, along a concentration gradient of a chemotactic agent, such as a protein which causes, mediates or responds to chemotaxis. Chemotactic molecules such as sugars, peptides, cell metabolites, cell-wall or membrane lipids bind to cell surface receptors and trigger activation of intracellular signaling pathways, as well as remodeling of the cytoskeleton through the activation or inhibition of various actin-binding proteins.
subclass of: Biological process
category: Biological process

chemotaxis
type: Class
database: go

Chitin degradation
type: Concept
alternative label: Chitin breakdown
alternative label: Chitin catabolic process
alternative label: Chitin catabolism
comment: Protein involved in the breakdown of chitin, a linear polysaccharide consisting of (1->4)-beta-linked D-glucosamine residues, most of which are N-acetylated.
subclass of: Polysaccharide degradation
category: Biological process

chitin catabolic process
type: Class
database: go

Chitin-binding
type: Concept
comment: Protein which binds chitin, a linear polysaccharide consisting of (1->4)-beta-linked D-glucosamine residues, most of which are N-acetylated. The 30-43 amino acids long chitin-binding domain contains several conserved glycine and cysteines residues. The conserved cysteines form disulfide bonds. Chitin-binding domains have been found in plant, fungal and bacterial proteins.
subclass of: Ligand
category: Ligand

chitin binding
type: Class
database: go

Chloride
type: Concept
alternative label: Chloride anion
alternative label: Chloride ion
alternative label: Cl-
comment: Protein which binds at least one chloride, or protein whose function is chloride-dependent. Chloride is a negatively-charged ion, which is abbreviated Cl(-).
subclass of: Ligand
narrower: Chloride channel
category: Ligand

Chloride channel
type: Concept
alternative label: Chloride anion channel
alternative label: Chloride ion channel
alternative label: Cl- channel
comment: Protein which is part of an anion channel found in the plasma membrane and in intracellular membranes. These channels are permeable for various anions, such as iodide, bromide, but also for nitrates, phosphates and even negatively charged amino acids. They are called chloride channels, because chloride is the most abundant anion and the predominant permeating species in all organisms. They have been classified according to their gating mechanisms, which may depend on changes in the transmembrane electric field (voltage-dependent/gated chloride channels, e.g. ClC family), on a protein kinase/nucleotide mediated mechanism (CFTR), an increase in intracellular calcium (calcium activated chloride channels, e.g. CaCC), cell swelling (volume-regulated anion channels, e.g. VRAC) or binding of a ligand, e.g. glycine or - aminobutyric acid (GABA) activated channels. In contrast with cation channels, they are not involved in the initiation or spread of excitation, but in the regulation of excitability in nerve and muscle. They also participate in many housekeeping processes, such as volume regulation, pH regulation in organelles, electrogenesis and control of synaptic activity. The chloride channels are crucial for transepithelial transport and the control of water flow, and often provide unexpected permeation pathways for a large variety of anions.
subclass of: Ion transport
subclass of: Ion channel
subclass of: Chloride
category: Molecular function

chloride channel activity
type: Class
database: go

chloride transport
type: Class
database: go

chloride channel complex
type: Class
database: go

Chloride channel impairing toxin
type: Concept
alternative label: Chloride anion channel inhibitor
alternative label: Chloride ion channel inhibitor
alternative label: Cl- channel inhibitor
comment: Protein which interferes with the function of chloride channels which are membrane proteins forming a channel in a biological membrane selectively permeable to chloride ions. Chloride channels include voltage-gated chloride channels (ClC), ionotropic GABA receptors (ligand-gated ion channels activated by GABA) and CFTR ion channels (ABC transporter-class ion channels). Toxins that target these channels are found in venom of several species including scorpions and snakes.
subclass of: Ion channel impairing toxin
narrower: Voltage-gated chloride channel impairing toxin
category: Molecular function

Chlorophyll
type: Concept
comment: Protein which interacts with chlorophyll, the major light-absorbing pigment in most oygenic green organisms. Higher plants contain chlorophyll a and chlorophyll b which are magnesium-porphyrin complexes esterified to a long hydrophobic terpenoid side chain (the alcohol phytol).
subclass of: Chromophore
narrower: Bacteriochlorophyll
category: Ligand

chlorophyll binding
type: Class
database: go

Chlorophyll biosynthesis
type: Concept
alternative label: Chlorophyll anabolism
alternative label: Chlorophyll biosynthetic process
alternative label: Chlorophyll formation
alternative label: Chlorophyll synthesis
comment: Protein involved in the synthesis of chlorophylls. These photosynthetic pigments are magnesium-porphyrin complexes with a long hydrophobic terpenoid side chain (the alcohol phytol). Angiosperms have only a light-dependent pathway for chlorophyll biosynthesis, other oxygenic organisms seem to have both the light-dependent and the light-independent pathways. Non-oxygenic organisms, which make bacteriochlorophyll, only have a light-independent pathway.
subclass of: Biological process
narrower: Bacteriochlorophyll biosynthesis
category: Biological process

chlorophyll biosynthetic process
type: Class
database: go

Chlorophyll catabolism
type: Concept
alternative label: Chlorophyll breakdown
alternative label: Chlorophyll catabolic process
alternative label: Chlorophyll degradation
comment: Protein involved in the degradation of chlorophylls. These photosynthetic pigments are magnesium-porphyrin complexes with a long hydrophobic terpenoid side chain (the alcohol phytol).
subclass of: Biological process
category: Biological process

chlorophyll catabolic process
type: Class
database: go

Chloroplast
type: Concept
comment: Protein encoded by or localized in the chloroplast, the most common form of plastid, found in all photosynthetic organisms except glaucophyte algae. In green (photosynthesizing) tissue they house the machinery necessary for photosynthesis and CO(2) fixation. They are surrounded by between 2 and 4 membranes and contain thylakoids in green tissue.
subclass of: Plastid
category: Cellular component

chloroplast
type: Class
database: go

Chlorosome
type: Concept
comment: Photosynthetic light-harvesting complexes found in green bacteria. Chlorosomes are sac-like organelles appressed to the cytoplasmic membrane of the cell membrane.
subclass of: Photosynthesis
subclass of: Cellular component
category: Cellular component

chlorosome
type: Class
database: go

Cholesterol biosynthesis
type: Concept
alternative label: Cholesterol anabolism
alternative label: Cholesterol biosynthetic process
alternative label: Cholesterol formation
alternative label: Cholesterol synthesis
comment: Protein involved in the synthesis of cholesterol, the major sterol of higher animals. It is a component of cell membranes, especially of the plasma membrane.
subclass of: Cholesterol metabolism
subclass of: Sterol biosynthesis
category: Biological process

cholesterol biosynthetic process
type: Class
database: go

Cholesterol metabolism
type: Concept
alternative label: Cholesterol metabolic process
comment: Protein which participates in the biochemical reactions where cholesterol is involved, including transport. Cholesterol is the major sterol of higher animals and an important component of cell membranes, especially of the plasma membrane.
subclass of: Sterol metabolism
narrower: Cholesterol biosynthesis
category: Biological process

cholesterol metabolic process
type: Class
database: go

Chondrogenesis
type: Concept
alternative label: Cartilage biogenesis
alternative label: Cartilage biosynthesis
alternative label: Cartilage development
alternative label: Cartilage formation
comment: Protein involved in chondrogenesis, the mechanism of cartilage formation. Chondrogenesis proceeds through determination of cells and their aggregation into prechondrogenic condensations, differentiation into chondrocytes, and later maturation. The formation of the long bones requires a cartilage template.
subclass of: Biological process
category: Biological process

cartilage development
type: Class
database: go

Chromate resistance
type: Concept
alternative label: Resistance to chromate
comment: Protein that enables bacteria and other microorganisms to withstand chromate, a salt of chromic acid (H2CrO4).
subclass of: Biological process
category: Biological process

response to chromate
type: Class
database: go

Chromatin regulator
type: Concept
comment: Protein controlling the opening or closing of chromatin.
subclass of: Molecular function
category: Molecular function

chromatin organization
type: Class
database: go

Chromophore
type: Concept
comment: Protein which interacts with one or more chromophores. A chromophore absorbs and transmits light energy. Originally it was used for visibly colored molecules, but it applies also to UV- and IR-absorbing molecules.
subclass of: Ligand
narrower: Bile pigment
narrower: Chlorophyll
narrower: Photoreceptor protein
narrower: Retinal protein
category: Ligand

Chromoplast
type: Concept
comment: Protein found in or associated with a chromoplast, a plastid containing pigments other than chlorophyll. Found in flower, petals and fruit.
subclass of: Plastid
category: Cellular component

chromoplast
type: Class
database: go

Chromosomal rearrangement
type: Concept
comment: Protein which can be altered by a structural chromosomal rearrangement. Structural rearrangements result from chromosome breakage, followed by reconstitution in an abnormal combination. Classes of chromosomal rearrangements include: deletions, duplications, insertions, inversions, translocations and transpositions.
subclass of: Coding sequence diversity
category: Coding sequence diversity

Chromosome
type: Concept
alternative label: Chromosomal protein
comment: Protein which is associated with chromosomal DNA, including histones, protamines and high mobility group proteins.
subclass of: Cellular component
narrower: Nucleosome core
narrower: Telomere
category: Cellular component

chromosome
type: Class
database: go

Chromosome partition
type: Concept
alternative label: Chromosome segregation
comment: Protein involved in chromosome partition, the process by which newly replicated plasmids and chromosomes are actively segregated prior to cell division. E.g., par and soj which contribute to efficient chromosome partitioning by serving functions analogous to centromeres (i.e. pairing or positioning of sister chromosomes).
subclass of: Biological process
category: Biological process

chromosome segregation
type: Class
database: go

Chronic granulomatous disease
type: Concept
alternative label: CGD
comment: Protein which, if defective, causes chronic granulomatous disease (CGD), a disease characterized by the failure of activated phagocytes to generate superoxide.
subclass of: Disease
category: Disease

Chylomicron
type: Concept
comment: 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.
subclass of: Cellular component
category: Cellular component

chylomicron
type: Class
database: go

Ciliopathy
type: Concept
comment: Protein which, if defective, causes any one of a group of diseases associated with either abnormal formation or function of cilia. Ciliopathies cover a large spectrum of often overlapping phenotypes ranging from relatively mild, tissue-restricted pathologies to severe defects in multiple organs. Although cilia play important roles in many tissues, the predominantly affected organs are kidney, eye, liver and brain. Clinical features typically include retinal degeneration, renal disease and cerebral anomalies. Additional manifestations include congenital fibrocystic diseases of the liver, diabetes, obesity and skeletal dysplasias. Ciliary dysfunction in the embryo may cause randomization of left-right body asymmetry or situs inversus, as well as severe malformations leading to embryonic lethality.
subclass of: Disease
narrower: Bardet-Biedl syndrome
narrower: Joubert syndrome
narrower: Senior-Loken syndrome
narrower: Meckel syndrome
narrower: Primary ciliary dyskinesia
category: Disease

Cilium
type: Concept
alternative label: Cilia
comment: Protein found in or associated with a cilium, a cell surface projection found at the surface of a large proportion of eukaryotic cells. The two basic types of cilia, motile (alternatively named flagella) and non-motile, collectively perform a wide variety of functions broadly encompassing cell/fluid movement and sensory perception. Their most prominent structural component is the axoneme which consists of nine doublet microtubules, with all motile cilia - except those at the embryonic node - containing an additional central pair of microtubules. The axonemal microtubules of all cilia nucleate and extend from a basal body, a centriolar structure most often composed of a radial array of nine triplet microtubules. In most cells, basal bodies associate with cell membranes and cilia are assembled as 'extracellular' membrane-enclosed compartments.
subclass of: Cell projection
narrower: Flagellum
category: Cellular component

cilium
type: Class
database: go

Cilium biogenesis/degradation
type: Concept
comment: Protein which is involved in the formation, organization, maintenance and degradation of the cilium, a cell surface projection found at the surface of a large proportion of eukaryotic. Their most prominent structural component is the axoneme which consists of nine doublet microtubules, with all motile cilia - except those at the embryonic node - containing an additional central pair of microtubules.
subclass of: Biological process
category: Biological process

cell projection organization
type: Class
database: go

Citrate utilization
type: Concept
comment: Protein which allows the utilization of the 6-carbon tricarboxylic acid citrate as a sole source of carbon and energy.
subclass of: Biological process
category: Biological process

citrate metabolic process
type: Class
database: go

Citrullination
type: Concept
alternative label: 2-amino-5-(carbamoylamino)pentanoic acid
alternative label: Citrulline
alternative label: N5-carbamoylornithine
comment: Protein which is posttranslationally modified by the deimination of one or more arginine residues.
subclass of: PTM
category: PTM

Clathrin- and caveolin-independent endocytosis of virus by host
type: Concept
alternative label: Non-clathrin/non caveolin-mediated endocytosis by host
comment: Viral protein involved in virus internalization into the host cell via endocytic pathways that involve neither clathrin nor caveolins. These pathways can be further defined by their dependency on various molecules such as cholesterol, DNM2/Dynamin-2, small GTPases or tyrosine kinase and possibly involve non-caveolar lipid rafts. Clathrin- and caveolin-independent pathways are used by viruses including poliovirus, human rhinovirus 14, lymphocytic choriomeningitis virus, murine norovirus-1 and SV40.
subclass of: Virus endocytosis by host
category: Biological process

receptor-mediated endocytosis of virus by host cell
type: Class
database: go

Clathrin-mediated endocytosis of virus by host
type: Concept
alternative label: Virion endocytosis by clathrin-coated vesicle
comment: Viral protein involved in virus internalization by the host cell via clathrin-mediated endocytosis. In response to an internalization signal, clathrin is assembled on the inside face of the cell membrane to form characteristic invaginations or clathrin coated pits that pinch off through the action of DNM1/Dynamin-1 or DNM2/Dynamin-2. The virus bound to its host cell receptor is internalized into clathrin-coated vesicles (CCV). Endocytic CCV deliver their viral content to early endosomes. The endosomal acidic pH and/or receptor binding usually induces structural modifications of the virus surface proteins that lead to penetration of the endosomal membrane via fusion or permeabilization mechanisms.
subclass of: Virus endocytosis by host
category: Biological process

clathrin-dependent endocytosis of virus by host cell
type: Class
database: go

Cleavage on pair of basic residues
type: Concept
comment: Protein which is posttranslationally modified by the cleavage on at least one pair of basic residues, in order to release one or more mature active peptides (such as hormones).
subclass of: PTM
category: PTM

Coated pit
type: Concept
comment: Protein which is a component of a coated pit. Coated pits are regions of the donor membrane where the assembly of the vesicle coat take place. The coat assembles from soluble protomers such as coat protein complex-I and coat protein complex-II. The components of the coat often define the intracellular sorting station, and contribute to both membrane deformation and local movement of the resulting transport intermediate following scission. During the first steps of the vesicle-mediated membrane transport, coated pits are internalized to form coated vesicles which transport proteins between distinct membrane-bound organelles.
subclass of: Membrane
category: Cellular component

clathrin-coated pit
type: Class
database: go

Cobalamin
type: Concept
alternative label: Vitamin B12
comment: Protein which contains at least one cobalamin as cofactor, e.g. methylmalonyl-CoA mutase, or which binds and/or transports cobalamin, such as intrinsic factor or transcobalamins. Cobalamin, which is synthesized by microorganisms, has equatorial sites occupied by a tetrapyrrol ring structure (corrin ring) with a cobalt(III) ion in the center, one axial site occupied by an intramolecularly-bound dimethylbenzimidazole and the other axial site occupied by a number of different ligands such as water (aquacobalamin), cyanide (cyanocobalamin=vitamin B12), glutathione (glutathionylcobalamin), 5'deoxyadenosine (adenosylcobalamin=coenzyme B12) or a methyl group (methylcobalamin). It is a prosthetic group of certain mammalian enzymes, where it is essential for the normal maturation and development of erythrocytes. A deficiency in the diet or more frequently the failure to absorb the vitamin give rise to pernicious anemia.
subclass of: Cobalt
category: Ligand

cobalamin binding
type: Class
database: go

Cobalamin biosynthesis
type: Concept
alternative label: Cobalamin anabolism
alternative label: Cobalamin biosynthetic process
alternative label: Cobalamin formation
alternative label: Cobalamin synthesis
alternative label: Vitamin B12 anabolism
alternative label: Vitamin B12 biosynthesis
alternative label: Vitamin B12 biosynthetic process
alternative label: Vitamin B12 formation
alternative label: Vitamin B12 synthesis
comment: Protein involved in the synthesis of cobalamin. Cobalamin, which is synthesized by microorganisms, has equatorial sites occupied by a modified porphyrin ring system, with two of the four pyrrol rings fused directly (without an intervening methine bridge). The modified porphyrin system binds a cobalt(III) ion in the center, and this is called a corrin ring system. One axial site is occupied usually by an intramolecularly-bound dimethylbenzimidazole nucleotide and the other axial site is occupied by a number of different ligands such as water (aquacobalamin), cyanide (cyanocobalamine=vitamin B12), glutathione (glutathionylcobalamine), 5'deoxyadenosine (adenosylcobalamine=coenzyme B12) or a methyl group (methylcobalamin). Vitamin B12, for instance, is a prosthetic group of certain mammalian enzymes, where it is essential for the normal maturation and development of erythrocytes. A deficiency in the diet or more frequently the failure to absorb the vitamin B12 give rise to pernicious anemia.
subclass of: Biological process
category: Biological process

cobalamin biosynthetic process
type: Class
database: go

Cobalt
type: Concept
alternative label: Co
alternative label: Cobalt cation
alternative label: Cobalt ion
alternative label: Co cation
alternative label: Co ion
comment: Protein which binds at least one cobalt atom, or protein whose function is cobalt-dependent. Cobalt is a metallic element, chemical symbol Co.
subclass of: Ligand
narrower: Cobalt transport
narrower: Cobalamin
category: Ligand

Cobalt transport
type: Concept
alternative label: Cobalt cation transport
alternative label: Cobalt ion transport
alternative label: Co cation transport
alternative label: Co ion transport
alternative label: Co transport
comment: Protein involved in the transport of the trace element cobalt, which is a component of vitamin B12.
subclass of: Cobalt
subclass of: Ion transport
category: Biological process

cobalt ion transport
type: Class
database: go

Cockayne syndrome
type: Concept
alternative label: Cockayne's syndrome
alternative label: CS
comment: Protein which, if defective, causes Cockayne's syndrome (CS), an autosomal recessive disease characterized by UV-sensitive skin (without pigmentation abnormalities), neurological dysfunction due to demyelination of neurons and calcification of basal ganglia (psychomotor retardation, deafness, optic atrophy, retinal pigmentation and hyperreflexes) and dysmorphic dwarfism (immature sexual development and microcephaly).
subclass of: Disease
category: Disease

Coding sequence diversity
type: Concept
comment: Keywords assigned to proteins because their sequences can differ, due to differences in the coding sequences such as polymorphisms, RNA-editing, alternative splicing.
narrower: Alternative initiation
narrower: Alternative splicing
narrower: Chromosomal rearrangement
narrower: Disease variant
narrower: Pyrrolysine
narrower: Ribosomal frameshifting
narrower: RNA editing
narrower: Selenocysteine
narrower: Triplet repeat expansion
narrower: Alternative promoter usage
narrower: RNA translational shunting
narrower: RNA termination-reinitiation
narrower: RNA suppression of termination
narrower: Ribosomal skipping
subclass of: Concept

Coenzyme A biosynthesis
type: Concept
alternative label: CoA anabolism
alternative label: CoA biosynthesis
alternative label: CoA biosynthetic process
alternative label: CoA formation
alternative label: CoASH anabolism
alternative label: CoASH biosynthesis
alternative label: CoASH biosynthetic process
alternative label: CoASH formation
alternative label: CoASH synthesis
alternative label: CoA synthesis
alternative label: Coenzyme A anabolism
alternative label: Coenzyme A biosynthetic process
alternative label: Coenzyme A formation
alternative label: Coenzyme A synthesis
comment: Protein involved in the biosynthetic pathway leading from pantothenate to coenzyme A (CoA). CoA has two halves in phosphodiester linkage: a 3',5'-ADP residue, and 4-phosphopantetheine. The phosphopantetheine moiety is itself composed of three structural entities: a branched chain dihydroxy acid in amide linkage to a beta-alanyl residue, which is in turn linked to a cysteamide containing the reactive thiol. Coenzyme A functions as a carrier of acetyl and acyl groups and is essential for numerous biosynthetic, energy-yielding, and degradative metabolic pathways. Acetyl-CoA is the common cellular currency for acetyl transfers.
subclass of: Biological process
category: Biological process

coenzyme A biosynthetic process
type: Class
database: go

Coenzyme M biosynthesis
type: Concept
alternative label: 2-mercaptoethanesulfonic acid anabolism
alternative label: 2-mercaptoethanesulfonic acid biosynthesis
alternative label: 2-mercaptoethanesulfonic acid biosynthetic process
alternative label: 2-mercaptoethanesulfonic acid formation
alternative label: 2-mercaptoethanesulfonic acid synthesis
alternative label: Coenzyme M anabolism
alternative label: Coenzyme M biosynthetic process
alternative label: Coenzyme M formation
alternative label: Coenzyme M synthesis
alternative label: CoM anabolism
alternative label: CoM biosynthesis
alternative label: CoM biosynthetic process
alternative label: CoM formation
alternative label: CoM synthesis
comment: Protein involved in the biosynthesis of coenzyme M. Coenzyme M (2-mercaptoethanesulfonic acid) is the smallest known organic cofactor. CoM serves as a methyl group carrier in key reactions within the pathway of methane formation from C1 precursors. In the alkene metabolism pathway, it is involved in aliphatic epoxyde carboxylation.
subclass of: Biological process
category: Biological process

coenzyme M biosynthetic process
type: Class
database: go

Coiled coil
type: Concept
alternative label: Heptad repeat pattern
comment: Protein which contains at least one coiled coil domain, a type of secondary structure composed of two or more alpha helices which entwine to form a cable structure. In proteins, the helical cables serve a mechanical role in forming stiff bundles of fibres.
subclass of: Domain
category: Domain

Collagen
type: Concept
comment: 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. It forms insoluble fibres of high tensile strength and which contains the unusual amino acids hyroxyproline and hydroxylysine. It is rich in glycine but lacks cysteine and tryptophan, and has an unusually regular amino-acid domain.
subclass of: Domain
category: Domain

collagen trimer
type: Class
database: go

Collagen degradation
type: Concept
alternative label: Collagen breakdown
alternative label: Collagen catabolic process
alternative label: Collagen catabolism
comment: Protein involved in the degradation of collagen, a family of fibrous proteins found in skin, bones, teeth, cartilage and other tissues of vertebrates.
subclass of: Biological process
category: Biological process

collagen catabolic process
type: Class
database: go

Competence
type: Concept
comment: Protein involved in competence, the state in which a cell or organism is able to take up DNA and become genetically transformed.
subclass of: Biological process
category: Biological process

establishment of competence for transformation
type: Class
database: go

Complement activation lectin pathway
type: Concept
alternative label: Lectin complement pathway
alternative label: Lectin pathway
comment: Protein involved in the complement activation lectin pathway which activates the proteins of the complement system. This pathway can be activated mainly by mannose-binding lectin (MBL) interacting with carbohydrate structures on microbial surfaces and by ficolins with different fine carbohydrate binding specificity.
subclass of: Innate immunity
category: Biological process

complement activation, lectin pathway
type: Class
database: go

Complement alternate pathway
type: Concept
alternative label: Alternate complement pathway
alternative label: Complement activation alternative pathway
alternative label: Properdin system
comment: Protein involved in the complement alternate pathway which activates the proteins of the complement system. This pathway can be activated by IgA immune complexes, but also by bacterial endotoxins, polysaccharides and cell walls, without participation of an antigen-antibody reaction.
subclass of: Innate immunity
category: Biological process

complement activation, alternative pathway
type: Class
database: go

Complement pathway
type: Concept
alternative label: Classical complement pathway
alternative label: Complement activation classical pathway
comment: 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. The pathway proceeds by a cascade reaction of successive binding and proteolytic cleavage of complement components. This pathway can be activated by either IgG or IgM binding to an antigen.
subclass of: Innate immunity
narrower: Membrane attack complex
category: Biological process

complement activation, classical pathway
type: Class
database: go

Complement system impairing toxin
type: Concept
comment: Toxin which interferes with the complement system. These toxins act by activating, inhibiting, or mimicking proteins of this system. They are mostly found in snake and spider venoms.
subclass of: Toxin
category: Molecular function

Cone-rod dystrophy
type: Concept
comment: Protein which, if defective, causes cone-rod dystrophy, a disease where dystrophy of cone-rod cells is characterized by the initial degeneration of cone photoreceptor cells, thus causing early loss of visual acuity and color vision, followed by the degeneration of rod photoreceptor cells and leading to progressive night blindness and peripheral visual field loss.
subclass of: Disease
category: Disease

Congenital adrenal hyperplasia
type: Concept
alternative label: CAH
comment: Protein which, if defective, causes congenital adrenal hyperplasia, a group of inherited disorders of cortisol biosynthesis. Defective cortisol biosynthesis results in compensatory hypersecretion of corticotropin with subsequent adrenal hyperplasia and excessive androgen production. Various clinical types are recognized: "salt wasting form" is the most severe type, "simple virilizing form" with normal aldosterone biosynthesis, "non-classic form" or late onset, and "cryptic form" or asymptomatic.
subclass of: Disease
category: Disease

Congenital disorder of glycosylation
type: Concept
comment: Protein which, if defective, causes a congenital disorder of glycosylation. In the endoplasmic reticulum (ER) of eukaryotes, N-linked glycans are first assembled on the lipid carrier dolichyl pyrophosphate. The GlcNAc(2)Man(9)Glc(3) oligosaccharide is transferred to selected asparagine residues of nascent polypeptides. Defects along the biosynthetic pathway of N-glycans are associated with severe multisystemic syndromes called congenital disorders of glycosylation (CDG). The characteristic biochemical feature of CDG is defective glycosylation of glycoproteins due to mutations in genes required for the biosynthesis of N-linked oligosaccharides. Defects of the assembly of dolichyl-linked oligosaccharides or their transfer on to nascent glycoproteins form type I forms of CDG, whereas CDG type II comprises all defects of the trimming and elongation of N-linked oligosaccharides.
subclass of: Disease
category: Disease

Congenital dyserythropoietic anemia
type: Concept
alternative label: CDA
comment: Protein which, if defective, causes congenital dyserythropoietic anemia, a heterogeneous group of disorders characterized by the occurrence of multinuclear erythroid precursors in the bone marrow, ineffective erythropoiesis, iron overload and anemia. Various forms are differentiated mainly by the morphological appearance of the erythroid precursors.
subclass of: Hereditary hemolytic anemia
category: Disease

Congenital erythrocytosis
type: Concept
alternative label: Congenital polycythemia
comment: Protein which, if defective, causes congenital absolute erythrocytosis, a disorder characterized by expansion of the erythrocyte compartment in the peripheral blood. Total red cell mass is increased in the absence of a reduction of plasma volume. Erythrocytoses are usually divided into primary and secondary forms. Primary erythrocytoses are due to defects in the erythroid progenitors and are characterized by low erythropoietin levels. Secondary erythrocytoses can be due to defects in hypoxia sensing, or to conditions that cause low tissue oxygen tension with consequent increase in erythropoietin secretion.
subclass of: Disease
category: Disease

Congenital generalized lipodystrophy
type: Concept
alternative label: Berardinelli-Seip syndrome
alternative label: Congenital generalized lipoatrophy
comment: Protein which, if defective, causes congenital generalized lipodystrophy, a disorder characterized by near complete absence of adipose tissue from birth. Affected patients manifest insulin resistance, early onset diabetes mellitus, hypertriglyceridemia, hepatic steatosis and acanthosis nigricans.
subclass of: Disease
category: Disease

Congenital hypothyroidism
type: Concept
comment: Protein which, if defective, causes congenital hypothyroidism, a condition due to thyroid hormones deficiency, presenting at birth. Congenital hypothyroidism occurs when the thyroid gland fails to develop or function properly. In most cases, the thyroid gland is absent, abnormally located, or severely reduced in size. In the remaining cases, a normal-sized or enlarged thyroid gland is present, but production of thyroid hormones is decreased or absent. If untreated, congenital hypothyroidism can lead to intellectual disability and growth failure.
subclass of: Disease
category: Disease

Congenital muscular dystrophy
type: Concept
comment: The congenital muscular dystrophies (CMD) are a heterogeneous group of disorders characterized by hypotonia, muscle weakness, dystrophic changes on skeletal muscle biopsy, and joint contractures that present at birth or during the first 6 months of life. Intellectual disability with or without structural brain changes is an additional feature of several CMD syndromes.
subclass of: Disease
category: Disease

Congenital myasthenic syndrome
type: Concept
alternative label: CMS
comment: Protein which, if defective, causes congenital myasthenic syndrome. Congenital myasthenic syndromes constitute a group of inherited diseases characterized by a congenital defect in neuromuscular transmission at the neuromuscular junction, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Congenital myasthenic syndromes are characterized by muscle weakness affecting the axial and limb muscles (with hypotonia in early-onset forms), the ocular muscles (leading to ptosis and ophthalmoplegia), and the facial and bulbar musculature (affecting sucking and swallowing, and leading to dysphonia). The symptoms fluctuate and worsen with physical effort.
subclass of: Disease
category: Disease

Congenital stationary night blindness
type: Concept
alternative label: CSNB
comment: Protein which, if defective, causes congenital stationary night blindness that is the failure or imperfection of vision at night or in dim light, with good vision only on bright days.
subclass of: Disease
category: Disease

Conidiation
type: Concept
alternative label: Conidia biosynthesis
alternative label: Conidia formation
alternative label: Conidium biosynthesis
alternative label: Conidium formation
comment: Protein involved in conidiation, the production of conidia which are asexual fungal spores.
subclass of: Sporulation
category: Biological process

conidium formation
type: Class
database: go

Conjugation
type: Concept
comment: Protein involved in the temporary fusion of two gametes or two cells leading to the transfer of genetic material. This process is seen in bacteria, ciliate protozoa and certain fungi.
subclass of: Biological process
narrower: Mobility protein
category: Biological process

Copper
type: Concept
alternative label: Copper cation
alternative label: Copper ion
alternative label: Cu
alternative label: Cu cation
alternative label: Cu ion
comment: Protein which binds at least one copper atom, or protein whose function is copper-dependent. Copper is a trace metallic element, chemical symbol Cu.
subclass of: Ligand
narrower: Copper transport
category: Ligand

Copper transport
type: Concept
alternative label: Copper cation transport
alternative label: Copper ion transport
alternative label: Cu transport
comment: Protein involved in the transport of ions of the trace element copper.
subclass of: Copper
subclass of: Ion transport
category: Biological process

copper ion transport
type: Class
database: go

Copulatory plug
type: Concept
comment: Protein involded in the formation of the copulatory plug, a plug composed of a number of proteins which are secreted by the seminal vesicle under the influence of testosterone. Found in rodents.
subclass of: Cellular component
category: Cellular component

mating plug formation
type: Class
database: go

Corneal dystrophy
type: Concept
comment: Protein which, if defective, causes corneal dystrophy. The term corneal dystrophy includes a heterogeneous group of bilateral, primary alterations of the cornea that are not associated with prior inflammation or secondary to systemic disease. Most corneal dystrophies present with variable shaped corneal opacities in a clear or cloudy cornea and they affect visual acuity to different degrees. Corneal dystrophies may be present at birth but more frequently develop during adolescence and progress slowly throughout life.
subclass of: Disease
category: Disease

Covalent protein-DNA linkage
type: Concept
alternative label: DNA-protein covalent cross-linking
comment: Protein covalently attached to a DNA molecule. For example some viruses contains proteins that are attached to the end of a viral replicating DNA and which are necessary for DNA replication.
subclass of: PTM
category: PTM

Covalent protein-RNA linkage
type: Concept
alternative label: RNA-protein covalent cross-linking
comment: Protein covalently attached to a RNA molecule. For example some viruses contains proteins that are attached to the end of a viral replicating RNA and which are necessary for RNA replication.
subclass of: PTM
category: PTM

RNA-protein covalent cross-linking
type: Class
database: go

Craniosynostosis
type: Concept
alternative label: Craniostosis
comment: Protein which, if defective, causes craniosynostosis, the premature closure of one or more cranial sutures which results in an abnormal head shape. Different types of craniosynostosis are known. All are characterized by skull deformities, with face and often limb involvement in the syndromic forms.
subclass of: Disease
category: Disease

CRISPR-cas system evasion by virus
type: Concept
comment: Viral protein that inhibits host defense CRISPR-cas system (Clustered Regularly Interspaced Short Palindromic Repeats). The CRISPR-cas system is composed of genomic sensors that allow prokaryotes to acquire DNA fragments from invading viruses and plasmids into the CRISPR locus. These stored fragments (called spacers) are transcribed and processed into small crRNA which are used to destroy matching DNA in future viral and plasmid invasion. Some prokaryotic viruses express specific genes that allow them to evade CRISPR-cas system.
subclass of: Host-virus interaction
category: Biological process

inhibition of host CRISPR-cas system by virus
type: Class
database: go

Crown gall tumor
type: Concept
comment: Protein involved in crown gall tumor formation, a plant tumor caused by the bacterium Agrobacterium tumefaciens.
subclass of: Disease
category: Disease

CTQ
type: Concept
alternative label: Cysteine tryptophylquinone
comment: Protein which contains at least one cysteine tryptophylquinone (CTQ) cross-link modification. CTQ is formed by oxidation of the indole ring of a tryptophan to form tryptophylquinone followed by covalent cross-linking with a cysteine residue. In the quinohemoprotein amine dehydrogenase, CTQ mediates during the catalytic cycle electron transfer from the substrate to either a copper protein, azurin, or cytochrome c-550.
subclass of: PTM
category: PTM

Cushing syndrome
type: Concept
alternative label: Cushing's syndrome
alternative label: Hyperadrenocorticism
alternative label: Hypercortisolism
comment: Protein which, if defective, causes Cushing syndrome, a condition caused by prolonged exposure to excess levels of cortisol from endogenous or exogenous sources. Endogenous Cushing syndrome is due to excess production of cortisol by the adrenal glands. It may be caused by pituary hypersecretion of adrenocorticotropic hormone (ACTH), ectopic ACTH secretion by non-pituary tumors, or may result from cortisol hypersecretion by adrenal gland tumors (ACTH-independent Cushing syndrome). Cushing syndrome is clinically characterized by upper body obesity, osteoporosis, hypertension, diabetes mellitus, hirsutism, amenorrhea, and excess body fluid.
subclass of: Disease
category: Disease

Cuticle
type: Concept
comment: Protein which is a component of the cuticle, the outer protective layer produced by epidermal cells that covers the body of many invertebrates.
subclass of: Cellular component
category: Cellular component

structural constituent of cuticle
type: Class
database: go

Cyanelle
type: Concept
alternative label: Cyanoplast
alternative label: Muroplast
comment: Protein encoded by the cyanelle genome or protein located in the cyanelle. Cyanelles are the plastids of glaucocystophyte algae. They are surrounded by a double membrane and, in between, a peptidoglycan wall. The cyanelle genome is of chloroplast size and contains genes for tRNAs, rRNAs and approx. 150 proteins, which is more than found in higher plant chloroplast genomes (this feature is also shared by other primitive plastids). Thylakoid membrane architecture is cyanobacteria-like. Historically, the term cyanelle is derived from a classification as endosymbiotic cyanobacteria, and thus is not fully correct.
subclass of: Plastid
category: Cellular component

cyanelle
type: Class
database: go

Cyclin
type: Concept
comment: Protein that belongs to the cyclin family or that contains a cyclin box-like domain. Cyclins are regulatory subunits of the cyclin-dependent protein kinases. They form kinase holoenzymes, with distinct biochemical characteristics and nonredundant biological functions, which mediate phosphorylation of cellular proteins, including key cell cycle regulatory molecules. In this way, the kinase holoenzymes promote the transit of cells through the division cycle. Cyclins accumulate during interphase of eukaryotic cell cycle and are destroyed at the end of mitosis.
subclass of: Molecular function
category: Molecular function

Cycloheximide resistance
type: Concept
alternative label: Resistance to cycloheximide
comment: Protein that confers, on an organism, the ability to withstand cycloheximide, an antibiotic produced by Streptomyces griseus, which inhibits eukaryotic elongation during protein synthesis. The resistance is often due to mutations that prevent antibiotic binding to the protein.
subclass of: Antibiotic resistance
category: Biological process

response to cycloheximide
type: Class
database: go

Cysteine biosynthesis
type: Concept
alternative label: Cysteine anabolism
alternative label: Cysteine biosynthetic process
alternative label: Cysteine formation
alternative label: Cysteine synthesis
comment: Protein involved in the synthesis of cysteine, the amino acid with the highly reactive sulfhydryl group (-SH). It is derived from the amino acids methionine and serine. Cysteine plays a special role in shaping some proteins by forming disulfide bonds. In enzymes the unique reactivity of this group is frequently exploited at the catalytic site.
subclass of: Amino-acid biosynthesis
category: Biological process

cysteine biosynthetic process
type: Class
database: go

Cystinuria
type: Concept
alternative label: CSNU
comment: Protein which, if defective, causes cystinuria (CSNU), an autosomal recessive condition of persistent excessive urinary excretion of cystine and three other dibasic amino acids: lysine, ornithine, and arginine. CSNU arises from impaired reabsorption of these amino acids through the epithelial cells of the renal tubule and gastrointestinal tract. It is characterized by cystine stones in the kidney, ureter and bladder. Three clinical types of cystinuria have been described: cystinuria type-I (CSNU1), type-II (CSNU2) and type-III (CSNU3).
subclass of: Disease
category: Disease

Cytadherence
type: Concept
comment: Protein involved in cytadherence, the attachment of mycoplasma to the epithelium.
subclass of: Biological process
category: Biological process

adhesion of symbiont to microvasculature
type: Class
database: go

Cytochrome c-type biogenesis
type: Concept
alternative label: Cytochrome c-type formation
alternative label: Cytochrome c-type synthesis
comment: Protein involved in the biogenesis of c-type cytochromes. Cytochromes c are electron-transfer proteins having one or several heme c groups, bound to the protein by one or, more commonly two, thioether bonds involving sulphydryl groups of cysteine residues.
subclass of: Biological process
category: Biological process

cytochrome complex assembly
type: Class
database: go

Cytokine
type: Concept
comment: Small secreted proteins from higher eukaryotes which affect the growth, division and functions of other cells, e.g. interleukins, lymphokines, TNF and interferons. Generally, growth factors are not classified as cytokines, though TGF is an exception. Chemokines are a subset of cytokines. They differ from classical hormones in that they are produced by a number of tissues or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.
subclass of: Molecular function
category: Molecular function

cytokine activity
type: Class
database: go

extracellular space
type: Class
database: go

Cytokinin biosynthesis
type: Concept
alternative label: Cytokinin anabolism
alternative label: Cytokinin biosynthetic process
alternative label: Cytokinin formation
alternative label: Cytokinin synthesis
comment: Protein involved in the synthesis of cytokinins, a class of plant hormones which promote cell division (e.g. kinetin, zeatin, benzyl adenine). They are also involved in cell growth, cell differentiation and in other physiological processes.
subclass of: Biological process
category: Biological process

cytokinin biosynthetic process
type: Class
database: go

Cytokinin signaling pathway
type: Concept
alternative label: Cytokinin mediated signaling
comment: Protein involved in the cytokinin signaling pathway (i.e. transport or signal transduction). Cytokinins (i.e. kinetin and zeatin) are defined more by their biological activity (e.g. inducing cell division in tissue culture) rather than by structure. These phytohormones are synthesized in the root apical meristem and transported through the plant in the xylem sap. Cytokinins are involved in several physiological processes such as promoting cell division and chloroplast maturation, regulating cell growth and differentiation, and monitoring nutrient uptake and senescence. Together with auxin, they also regulate the cell cycle and tissue morphogenesis.
subclass of: Biological process
category: Biological process

cytokinin-activated signaling pathway
type: Class
database: go

Cytolysis
type: Concept
alternative label: Cell lysis
comment: Protein involved in the rupture of cell membranes and loss of cytoplasm, e.g. exotoxin, cytolysin.
subclass of: Biological process
narrower: Hemolysis
narrower: Membrane attack complex
narrower: Host cell lysis by virus
category: Biological process

Cytoplasm
type: Concept
comment: Protein found in the cytoplasm, the content of a cell within the plasma membrane and, in eukaryotics cells, surrounding the nucleus. This three-dimensional, jelly-like lattice interconnects and supports the other solid structures. The cytosol (the soluble portion of the cytoplasm outside the organelles) is mostly composed of water and many low molecular weight compounds. In eukaryotes, the cytoplasm also contains a network of cytoplasmic filaments (cytoskeleton).
subclass of: Cellular component
narrower: Cytoskeleton
narrower: Inflammasome
category: Cellular component

cytoplasm
type: Class
database: go

Cytoplasmic inwards viral transport
type: Concept
comment: Viral protein that allows the active transport of viral components along cytoskeletal filaments toward the intracellular replication sites during virus entry. Viruses such as adenoviruses, adeno-associated virus, vaccinia virus, poliovirus, canine parvovirus, African swine fever virus, rabies virus, human herpes virus 1, foamy virus are thought to use active intracellular transport of viral components.
subclass of: Virus entry into host cell
narrower: Microtubular inwards viral transport
narrower: Actin-dependent inwards viral transport
category: Biological process

transport of viral material towards nucleus
type: Class
database: go

Cytoplasmic vesicle
type: Concept
comment: Protein found in or associated with cytoplasmic vesicles, which mediate vesicular transport among the organelles of secretory and endocytic systems. These transport vesicles are classified by the identity of the protein coat used in their formation and also by the cargo they contain, e.g. clathrin-, COPI-, and COPII-coated vesicles, synaptic vesicles, secretory vesicles, phagosomes, etc.
subclass of: Cellular component
category: Cellular component

cytoplasmic vesicle
type: Class
database: go

Cytosine metabolism
type: Concept
alternative label: Cytosine metabolic process
comment: Protein involved in the biochemical reactions with the pyrimidine base cytosine.
subclass of: Biological process
category: Biological process

cytosine metabolic process
type: Class
database: go

Cytoskeleton
type: Concept
comment: Protein which is a component or which is associated with the cytoskeleton, a dynamic three-dimensional filamentous structure in the cytoplasm. The cytoskeleton is both a muscle and a skeleton, and its roles include maintenance of cell shape, cell movement (in eukaryotes), cytokinesis, and the organization of the organelles within the cell. This includes the major components of cytoskeleton; microfilaments (actin-like proteins), microtubules (tubulin-like proteins) and intermediate filaments (mostly in eukaryotes) and prokaryotic MinD-ParA proteins. Originally not thought to exist in prokaryotes, but now known to have the same functions as in eukyaryotes.
subclass of: Cytoplasm
category: Cellular component

cytoskeleton
type: Class
database: go

D-amino acid
type: Concept
comment: Protein which contains at least one D-amino acid. All of the amino acids derived from natural proteins are of the L configuration. D-amino acids are found in nature, especially as components of certain peptide antibiotics and in walls of certain microorganisms.
subclass of: PTM
category: PTM

Deafness
type: Concept
comment: Protein which, if defective, causes a partial or total inability to hear. The two principal types of deafness are conductive deafness that results from changes in the middle ear, and nerve or sensorineural deafness that is caused by damages to the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information.
subclass of: Disease
narrower: Usher syndrome
narrower: Waardenburg syndrome
narrower: Non-syndromic deafness
category: Disease

Decarboxylase
type: Concept
comment: Enzyme that belongs to the lyase family and which catalyzes the spliting of CO(2) from the carboxylic group of amino acids, beta-keto acids and alpha-keto acids.
subclass of: Lyase
category: Molecular function

carboxy-lyase activity
type: Class
database: go

Decay of host mRNAs by virus
type: Concept
comment: Viral protein involved in the degradation of host mRNAs. Viruses have evolved ways of degrading host mRNAs to inhibit cellular translation. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. Decay of host mRNAs can be achieved by endonucleotic RNA cleavage or associated with PABPC1 nuclear relocalization.
subclass of: Host mRNA suppression by virus
category: Biological process

induction by virus of catabolism of host mRNA
type: Class
database: go

Defensin
type: Concept
comment: Families of microbicidal and cytotoxic peptides. Defensins have antibacterial, antifungal and antiviral properties. Defensins kills cells by forming voltage-regulated multimeric channels in the susceptible cell's membrane.
subclass of: Antimicrobial
category: Molecular function

Degradation of host capsule during virus entry
type: Concept
comment: Virion protein involved in breaking down host cell capsule to reach the host cell wall, and finally the host cytoplasmic membrane. Many prokaryotic viruses carry for example glycanase, polysaccharide lyase or deacetylase activities to specifically digest host capsule.
subclass of: Virion
subclass of: Degradation of host cell envelope components during virus entry
category: Biological process

disruption of host cell glycocalyx during viral entry
type: Class
database: go

Degradation of host cell envelope components during virus entry
type: Concept
comment: Virion protein involved in breaking down host cell surface components to reach the host cytoplasmic membrane. Many prokaryotic viruses for example carry enzymatic activities to degrade the host cell lipopolysaccharide layer, cell wall, or capsule.
subclass of: Virion
subclass of: Virus entry into host cell
narrower: Degradation of host peptidoglycans during virus entry
narrower: Degradation of host lipopolysaccharides during virus entry
narrower: Degradation of host capsule during virus entry
category: Biological process

disruption of host cell envelope during viral entry
type: Class
database: go

Degradation of host chromosome by virus
type: Concept
comment: Viral protein that rapidly degrades the host DNA at the onset of infection. The breakdown products can be reused to synthesize viral DNA or can be excreted from the host cell. Degrading host chromosome provides an advantage during the virus life cycle by reducing or eliminating competing host macromolecular synthesis. Bacteriophages such as T4 or T5 for example are known to induce degradation of the host chromosome and excretion of the host DNA degradation products.
subclass of: Bacterial host gene expression shutoff by virus
category: Biological process

degradation of host chromosome by virus
type: Class
database: go

Degradation of host lipopolysaccharides during virus entry
type: Concept
comment: Virion protein involved in breaking down host cell lipopolysaccharides (LPS) to reach the cytoplasmic membrane of prokaryotes with 2 membranes. Many prokaryotic viruses carry glycanase or deacetylase activities to digest host LPS.
subclass of: Degradation of host cell envelope components during virus entry
category: Biological process

disruption by virus of host envelope lipopolysaccharide during virus entry
type: Class
database: go

Degradation of host peptidoglycans during virus entry
type: Concept
comment: Virion exolysin involved in breaking down host cell peptidoglycans (e.g. murein, pseudomurein) to reach the host cytoplasmic membrane during virus entry. Exolysins are usually part of the tail or the base plate of prokaryotic viruses. Exolysins can display various enzymatic activities such as lysozyme, transglycosylase, muramidase or even protease activity. Murein hydrolases for example are widespread in bacteriophages infecting Gram-positive or Gram-negative bacteria.
subclass of: Virion
subclass of: Degradation of host cell envelope components during virus entry
category: Biological process

disruption by virus of host cell wall peptidoglycan during virus entry
type: Class
database: go

Dejerine-Sottas syndrome
type: Concept
alternative label: DSS
comment: Protein which, if defective, causes Dejerine-Sottas disease. DSS is a hereditary motor and sensory neuropathy (HMSN) of the Charcot-Marie-Tooth disease type 1 class. DSS is characterized by severe early onset, very slow nerve conduction velocities (less than 12m/sec) and raised cerebrospinal fluid protein concentrations (0.7 g/l). Clinical signs are delayed age of walking as well as areflexia.
subclass of: Neuropathy
category: Disease

Dental caries
type: Concept
comment: Protein involved in dental caries or important in the prevention of dental caries. Dental caries are localized destruction of the tooth surface, initiated by decalcification of the enamel and followed by enzymatic lysis of organic structures, the result of which is cavity formation. The cavity may penetrate the enamel and dentin, and reach the pulp. The disease may be caused by acids produced by bacteria which lead to decalcification, or by microorganisms that destroy the enamel protein, or by keratolytic microorganisms producing chelates that lead to decalcification.
subclass of: Disease
category: Disease

Deoxyribonucleotide synthesis
type: Concept
alternative label: Deoxyribonucleotide anabolism
alternative label: Deoxyribonucleotide biosynthesis
alternative label: Deoxyribonucleotide biosynthetic process
alternative label: Deoxyribonucleotide formation
comment: Protein involved in the synthesis of deoxyribonucleotides, the basic repeating units in DNA. Deoxyribonucleotides consist of a purine or a pyrimidine base bonded to deoxyribose, which in turn is bound to a phosphate group. They are synthesised by reduction of ribonucleoside diphosphates.
subclass of: Biological process
category: Biological process

deoxyribonucleotide biosynthetic process
type: Class
database: go

Dermonecrotic toxin
type: Concept
comment: Protein involved in the necrosis of the skin.
subclass of: Toxin
category: Molecular function

Desmin-related myopathy
type: Concept
comment: Protein which, if defective, causes desmin-related myopathy (DRM), a clinically and genetically heterogeneous group of muscular disorders defined morphologically by intrasarcoplasmic aggregates of desmin, usually accompanied by other protein aggregates. Both autosomal dominant and autosomal recessive inheritance have been reported. Approximately one-third of DRMs are thought to be caused by mutations in the desmin gene.
subclass of: Myofibrillar myopathy
category: Disease

Detoxification
type: Concept
comment: Protein involved in degrading toxic compounds. Detoxification generally takes place in the liver or kidney and inactivates toxins, either by degradation or by conjugation of residues to a hydrophilic moiety in order to promote excretion.
subclass of: Biological process
category: Biological process

response to toxic substance
type: Class
database: go

Developmental protein
type: Concept
comment: Protein involved in development, the process whereby a multicellular organism develops from its early immature forms, e.g., zygote, larva, embryo, into an adult.
subclass of: Molecular function
narrower: Gap protein
narrower: Gastrulation
narrower: Pair-rule protein
narrower: Segmentation polarity protein
category: Molecular function

multicellular organism development
type: Class
database: go

Developmental stage
type: Concept
comment: Keywords assigned to proteins because they are expressed specifically in a given developmental stage.
narrower: Early protein
narrower: Fruiting body
narrower: Heterocyst
narrower: Late protein
narrower: Merozoite
narrower: Sporozoite
narrower: Bradyzoite
narrower: Tachyzoite
narrower: Trophozoite
subclass of: Concept

Diabetes insipidus
type: Concept
comment: Protein which, if defective, causes diabetes insipidus, a rare form of diabetes in which the kidney tubules do not reabsorb enough water resulting in excessive urine excretion (polyuria). Two types of diabetes insipidus are recognized: central or neurohypophyseal diabetes insipidus which is due to defects in the neurohypophyseal system and results in a deficient quantity of anti-diuretic hormone being produced or released; nephrogenic diabetes insipidus, a vasopressin unresponsive condition of polyuria and hyposthenuria.
subclass of: Disease
category: Disease

Diabetes mellitus
type: Concept
comment: Protein which, if defective, causes diabetes mellitus, a disorder of impaired carbohydrate, protein, and fat metabolism due to insufficient secretion of insulin or to target tissue insulin resistance. Diabetes mellitus can be divided into two main types, type I or insulin-dependent diabetes mellitus (IDDM), and type II, or non insulin-dependent diabetes mellitus (NIDDM). Type I diabetes mellitus normally starts in childhood or adolescence and is caused by the body's own immune system which destroys the insulin-producing beta cells in the pancreas. Classical features are polydipsia, polyphagia and polyuria, due to hyperglycemia-induced osmotic diuresis. Type II diabetes mellitus normally starts in adulthood and is caused by a lack of sensitivity to the body's own insulin. It is usually characterized by a gradual onset with minimal or no symptoms of metabolic disturbance. Both forms of diabetes mellitus lead to secondary complications (notably cardiovascular, nephropathy, retinopathy, neuropathy). Two other major subcategories of diabetes mellitus are gestational diabetes and diabetes secondary to other medical conditions. In common usage, the term diabetes, when used alone, refers to diabetes mellitus and not diabetes insipidus.
subclass of: Disease
category: Disease

Diaminopimelate biosynthesis
type: Concept
alternative label: Diaminopimelate anabolism
alternative label: Diaminopimelate biosynthetic process
alternative label: Diaminopimelate formation
alternative label: Diaminopimelate synthesis
comment: Protein involved in the synthesis of diaminopimelate, the ionic form of the amino acid diaminopimelic acid (DAP) which is found in the murein peptidoglycans of bacterial cell walls. Diaminopimelic acid is synthesised from aspartate.
subclass of: Biological process
category: Biological process

diaminopimelate biosynthetic process
type: Class
database: go

Diamond-Blackfan anemia
type: Concept
alternative label: Aase-Smith syndrome II
alternative label: Aase syndrome
alternative label: BDS
alternative label: Blackfan-Diamond disease
alternative label: Blackfan-Diamond syndrome
alternative label: Chronic congenital aregenerative anemia
alternative label: Congenital erythroid hypoplastic anemia
alternative label: Congenital hypoplastic anemia of Blackfan and Diamond
alternative label: DBA
alternative label: Erythrogenesis imperfecta
alternative label: Pure red cell aplasia
comment: Protein which, if defective, causes Diamond-Blackfan anemia, a rare congenital non-regenerative hypoplastic anemia that usually presents early in infancy. The disease is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of developing leukemia. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies.
subclass of: Disease
category: Disease

Differentiation
type: Concept
alternative label: Cell differentiation
comment: Protein involved in differentiation, the developmental process of a multicellular organism by which cells become specialized for particular functions. Differentiation requires selective expression of the genome; the fully differentiated state may be preceded by a stage in which the cell is already programmed for differentiation but is not yet expressing the characteristic phenotype determination. Also used for fungal conidiation proteins, and for some bacteria that present specialization of function in cell types, such as Caulobacter crescentus.
subclass of: Biological process
narrower: Gonadal differentiation
narrower: Sexual differentiation
narrower: Spermatogenesis
narrower: Oogenesis
category: Biological process

cell differentiation
type: Class
database: go

Digestion
type: Concept
comment: 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.
subclass of: Biological process
category: Biological process

digestion
type: Class
database: go

Dioxygenase
type: Concept
comment: Enzyme that reduces molecular oxygen by incorporating both atoms into its substrate(s).
subclass of: Oxidoreductase
category: Molecular function

dioxygenase activity
type: Class
database: go

Dipeptidase
type: Concept
comment: Enzyme that hydrolyzes a dipeptide into its constituent amino acids.
subclass of: Protease
category: Molecular function

dipeptidase activity
type: Class
database: go

Direct protein sequencing
type: Concept
comment: Protein, whose amino acid sequence has been partially (more than one residue) or completely determined experimentally by Edman degradation or by mass spectrometry.
subclass of: Technical term
category: Technical term

Disease
type: Concept
comment: Keywords assigned to proteins because they are involved in a specific disease.
narrower: AIDS
narrower: Albinism
narrower: Allergen
narrower: Alport syndrome
narrower: Alzheimer disease
narrower: Ectodermal dysplasia
narrower: Tumor suppressor
narrower: Atherosclerosis
narrower: Autoimmune encephalomyelitis
narrower: Autoimmune uveitis
narrower: Bernard Soulier syndrome
narrower: Cardiomyopathy
narrower: Chronic granulomatous disease
narrower: Cockayne syndrome
narrower: Cone-rod dystrophy
narrower: Crown gall tumor
narrower: Cystinuria
narrower: Deafness
narrower: Dental caries
narrower: Diabetes insipidus
narrower: Diabetes mellitus
narrower: Disease variant
narrower: Down syndrome
narrower: Dwarfism
narrower: Ehlers-Danlos syndrome
narrower: Epidermolysis bullosa
narrower: Gaucher disease
narrower: Glutaricaciduria
narrower: Glycogen storage disease
narrower: Gangliosidosis
narrower: Gout
narrower: Hemophilia
narrower: Hereditary hemolytic anemia
narrower: Hereditary multiple exostoses
narrower: Hereditary nonpolyposis colorectal cancer
narrower: Hirschsprung disease
narrower: Holoprosencephaly
narrower: Hyperlipidemia
narrower: Li-Fraumeni syndrome
narrower: Lissencephaly
narrower: Long QT syndrome
narrower: Malaria
narrower: Maple syrup urine disease
narrower: Mucopolysaccharidosis
narrower: Neurodegeneration
narrower: Obesity
narrower: Oncogene
narrower: Phenylketonuria
narrower: Neuropathy
narrower: Proto-oncogene
narrower: Pseudohermaphroditism
narrower: Retinitis pigmentosa
narrower: Rhizomelic chondrodysplasia punctata
narrower: SCID
narrower: Stargardt disease
narrower: Stickler syndrome
narrower: Systemic lupus erythematosus
narrower: Thrombophilia
narrower: Trypanosomiasis
narrower: von Willebrand disease
narrower: Whooping cough
narrower: Williams-Beuren syndrome
narrower: Xeroderma pigmentosum
narrower: Epilepsy
narrower: Cataract
narrower: Congenital disorder of glycosylation
narrower: Leber congenital amaurosis
narrower: Primary microcephaly
narrower: Parkinson disease
narrower: Parkinsonism
narrower: Bartter syndrome
narrower: Congenital muscular dystrophy
narrower: Age-related macular degeneration
narrower: Fanconi anemia
narrower: Short QT syndrome
narrower: Mucolipidosis
narrower: Limb-girdle muscular dystrophy

Disease variant
type: Concept
comment: Protein for which at least one genetic variant involved in a disease is reported in the feature table of the UniProtKB/Swiss-Prot entry.
subclass of: Disease
subclass of: Coding sequence diversity
category: Disease

Disulfide bond
type: Concept
comment: Protein which is modified by the formation of a bond between the thiol groups of two peptidyl-cysteine residues. The process of chemical oxidation that forms interchain disulfide bonds can produce stable, covalently linked protein dimers, multimers or complexes, whereas intrachain disulfide bonds can contribute to protein folding and stability. Depending on the protein environment, some disulfide bonds are more labile, forming transient redox-active disulfide bonds that are alternately reduced and oxidized in the course of an enzymatic reaction.
subclass of: PTM
category: PTM

DNA condensation
type: Concept
comment: 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 30 nm chromatin fibre. DNA condensation takes place as cells enter mitosis or when germ cells enter meiosis.
subclass of: Biological process
category: Biological process

chromosome condensation
type: Class
database: go

DNA damage
type: Concept
alternative label: DNA damage response
alternative label: Response to DNA damage stimulus
comment: Protein induced by DNA damage or protein involved in the response to DNA damage. Drug- or radiation-induced injuries in DNA introduce deviations from its normal double-helical conformation. These changes include structural distortions which interfere with replication and transcription, as well as point mutations which disrupt base pairs and exert damaging effects on future generations through changes in DNA sequence. Response to DNA damage results in either repair or tolerance.
subclass of: Biological process
narrower: DNA repair
narrower: SOS response
category: Biological process

cellular response to DNA damage stimulus
type: Class
database: go

DNA end degradation evasion by virus
type: Concept
comment: Viral protein that inhibits or counteracts prokaryotic host helicase/nuclease proteins in order to escape the antiviral activity of the latter. When functioning in their exonuclease mode, helicase/nuclease proteins such as bacterial RecBCD or AddAB degrade any free DNA end as well as the linear dsDNA products resulting from restriction Type II cleavage. Any prokaryotic virus that exposes free dsDNA ends as part of its life cycle must find the means to evade destruction by these host enzymes. Prokaryotic viruses escape this host defense by expressing inhibitors or by protecting the ends of their linear genomes from digestion.
subclass of: Host-virus interaction
category: Biological process

evasion by virus of DNA end degradation
type: Class
database: go

DNA excision
type: Concept
comment: Protein involved in the repair of damages to one strand of DNA (loss of purines due to thermal fluctuations, formation of pyrimidine dimers by UV irradiation, for instance). The site of damage is recognized, excised by an endonuclease, the correct sequence is copied from the complementary strand by a polymerase and the ends of this correct sequence are joined to the rest of the strand by a ligase. In bacterial systems, the polymerase also acts as endonuclease. Excisase A and other proteins involved in recombination mediate DNA excision; a process whereby abnormal or mismatched nucleotides are enzymatically cut out of a strand of a DNA molecule.
subclass of: Biological process
category: Biological process

DNA repair
type: Class
database: go

DNA integration
type: Concept
comment: Protein involved in DNA integration, a process that mediates the insertion of foreign genetic material, or other duplex DNA, into a chromosome, or another replicon, in order to form a covalently linked DNA continuous with the host DNA.
subclass of: Biological process
narrower: Viral genome integration
category: Biological process

DNA integration
type: Class
database: go

DNA invertase
type: Concept
comment: Specific recombinases which catalyze the inversion of a DNA segment within a nucleoprotein structure termed invertasome.
subclass of: DNA recombination
subclass of: DNA-binding
subclass of: Molecular function
category: Molecular function

DNA strand exchange activity
type: Class
database: go

DNA binding
type: Class
database: go

DNA recombination
type: Class
database: go

DNA recombination
type: Concept
comment: Protein involved in DNA recombination, i.e. any process in which DNA molecules are cleaved and the fragments are rejoined to give a new combination.
subclass of: Biological process
narrower: DNA invertase
category: Biological process

DNA repair
type: Concept
comment: Protein involved in the repair of DNA, the various biochemical processes by which damaged DNA can be restored. DNA repair embraces, for instance, not only the direct reversal of some types of damage (such as the enzymatic photoreactivation of thymine dimers), but also multiple distinct mechanisms for excising damaged base; termed nucleotide excision repair (NER), base excision repair (BER) and mismatch repair (MMR); or mechanisms for repairing double-strand breaks.
subclass of: DNA damage
narrower: Excision nuclease
category: Biological process

DNA replication
type: Concept
comment: Protein involved in DNA replication, i.e. the duplication of DNA by making a new copy of an existing molecule. The parental double-stranded DNA molecule is replicated semi conservatively, i.e. each copy contains one of the original strands paired with a newly synthesized strand that is complementary in terms of AT and GC base pairing.
subclass of: Biological process
narrower: Viral DNA replication
category: Biological process

DNA replication
type: Class
database: go

DNA replication inhibitor
type: Concept
alternative label: Negative regulation of DNA replication
comment: Protein involved in the inhibition of DNA replication.
subclass of: Molecular function
category: Molecular function

negative regulation of DNA replication
type: Class
database: go

DNA synthesis
type: Concept
alternative label: DNA biosynthesis
alternative label: DNA biosynthetic process
comment: Protein involved in the synthesis of DNA from deoxyribonucleic acid monomers.
subclass of: Biological process
category: Biological process

DNA biosynthetic process
type: Class
database: go

DNA-binding
type: Concept
comment: 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. Many DNA-binding domains are described in PROSITE.
subclass of: Molecular function
narrower: DNA invertase
narrower: Nucleosome core
category: Molecular function

DNA-directed DNA polymerase
type: Concept
comment: Enzyme that catalyzes DNA synthesis by addition of deoxyribonucleotide units to a DNA chain using DNA as a template. They can also possess exonuclease activity and therefore function in DNA repair.
subclass of: Nucleotidyltransferase
category: Molecular function

DNA-directed DNA polymerase activity
type: Class
database: go

DNA-directed RNA polymerase
type: Concept
comment: Protein of the DNA-directed RNA polymerase complexes, 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. Prokaryotes have a single enzyme for the three RNA types that is subject to stringent regulatory mechanisms. Eukaryotes have type I that synthesizes all rRNA except the 5S component, type II that synthesizes mRNA and hnRNA and type III that synthesizes tRNA and the 5S component of rRNA.
subclass of: Transcription
subclass of: Cellular component
category: Cellular component

DNA-directed RNA polymerase complex
type: Class
database: go

Domain
type: Concept
comment: Keywords assigned to proteins because they have at least one specimen of a specific domain.
narrower: ANK repeat
narrower: Annexin
narrower: Bait region
narrower: Bromodomain
narrower: CBS domain
narrower: Coiled coil
narrower: Collagen
narrower: EGF-like domain
narrower: Glutamine amidotransferase
narrower: Homeobox
narrower: Immunoglobulin domain
narrower: Kringle
narrower: Laminin EGF-like domain
narrower: Leucine-rich repeat
narrower: LIM domain
narrower: Lipoyl
narrower: Paired box
narrower: Redox-active center
narrower: Repeat
narrower: SH2 domain
narrower: SH3 domain
narrower: SH3-binding
narrower: Signal
narrower: Sushi
narrower: TonB box
narrower: TPR repeat
narrower: Transit peptide
narrower: Transmembrane
narrower: WD repeat
narrower: Zinc-finger
narrower: Kelch repeat
narrower: Knottin
subclass of: Concept

Down syndrome
type: Concept
alternative label: Down's syndrome
comment: Protein which, if defective, causes Down's syndrome, a condition due to the presence of three copies of chromosome 21 (trisomy 21), characterized by some degree of intellectual disability, short stature and poor muscle tone. Common (1 in 700 live births); incidence increases with maternal age. The cause is usually non-disjunction at meiosis but occasionally a translocation of fused chromosomes 21 and 14.
subclass of: Disease
category: Disease

Dwarfism
type: Concept
comment: Protein which, if defective, causes dwarfism, a skeletal growth defect resulting in the condition of being undersized.
subclass of: Disease
category: Disease

Dynein
type: Concept
comment: Large multimeric complex with ATPase activity, responsible for the movement of eukaryotic cilia and flagella (axonemal dynein) and for the intracellular retrograde motility of vesicles, organelles and chromosomes along microtubules (cytosolic dynein). Constitutes the side arms of the outer microtubule doublets in the ciliary axoneme and is responsible for the sliding. Also used for the dynein-associated microtubule-binding proteins (MTBs), e.g. dynactin.
subclass of: Cellular component
category: Cellular component

dynein complex
type: Class
database: go

Dyskeratosis congenita
type: Concept
alternative label: DKC
comment: Protein which, if defective, causes dyskeratosis congenita, a clinically and genetically heterogeneous disorder characterized by abnormal skin pigmentation, mucosal leukoplakia, nail dystrophy, progressive bone marrow failure, and increased predisposition to cancer.
subclass of: Disease
category: Disease

Dystonia
type: Concept
comment: Protein which, if defective, causes dystonia or dystonic conditions that feature persistent or recurrent episodes of dystonia as a major manifestation of disease. Dystonia is a movement disorder with a neurological basis, due to disordered tonicity of muscle. It is characterized by sustained involuntary muscle contractions that cause abnormal postures, twisting, repetitive and patterned movements. It may affect muscles throughout the body (generalized), in certain parts of the body (segmental), or may be confined to particular muscles or muscle groups (focal).
subclass of: Disease
category: Disease

Dystroglycanopathy
type: Concept
comment: Protein which, if defective, causes any of the muscular disorders caused by aberrant glycosylation of dystroglycan. These genetically heterogeneous diseases include a range of conditions with different degrees of severity. At the most severe end of the clinical spectrum, Walker-Warburg syndrome (WWS), muscle-eye-brain disease (MEB) and Fukuyama congenital muscular dystrophy (FCMD) are characterized by congenital muscular dystrophy and severe structural brain and eye abnormalities, which in WWS result in early infantile death. At the mildest end of the clinical spectrum, affected individuals present with limb girdle muscular dystrophy (LGMD), without brain and eye involvement.
subclass of: Disease
category: Disease

Early protein
type: Concept
comment: Bacteriophage or viral protein expressed in the first phase of the infectious cycle.
subclass of: Developmental stage
category: Developmental stage

Ectodermal dysplasia
type: Concept
alternative label: ED
comment: Protein which, if defective, causes ectodermal dysplasia, a heterogeneous group of developmental disorders affecting tissues of ectodermal origin. Ectodermal dysplasias are characterized by abnormal development of two or more ectodermal structures such as hair, teeth, nails and sweat glands, with or without any additional clinical sign. Each combination of clinical features represents a different type of ectodermal dysplasia.
subclass of: Disease
narrower: Lacrimo-auriculo-dento-digital syndrome
category: Disease

EGF-like domain
type: Concept
comment: Protein containing at least one EGF-like domain, a sequence of about thirty to forty amino-acid residues long found in the sequence of epidermal growth factor (EGF). It has been shown to be present, in a more or less conserved form, in a large number of proteins. The EGF-like domain contains six cysteines which form disulfide bonds within the domain (C1-C3, C2-C4, C5-C6).
subclass of: Domain
category: Domain

Ehlers-Danlos syndrome
type: Concept
alternative label: EDS
comment: Protein which, if defective, causes Ehlers-Danlos syndrome (EDS), a genetically and phenotypically heterogeneous group of connective-tissue disorders. It affects primarily the skin, ligaments, joints, and blood vessels. Typical features include skin hyperextensibility, joint hypermobility, easy bruisability, friability of tissues with bleeding and poor wound healing. Inheritance can be autosomal dominant, autosomal recessive, or X-linked recessive.
subclass of: Disease
category: Disease

Electron transport
type: Concept
comment: Protein involved in the transport of electrons, a process by which electrons are transported through a series of reactions from the reductant, or electron donor, to the oxidant, or electron acceptor, with concomitant energy conversion. Necessary for both photosynthesis and aerobic respiration.
subclass of: Transport
narrower: Respiratory chain
category: Biological process

Elliptocytosis
type: Concept
comment: Protein which, if defective, causes elliptocytosis, a disorder characterized by variable haemolytic anaemia and elliptical red blood cell shape. Caused by deficiency/dysfunction of red blood cell membrane proteins.
subclass of: Hereditary hemolytic anemia
category: Disease

Elongation factor
type: Concept
alternative label: Translation elongation factor activity
comment: Protein that associates with ribosomes cyclically during the elongation phase of protein synthesis, and catalyze formation of the acyl bond between the incoming amino-acid residue and the peptide chain.
subclass of: Protein biosynthesis
subclass of: Molecular function
category: Molecular function

translation elongation factor activity
type: Class
database: go

translational elongation
type: Class
database: go

Emery-Dreifuss muscular dystrophy
type: Concept
alternative label: Scapuloperoneal muscular dystrophy
comment: Protein which, if defective, causes Emery-Dreifuss muscular dystrophy, a heterogenous group of inherited muscular dystrophy without the involvement of nervous system. The disease is characterized by slowly progressive muscle weakness, contracture of the elbows, Achilles tendon and posterior cervical muscles, and cardiac features.
subclass of: Disease
category: Disease

Encapsulin nanocompartment
type: Concept
comment: Protein located in or on an encapsulin nanocompartment, proteinaceous shells that encapsulate enzymes. The selectively permeable, self-assembling 25-42 nm shell is made of only 1 protein, unlike the larger bacterial microcompartment. The shell protein has an HK97-like fold and probably evolved from a viral protein. Artificial encapsulin nanocompartments can be expressed and filled with cargo proteins for biotechnological uses. They are found in many bacterial and a few archaeal phyla.
subclass of: Cellular component
category: Cellular component

Endocytosis
type: Concept
comment: Protein involved in endocytosis, a process by which extracellular materials are taken up into a cell by invagination of the plasma membrane to form vesicles enclosing these materials.
subclass of: Biological process
category: Biological process

endocytosis
type: Class
database: go

Endonuclease
type: Concept
comment: Phosphodiesterase capable of cleaving at phosphodiester internal bonds within a DNA or RNA substrate.
subclass of: Nuclease
narrower: Intron homing
category: Molecular function

endonuclease activity
type: Class
database: go

Endoplasmic reticulum
type: Concept
comment: 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. The rough-surface portion is studded with ribosomes.
subclass of: Cellular component
narrower: Microsome
category: Cellular component

endoplasmic reticulum
type: Class
database: go

Endorphin
type: Concept
comment: Morphine-like peptides produced by the brain in response to neurotransmitters. They bind to neuron receptors that mediate the action of opiates and induce analgesia and sedation.
subclass of: Molecular function
category: Molecular function

neuropeptide signaling pathway
type: Class
database: go

Endosome
type: Concept
comment: Protein found in or associated with endosomes. Endosomes are highly dynamic membrane systems involved in transport within the cell, they receive endocytosed cell membrane molecules and sort them for either degradation or recycling back to the cell surface. They also receive newly synthesised proteins destined for vacuolar/lysosomal compartments. In certain cell types, endosomal multivesicular bodies may fuse with the cell surface in an exocytic manner. These released vesicles are called exosomes.
subclass of: Cellular component
category: Cellular component

endosome
type: Class
database: go

Enterobactin biosynthesis
type: Concept
alternative label: Enterobactin anabolism
alternative label: Enterobactin biosynthetic process
alternative label: Enterobactin formation
alternative label: Enterobactin synthesis
alternative label: Enterochelin anabolism
alternative label: Enterochelin biosynthesis
alternative label: Enterochelin biosynthetic process
alternative label: Enterochelin formation
alternative label: Enterochelin synthesis
comment: Protein involved in the synthesis of enterobactin, a compound that transports iron from the bacterial environment into the cell cytoplasm.
subclass of: Biological process
category: Biological process

enterobactin biosynthetic process
type: Class
database: go

Enterotoxin
type: Concept
comment: Toxin which, either when ingested or when produced by enterobacteria within the intestine, acts on the intestinal mucosa and induces diarrhea by perturbing ion and water transport systems.
subclass of: Toxin
category: Molecular function

Epidermolysis bullosa
type: Concept
comment: Protein which, if defective, causes epidermolysis bullosa, any of a group of mechano-bullous disorders characterized by blistering and/or erosion of the skin and mucous membranes which occur spontaneously or as a result of mild physical trauma. Traditionally, epidermolysis bullosa is divided into three broad categories based on the level of tissue separation: in epidermolysis bullosa simplex (EBS), tissue separation is intraepidermal and occurs within the basal keratinocytes at the bottom layer of epidermis; the junctional forms (JEB) display tissue separation within the dermo-epidermal basement membrane (basement membrane zone, BMZ), primarily within the lamina lucida; in the dystrophic forms (DEB), tissue separation occurs below the lamina densa within the upper papillary dermis. Some forms of epidermolysis bullosa display tissue separation at the basal cell/lamina lucida interface, at the level of the hemidesmosomes (hemidesmosomal variants). The hemidesmosomal variants overlap with the traditional subtypes, particularly the simplex and junctional forms. In addition to skin involvement, various extracutaneous manifestations can be associated with distinct subtypes of epidermolysis bullosa.
subclass of: Disease
category: Disease

Epilepsy
type: Concept
comment: Protein which, if defective, causes epilepsy, any of a group of disorders characterized by paroxysmal transient disturbances of the electrical activity of the brain that may be manifested as episodic impairment or loss of consciousness, abnormal motor phenomena, psychic or sensory disturbances, or perturbation of the autonomic nervous system. Epilepsy is classified as either symptomatic or idiopathic according to whether the cause is known or unknown. Both of these types can be classified into partial and generalized epilepsy, depending on whether the seizures are due to limited or to widespread brain lesions, respectively.
subclass of: Disease
category: Disease

ER-Golgi transport
type: Concept
alternative label: ER/Golgi transport
alternative label: ER to Golgi transport
alternative label: Golgi-to-ER transport
comment: Protein involved in the 'ER-to-Golgi' transport, a bidirectional membrane traffic between the endoplasmic reticulum and the Golgi apparatus which mediates the transfer of cargo molecules by means of small vesicles or tubular-saccular extensions.
subclass of: Transport
category: Biological process

vesicle-mediated transport
type: Class
database: go

ERV
type: Concept
alternative label: Endogenous retrovirus
alternative label: Fossil virus
comment: Protein encoded by proviral genes of endogenous retroviruses. When a retrovirus infects a host cell, viral reverse transcriptase (RT) makes a DNA copy of the RNA viral genome. The integrated DNA form of a retrovirus is referred to as a provirus. Proviral genes are expressed by cellular mechanisms. Retroviruses that enter the germline are referred to as endogenous retroviruses (ERVs) to distinguish them from horizontally transmitted, not passed on to host progeny, "exogenous" retroviruses. Amplification of ERV copy number via retrotransposition or reinfection has given rise to numerous ERV sequences in the vertebrate genomes. As much as 8% of the human genome, and 10% of the mouse genome, consists of sequences derived from ERV insertions.
subclass of: Technical term
category: Technical term

Erythrocyte maturation
type: Concept
alternative label: RBC maturation
alternative label: Red blood cell maturation
alternative label: Red blood corpuscle maturation
comment: Protein involved in the maturation of erythrocytes, the predominant type of cells present in vertebrate blood and which contain the gas-transporting protein, hemoglobin.
subclass of: Biological process
category: Biological process

erythrocyte maturation
type: Class
database: go

Ethylene biosynthesis
type: Concept
alternative label: Ethylene anabolism
alternative label: Ethylene biosynthetic process
alternative label: Ethylene formation
alternative label: Ethylene synthesis
comment: Protein involved in the synthesis of ethylene (C2H4), an unsaturated hydrocarbon gas mainly produced in plants. It has developmental effects as a hormone, including growth inhibition, regulation of fruit development, leaf abscission and aging.
subclass of: Biological process
category: Biological process

ethylene biosynthetic process
type: Class
database: go

Ethylene signaling pathway
type: Concept
alternative label: Ethylene mediated signaling pathway
comment: Protein involved in the ethylene signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth and development (e.g. seed germination, root and shoot growth, flower development, plant defense, senescence, abscission and ripening). This phytohormone can be synthesized from methionin.
subclass of: Biological process
category: Biological process

ethylene-activated signaling pathway
type: Class
database: go

Eukaryotic host gene expression shutoff by virus
type: Concept
comment: Viral protein which prevents host gene expression by blocking host transcription, mRNA export or translation. This gives viral transcripts a competitive edge to use the hijacked translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response.
subclass of: Host gene expression shutoff by virus
narrower: Eukaryotic host transcription shutoff by virus
narrower: Host mRNA suppression by virus
narrower: Eukaryotic host translation shutoff by virus
category: Biological process

Eukaryotic host transcription shutoff by virus
type: Concept
comment: Viral protein involved in inhibiting host transcription to ensure the shutoff of cellular proteins expression and give virus transcripts a competitive edge for access to the cellular translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response. Inhibition of transcription can be performed by interfering with host RNA pol-II function or interfering with general transcription factors.
subclass of: Eukaryotic host gene expression shutoff by virus
narrower: Inhibition of host RNA polymerase II by virus
narrower: Inhibition of eukaryotic host transcription initiation by virus
category: Biological process

suppression by virus of host transcription
type: Class
database: go

Eukaryotic host translation shutoff by virus
type: Concept
comment: Viral protein involved in inhibiting the host translational machinery to shutoff cellular gene expression. This gives virus transcripts a competitive edge to use the hijacked translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response. Several virus are known to inhibit host translation mostly by inactivating translation factors.
subclass of: Eukaryotic host gene expression shutoff by virus
narrower: Inhibition of eukaryotic host translation factors by virus
narrower: Inhibition of host poly(A)-binding protein by virus
category: Biological process

suppression by virus of host translation
type: Class
database: go

Evasion of bacteria-mediated translation shutoff by virus
type: Concept
comment: Viral protein that counteracts the translation shutoff set up by the bacterial host in order to inhibit viral replication. This antiviral defense system alters a crucial cellular process thereby blocking virus multiplication and ending up with host dormancy or even cell death. For example, some E.coli strains infected by bacteriophage T4 activate an anticodon nuclease which causes depletion of tRNA(Lys) and, consequently, abolishes T4 protein synthesis and causes cell death. However, this effect is counteracted by the repair of tRNA(Lys) in consecutive reactions catalyzed by the viral enzymes polynucleotide kinase and RNA ligase. The ToxIN system functions as a toxin-antitoxin (TA) tandem which is used as a antiviral defense mechanism.
subclass of: Host-virus interaction
category: Biological process

Evasion of host immunity by viral interleukin-like protein
type: Concept
comment: Viral protein sharing sequence homology with host interleukins. Interleukins are produced by immune system cells such as lymphocytes, macrophages and monocytes, and modulate inflammation and immunity by regulating growth, mobility and differentiation of lymphoid and other cells. Several viruses encode interleukin-like proteins playing a role in immune evasion. Additionally, viral interleukins have been shown to activate cellular signaling cascades that enhance virus replication.
subclass of: Viral immunoevasion
category: Biological process

mitigation of host antiviral defense response
type: Class
database: go

Excision nuclease
type: Concept
comment: Enzyme which excises abnormal or mismatched nucleotides from a DNA strand.
subclass of: DNA repair
subclass of: Molecular function
category: Molecular function

nuclease activity
type: Class
database: go

Exocytosis
type: Concept
alternative label: Vesicle exocytosis
comment: Protein involved in exocytosis, a process by which a material is transported out of a cell using a vesicle that first engulfs the material and then is extruded through an opening in the cell membrane. The exocyst protein complex plays an important role in exocytosis by directing exocytic vesicles to their precise sites of fusion in the plasma membrane.
subclass of: Biological process
category: Biological process

exocytosis
type: Class
database: go

Exonuclease
type: Concept
comment: Enzyme that degrades DNA or RNA by progressively splitting off single nucleotides from one end of the chain.
subclass of: Nuclease
category: Molecular function

exonuclease activity
type: Class
database: go

Exopolysaccharide synthesis
type: Concept
alternative label: EPS anabolism
alternative label: EPS biosynthesis
alternative label: EPS biosynthetic process
alternative label: EPS formation
alternative label: EPS synthesis
alternative label: Exopolysaccharide anabolism
alternative label: Exopolysaccharide biosynthesis
alternative label: Exopolysaccharide biosynthetic process
alternative label: Exopolysaccharide formation
comment: Protein involved in the synthesis of exopolysaccharide (EPS), a high molecular-weight polymer composed of saccharide subunits. An example is succinoglycan (EPS I) of Rhizobium meliloti, that is important for invasion of the nodules that it elicits on its host, Medicago sativa.
subclass of: Biological process
category: Biological process

polysaccharide biosynthetic process
type: Class
database: go

Exosome
type: Concept
comment: Protein which is a component of the exosome, a complex of proteins that includes 3->5 exoribonucleases and that plays a major role in diverse RNA processing and degradation pathways in eukaryotes and archaea.
subclass of: Cellular component
category: Cellular component

exosome (RNase complex)
type: Class
database: go

Extinct organism protein
type: Concept
comment: Protein originating from a species thought to be extinct, i.e. from a species for which no known surviving specimens are known to exist. Eg. Dodo, Mammoth or Neanderthal.
subclass of: Technical term
category: Technical term

Extracellular matrix
type: Concept
comment: 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. The extracellular matrix forms a supportive meshwork around cells and is largely composed of collagen, laminin, fibronectin and glycosaminoglycans. It can influence the properties of the cells that it supports. In certain tissues, specific modifications to the extracellular matrix occur. For instance, the matrix of bone is mineralized to resist compression.
subclass of: Secreted
narrower: Basement membrane
category: Cellular component

extracellular matrix
type: Class
database: go

Eye lens protein
type: Concept
comment: Protein found in the lens, a transparent body at the front of the vertebrate eye.
subclass of: Molecular function
category: Molecular function

structural constituent of eye lens
type: Class
database: go

FAD
type: Concept
alternative label: Flavin adenine dinucleotide
comment: Protein involved in flavin adenine dinucleotide synthesis or protein which contains at least one FAD as prosthetic group, cofactor (flavoprotein) or cosubstrate such as many oxidation-reduction enzymes. FAD is an electron carrier molecule that functions as a hydrogen acceptor. The generic term "flavin" derives from the Latin word flavius ("yellow") because of the brilliant yellow color they exhibit as solids and in neutral aqueous solutions.
subclass of: Flavoprotein
category: Ligand

Familial hemophagocytic lymphohistiocytosis
type: Concept
alternative label: FHL
alternative label: Hemophagocytic lymphohistiocytosis
alternative label: HPLH
comment: Protein which, if defective, causes familial hemophagocytic lymphohistiocytosis. FHL is a genetically heterogeneous, autosomal recessive disorder characterized by immune dysregulation with hypercytokinemia and defective natural killer cell function. The clinical features of the disease include fever, hepatosplenomegaly, cytopenia, hypertriglyceridemia, hypofibrinogenemia, and neurological abnormalities ranging from irritability and hypotonia to seizures, cranial nerve deficits and ataxia. Hemophagocytosis is a prominent feature of the disease, and non-malignant infiltration of macrophages and activated T lymphocytes in lymph nodes, spleen and other organs is also found.
subclass of: Disease
category: Disease

Fanconi anemia
type: Concept
alternative label: Fanconi pancytopenia
comment: Protein which, if defective, causes Fanconi anemia. Fanconi anemia is a rare recessive disorder characterized by progressive pancytopenia, hypoplasia of the bone marrow and patchy brown discoloration of the skin, due to melanin deposition. It is associated with multiple congenital anomalies of the musculoskeletal and genitourinary systems.
subclass of: Disease
category: Disease

Fatty acid biosynthesis
type: Concept
alternative label: Fatty acid anabolism
alternative label: Fatty acid biosynthetic process
alternative label: Fatty acid formation
alternative label: Fatty acid synthesis
comment: Protein involved in the synthesis of fatty acids, long chain organic acids of the general formula CH3(CnHx)COOH. They are constituents of lipids and can be saturated or unsaturated. The esterified forms are important both as energy storage molecules and structural molecules.
subclass of: Fatty acid metabolism
subclass of: Lipid biosynthesis
narrower: Prostaglandin biosynthesis
narrower: Oxylipin biosynthesis
category: Biological process

fatty acid biosynthetic process
type: Class
database: go

Fatty acid metabolism
type: Concept
alternative label: Fatty acid metabolic process
comment: Protein involved in the biochemical reactions with fatty acids. Fatty acids are long chain organic acids of the general formula CH3(CnHx)COOH. They are constituents of lipids and can be saturated or unsaturated. The esterified forms are important both as energy storage molecules and structural molecules.
subclass of: Lipid metabolism
narrower: Fatty acid biosynthesis
narrower: Prostaglandin metabolism
category: Biological process

fatty acid metabolic process
type: Class
database: go

Fertilization
type: Concept
comment: Protein involved in fertilization, the union of two haploid cells, the gametes, to form a diploid cell, the zygote.
subclass of: Biological process
category: Biological process

single fertilization
type: Class
database: go

Fibrinogenolytic toxin
type: Concept
comment: Toxin involved in fibrinogen degradation leading to a decrease of plasma fibrinogen concentration. Fibrinogenolytic toxins are mostly snake venom proteases.
subclass of: Hemostasis impairing toxin
category: Molecular function

Fibrinolysis
type: Concept
comment: Protein involved in fibrin degradation leading to the dissolving of blood clots.
subclass of: Blood coagulation
category: Biological process

fibrinolysis
type: Class
database: go

Fibrinolytic toxin
type: Concept
comment: Toxin involved in fibrin degradation leading to the dissolution of fibrin clots. Fibrinolytic toxins are mostly snake venom proteases.
subclass of: Hemostasis impairing toxin
category: Molecular function

Fimbrium
type: Concept
alternative label: Fimbria
alternative label: Pili
alternative label: Pilus
comment: Protein found in a fimbrium or pilus. A fimbrium or pilus is a hair-like, non-flagellar, polymeric filamentous appendage that extend from the bacterial or archaeal cell surface, such as type 1 pili, P-pili, type IV pili or curli. Pili perform a variety of functions, including surface adhesion, motility, cell-cell interactions, biofilm formation, conjugation, DNA uptake, and twitching motility.
subclass of: Cellular component
category: Cellular component

pilus
type: Class
database: go

Fimbrium biogenesis
type: Concept
alternative label: Fimbria biogenesis
alternative label: Pili biogenesis
alternative label: Pilus biogenesis
comment: Protein which is involved in the formation, organization or maintenance of the fimbrium, a long hair-like cell surface appendage. The flagellar apparatus consists of the flagellar filament made of polymerized flagellin, the hook-like structure near the cell surface and a system of rings embedded in the cell enveloppe (the basal body or flagellar motor). The basal body and the hook anchor the whip-like filament to the cell surface. The flagellum is a rotating structure whose switches propels the cell through a liquid medium.
subclass of: Biological process
category: Biological process

Flagellar rotation
type: Concept
alternative label: Flagella motility
alternative label: Flagellar motility
alternative label: Flagella rotation
alternative label: Flagellum motility
alternative label: Flagellum rotation
comment: Protein involved in the movement of the flagella.
subclass of: Biological process
category: Biological process

archaeal or bacterial-type flagellum-dependent cell motility
type: Class
database: go

Flagellum
type: Concept
alternative label: Flagella
alternative label: Motile cilia
alternative label: Motile cilium
alternative label: Undulipodia
alternative label: Undulipodium
comment: Protein present in the flagellum, a long whip-like or feathery structure which propels the cell through a liquid medium. This motile cilium is produced by unicellular eukaryotes and by the motile male gametes of many eukaryotic organisms. The flagella commonly have a characteristic axial '9+2' microtubular array (axoneme) and bends are generated along the length of the flagellum by restricted sliding of the nine outer doublets.
subclass of: Cilium
category: Cellular component

motile cilium
type: Class
database: go

Flavonoid biosynthesis
type: Concept
alternative label: Flavonoid anabolism
alternative label: Flavonoid biosynthetic process
alternative label: Flavonoid formation
alternative label: Flavonoid synthesis
comment: Protein involved in the synthesis of flavonoids, polyphenolic compounds possessing 15 carbon atoms; two benzene rings joined by a linear three carbon chain, a C6-C3-C6 skeleton. C6 presents a benzene ring, C3 often is part of of an oxygen-containing ring. Flavonoids are coloured phenolic pigments originally considered vitamins (Vitamins P, C2) but not shown to have any nutritional role. They are responsible for the red/purple colours of many higher plants.
subclass of: Biological process
category: Biological process

flavonoid biosynthetic process
type: Class
database: go

Flavoprotein
type: Concept
comment: Enzymes which contain one or more flavin nucleotides (FAD or FMN) as redox cofactors or cosubstrates. Flavoproteins are involved, for example, in the oxidative degradation of pyruvate, fatty acids and amino acids, and in the process of electron transport.
subclass of: Ligand
narrower: FAD
narrower: FMN
category: Ligand

Flight
type: Concept
alternative label: Flight behavior
comment: Protein which stimulates or which is involved in flight, the act of passing through the air by the use of wings.
subclass of: Biological process
category: Biological process

flight behavior
type: Class
database: go

Flowering
type: Concept
alternative label: Flower development
comment: Protein involved in the transition from vegetative to reproductive development in plants.
subclass of: Biological process
category: Biological process

flower development
type: Class
database: go

FMN
type: Concept
alternative label: Flavin adenine mononucleotide
alternative label: Flavin mononucleotide
alternative label: Riboflavin 5'-phosphate
comment: Protein involved in flavin adenine mononucleotide synthesis or protein which contains at least one FMN as prosthetic group/cofactor (flavoproteins) or cosubstrate, such as many oxidation-reduction enzymes. FMN is an electron carrier molecule that functions as a hydrogen acceptor. The generic term "flavin" derives from the Latin word flavius ("yellow") because of the brilliant yellow color they exhibit as solids and in neutral aqueous solutions.
subclass of: Flavoprotein
category: Ligand

Folate biosynthesis
type: Concept
alternative label: Folacin anabolism
alternative label: Folacin biosynthesis
alternative label: Folacin biosynthetic process
alternative label: Folacin formation
alternative label: Folacin synthesis
alternative label: Folate anabolism
alternative label: Folate biosynthetic process
alternative label: Folate formation
alternative label: Folate synthesis
alternative label: Folic acid anabolism
alternative label: Folic acid biosynthesis
alternative label: Folic acid biosynthetic process
alternative label: Folic acid formation
alternative label: Folic acid synthesis
alternative label: Pteroylglutamic acid anabolism
alternative label: Pteroylglutamic acid biosynthesis
alternative label: Pteroylglutamic acid biosynthetic process
alternative label: Pteroylglutamic acid formation
alternative label: Pteroylglutamic acid synthesis
comment: Protein involved in the synthesis of folate, the ionic form of folic acid (Latin folium, 'leaf'), first found in spinach leaves. Folate is converted in a two-step reduction into its coenzyme form tetrahydrofolate, often abbreviated FH4 or THF, which acts as a carrier of one-carbon units at several oxidation levels in a variety of biosyntheses.
subclass of: Biological process
category: Biological process

folic acid biosynthetic process
type: Class
database: go

Folate-binding
type: Concept
alternative label: Folacin-binding
alternative label: Folic acid-binding
alternative label: Pteroylglutamic acid-binding
comment: Protein that binds folate, the ionic form of folic acid.
subclass of: Ligand
category: Ligand

folic acid binding
type: Class
database: go

Formylation
type: Concept
alternative label: N-Formylated
comment: A protein in which either the N-terminal N-formylmethionine has not been processed by the methionyl-tRNA formyltransferase or which is posttranslationally modified by the attachment of at least one formyl group.
subclass of: PTM
category: PTM

Fruit ripening
type: Concept
comment: Protein involved in fruit ripening. The fruit is the matured ovary of a plant, enclosing the seed(s). The plant hormone ethylene stimulates fruit ripening.
subclass of: Biological process
category: Biological process

fruit ripening
type: Class
database: go

Fruiting body
type: Concept
comment: Protein involved in fruiting body formation or expressed in fruiting bodies, any specialized reproductive structure that produces spores or gametes in fungi, slime molds, algae, etc. Fruiting bodies are distinct in size, shape and coloration for each species.
subclass of: Developmental stage
category: Developmental stage

Fucose metabolism
type: Concept
alternative label: Fucose metabolic process
comment: Protein involved in the biochemical reactions with fucose. L-fucose (6-deoxy-L-galactose) is present in some algae and identified in the chains of glycoproteins; it is the only polysaccharides of certain bacterias.
subclass of: Carbohydrate metabolism
category: Biological process

fucose metabolic process
type: Class
database: go

Fungicide
type: Concept
alternative label: Anti-fungal
comment: Protein capable of killing or inhibiting growth of fungi.
subclass of: Antimicrobial
category: Molecular function

defense response to fungus
type: Class
database: go

Fusion of virus membrane with host cell membrane
type: Concept
alternative label: Viral entry into host cell via plasma membrane fusion
comment: Viral protein involved in the merging of the virus envelope with host cytoplasmic membrane during viral penetration into host cell. Virus fusion proteins drive this fusion reaction by undergoing a major conformational change that is triggered by interactions with the target cell. This pathway is used by viruses whose fusion protein is usually pH independent such as most paramyxoviruses, herpesviruses and retroviruses. MHV-JHM coronavirus has been shown to fuse directly with the host cytoplasmic membrane. Prokaryotic viruses such as Tectiviridae fuse their inner membrane with the host cytoplasmic membrane whereas Cystoviridae fuse their outer membrane with the host cytoplasmic membrane.
subclass of: Fusion of virus membrane with host membrane
category: Biological process

fusion of virus membrane with host plasma membrane
type: Class
database: go

Fusion of virus membrane with host endosomal membrane
type: Concept
alternative label: Viral entry into host cell via plasma membrane fusion
comment: Viral protein involved in the merging of the virus envelope with host endosomal membrane during viral penetration into host cell. Viral fusion proteins drive this fusion reaction by undergoing a major conformational change that is triggered by interactions with the target cell. The specific trigger is mainly endosome acidification which induce activation of the fusion protein by conformational change. This pathway is used by enveloped viruses which are endocytosed and whose fusion protein is usually pH-dependent like influenza A virus, rhabdoviruses, bornaviruses, filoviruses, asfarviridae, flaviviridae, alphaviruses, HIV-1, avian leukosis virus, SARS, 229E, and MHV-2 coronaviruses.
subclass of: Fusion of virus membrane with host membrane
category: Biological process

fusion of virus membrane with host endosome membrane
type: Class
database: go

Fusion of virus membrane with host membrane
type: Concept
alternative label: Viral entry into host cell via membrane fusion
comment: Viral protein involved in the merging of the virion membrane with a host membrane during viral penetration into host cell. Viral fusion proteins drive this fusion reaction by undergoing a major conformational change that is triggered by interactions with the target cell. The specific trigger depends on the virus and can be exposure to low pH in the endocytic pathway or interaction of the virion with the host receptor(s). In prokaryotic viruses, host-virus membrane fusion can occur either at the host outer membrane or plasma membrane. Bacteriophages such as cystoviridae fuse their external envelope with the host outer membrane, whereas others like tectiviridae fuse their inner envelope with the host plasma membrane.
subclass of: Viral penetration into host cytoplasm
narrower: Fusion of virus membrane with host cell membrane
narrower: Fusion of virus membrane with host endosomal membrane
narrower: Fusion of virus membrane with host outer membrane
category: Biological process

membrane fusion involved in viral entry into host cell
type: Class
database: go

Fusion of virus membrane with host outer membrane
type: Concept
alternative label: Viral entry into host cell via outer membrane fusion
comment: Viral protein involved in the merging of the virion external lipidic membrane (envelope) with the prokaryotic host outer membrane during viral penetration into host cell. Bacteriophages such as Cystoviridae for example fuse their membrane with the host outer membrane.
subclass of: Virion
subclass of: Fusion of virus membrane with host membrane
category: Biological process

fusion of virus membrane with host outer membrane
type: Class
database: go

G-protein coupled acetylcholine receptor impairing toxin
type: Concept
alternative label: mAChR regulator
alternative label: Muscarinic acetylcholine receptor regulator
comment: Toxin which interferes with the function of the muscarinic acetylcholine receptor (mAChR). The mAChR is a specific class of G-protein coupled receptor (GPCR) that binds acetylcholine. These toxins are mostly found in snake venoms.
subclass of: G-protein coupled receptor impairing toxin
category: Molecular function

G-protein coupled receptor
type: Concept
alternative label: 7TM receptor
alternative label: GPCR
comment: Receptors which transduce extracellular signals across the cell membrane. At the external side they receive a ligand (a photon in case of opsins), and at the cytosolic side they activate a guanine nucleotide-binding (G) protein. These receptors are hydrophobic proteins that cross the membrane seven times.
subclass of: Receptor
subclass of: Transducer
category: Molecular function

G protein-coupled receptor activity
type: Class
database: go

G protein-coupled receptor signaling pathway
type: Class
database: go

G-protein coupled receptor impairing toxin
type: Concept
alternative label: GPCR regulator
comment: Toxin which interferes with the function of G-protein coupled receptors (GPCRs). These toxins are mostly found in snake and scorpion venoms.
subclass of: Toxin
narrower: G-protein coupled acetylcholine receptor impairing toxin
narrower: Bradykinin receptor impairing toxin
category: Molecular function

G0/G1 host cell cycle checkpoint dysregulation by virus
type: Concept
comment: Viral protein involved in the modulation of host cell cycle progression by dysregulating the G0/G1 transition. Some viruses benefit from keeping cells in resting state (G0), while others favor entry through G1 and subsequent cell division to replicate more efficiently.
subclass of: Modulation of host cell cycle by virus
category: Biological process

modulation by virus of host G0/G1 transition checkpoint
type: Class
database: go

G1/S host cell cycle checkpoint dysregulation by virus
type: Concept
comment: Viral protein involved in the modulation of host cell cycle progression by dysregulating the G1/S transition. Some viruses benefit from an arrest in G1 to S phase transition, while others force through S phase to favor their own replication.
subclass of: Modulation of host cell cycle by virus
category: Biological process

modulation by virus of host G1/S transition checkpoint
type: Class
database: go

Galactitol metabolism
type: Concept
alternative label: Dulcitol metabolic process
alternative label: Dulcitol metabolism
alternative label: Galactitol metabolic process
comment: Protein involved in the biochemical reactions with galactitol. This sugar alcohol is derived from galactose. It can be found in certain bacteria, yeasts, fungi and plants. In humans, the congenital galactosemic cataracts are due to an accumulation of galactitol within the lens.
subclass of: Biological process
category: Biological process

galactitol metabolic process
type: Class
database: go

Galactose metabolism
type: Concept
alternative label: Galactose metabolic process
comment: Protein involved in the biochemical reactions with the monosaccharide galactose. This optical isomer (epimer) of glucose is a constituent of various oligosaccharides (e.g. lactose, raffinose), polysaccharides (e.g. galactans, agar, gum arabic) and also of sphingolipids (galactocerebrosides).
subclass of: Carbohydrate metabolism
category: Biological process

galactose metabolic process
type: Class
database: go

Gamma-carboxyglutamic acid
type: Concept
alternative label: 1-carboxyglutamic acid
comment: Protein which possesses at least one gamma-carboxyglutamic acid, a vitamin K dependent post-translational modification of a glutamate residue found in blood coagulation proteins and in the proteins of calcified tissues. Gamma-carboxyglutamyl residues are good chelators of calcium ions. There are two natural forms of vitamin K, 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). In infants, the primary symptom of a deficiency of this fat-soluble vitamin is a hemorrhagic syndrome.
subclass of: PTM
category: PTM

Gangliosidosis
type: Concept
comment: Protein which, if defective, causes gangliosidosis. Gangliosidosis defines any of a group of autosomal recessive lysosomal storage diseases characterized by the accumulation of gangliosides GM1 or GM2 and related glycoconiugates, and by progressive psychomotor deterioration. Subtypes include GM1-gangliosidoses and GM2-gangliosidoses.
subclass of: Disease
category: Disease

Gap junction
type: Concept
comment: Protein component of gap junctions which are specialized regions of the plasma membrane formed by a cluster of channels allowing small molecules to diffuse from the cytosol of one cell to that of an adjacent cell. A current model of the gap junction consists of a cluster of gap-junction channels. Both membranes contain connexon hemichannels, composed of a hexamer of an integral membrane protein which is often referred to as connexin. The junction of two adjacent connexons forms a gap-junction channel.
subclass of: Cell junction
category: Cellular component

gap junction
type: Class
database: go

Gap protein
type: Concept
comment: A group of insect proteins which are crucial for the development of proper embryonic segmentation. These are the first proteins that define the coarsest subdivisions. Generally, gap gene mutations are lethal and eliminate a large block of contiguous segments from the embryo.
subclass of: Developmental protein
category: Molecular function

segmentation
type: Class
database: go

Gas vesicle
type: Concept
comment: Protein of, or involved in synthesis of, gas vesicles. Gas vesicles (GV) are hollow, watertight, gas-permeable proteinaceous nanostructures found in some microorganisms. During planktonic growth they allow positioning of the organism at a favorable depth for light or nutrient acquisition. By regulating their relative GV content, aquatic microbes can perform vertical migrations. The GV is impermeable to liquid water but is highly permeable to gases and is normally filled with air. As they scatter light, they may also protect against UV light. Two main proteins are present in the gas vesicle: GvpA, an extremely hydrophobic protein which makes the ribs that form the structure, and GvpC, which binds to the outside of the ribs, helps shape GVs and stiffens the structure against collapse.
subclass of: Cellular component
category: Cellular component

gas vesicle
type: Class
database: go

Gaseous exchange
type: Concept
comment: Protein involved in the exchange of gases.
subclass of: Biological process
narrower: Surface film
category: Biological process

respiratory gaseous exchange by respiratory system
type: Class
database: go

Gastrulation
type: Concept
comment: Protein involved in gastrulation, a stage in early embryogenesis in which cell movements result in a massive reorganization of the embryo from an initially unstructured group of cells, the blastula, into a multi-layered organism. During gastrulation, the primary germ layers (endoderm, mesoderm, and ectoderm) are formed and organized in their proper locations for further development.
subclass of: Developmental protein
subclass of: Biological process
category: Biological process

gastrulation
type: Class
database: go

Gaucher disease
type: Concept
comment: Protein which, if defective, causes Gaucher disease, the most prevalent sphingolipid storage disorder caused by a recessively inherited deficiency of the enzyme glucocerebrosidase. Most common in Ashkenazi Jews, it is associated with hepatosplenomegaly (enlargement of liver and spleen) and, in severe early onset forms of the disease, with neurological dysfunction.
subclass of: Disease
category: Disease

Genetically modified food
type: Concept
comment: Any protein used in a biotechnological process that results in the modification of a naturally occurring food (crop or livestock). Examples include proteins introduced to enable herbicide or insect resistance or proteins that act in fruit ripening.
subclass of: Technical term
category: Technical term

Germination
type: Concept
comment: Protein involved in germination, the physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
subclass of: Biological process
category: Biological process

Gibberellin signaling pathway
type: Concept
alternative label: GA signalling pathway
alternative label: GA-signalling pathway
alternative label: Gibberellic acid signaling pathway
comment: Protein involved in the gibberellin (GA) signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth including seed germination, hypocotyl elongation, stem elongation, leaf expansion, trichome development, pollen maturation and flower and fruit development. GAs are tetracyclic diterpenoid phytohormones found in plants, fungi and bacteria. They are named GA1....GAn in order of discovery. The term "gibberellin" was first given to a substance, produced by the fungus Gibberella fujikuroi, which caused overgrowth symptoms in rice. This substance was later proven to be a mixture of GAs, with GA1 and GA3 being the active factors.
subclass of: Biological process
category: Biological process

gibberellic acid mediated signaling pathway
type: Class
database: go

Glaucoma
type: Concept
comment: Protein which, if defective, causes glaucoma, a group of eye diseases characterized by pathological changes in the optic disk, progressive loss of optic nerve axons and visual field defects. Most of the patients with glaucoma have an increased intraocular pressure. The disease is painless and often diagnosed at a late stage, when visual field defects are severe. Glaucoma is one of the leading causes of blindness worldwide.
subclass of: Disease
category: Disease

Gluconate utilization
type: Concept
comment: Protein involved in the biochemical pathway(s) in which gluconate is the carbon source.
subclass of: Biological process
category: Biological process

D-gluconate metabolic process
type: Class
database: go

Gluconeogenesis
type: Concept
alternative label: Glucose biosynthesis
alternative label: Glucose biosynthetic process
comment: Protein involved in the biosynthesis of "new" glucose from such noncarbohydrate precursors as pyruvate, lactate, certain amino acids and intermediates of the tricarboxylic acid cycle.
subclass of: Biological process
category: Biological process

gluconeogenesis
type: Class
database: go

Glucose metabolism
type: Concept
alternative label: Glucose metabolic process
comment: Protein involved in the biochemical reactions with the 6-carbon aldose sugar glucose.
subclass of: Carbohydrate metabolism
category: Biological process

glucose metabolic process
type: Class
database: go

Glutamate biosynthesis
type: Concept
alternative label: Glutamate anabolism
alternative label: Glutamate biosynthetic process
alternative label: Glutamate formation
alternative label: Glutamate synthesis
alternative label: Glutamic acid anabolism
alternative label: Glutamic acid biosynthesis
alternative label: Glutamic acid biosynthetic process
alternative label: Glutamic acid formation
alternative label: Glutamic acid synthesis
comment: 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.
subclass of: Amino-acid biosynthesis
category: Biological process

glutamate biosynthetic process
type: Class
database: go

Glutamine amidotransferase
type: Concept
alternative label: Glutamine metabolic process
comment: Enzyme that catalyzes the removal of the ammonia group from glutamine and transfers it to a substrate to form a new carbon-nitrogen group. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides or as domains in larger multifunctional proteins. There exist two classes of glutamine amidotransferases domains: I and II.
subclass of: Domain
category: Domain

glutamine metabolic process
type: Class
database: go

Glutaricaciduria
type: Concept
alternative label: GA
alternative label: Glutaric aciduria
comment: Protein which, if defective, causes glutaricaciduria (GA), a metabolic disorder characterized by the excretion of glutaric acid in the urine. Type I GA is caused by the deficiency of glutaryl-CoA dehydrogenase, a mitochondrial enzyme involved in the metabolism of lysine, hydroxylysine and tryptophan. Type II GA differs from type I in that multiple acyl-CoA dehydrogenase deficiencies result in a large excretion not only of glutaric acid but also of lactic, ethylmalonic, butyric, isobutyric, 2-methyl-butyric, and isovaleric acids. GA II can result from a deficiency of any one of 3 mitochondrial molecules: the alpha and beta subunits of electron transfer flavoprotein and electron transfer flavoprotein-ubiquinone oxidoreductase.
subclass of: Disease
category: Disease

Glutathione biosynthesis
type: Concept
alternative label: Glutathione anabolism
alternative label: Glutathione biosynthetic process
alternative label: Glutathione formation
alternative label: Glutathione synthesis
comment: Protein involved in the synthesis of the tripeptide glutathione (Gamma-Glu-Cys-Gly). Glutathione sulphydryl group is kept largely in the reduced state; this allows it to act as a sulphydryl buffer, reducing any disulphide bonds formed within cytoplasmic proteins to cysteines. Glutathione is also important as a cofactor for the enzyme glutathione peroxidase, in the uptake of amino acids and participates in leucotriene synthesis. Glutathione contains an unusual peptide linkage between the carboxyl group of the glutamate side chain and the amine group of cysteine.
subclass of: Biological process
category: Biological process

glutathione biosynthetic process
type: Class
database: go

Glutathionylation
type: Concept
alternative label: Glutathionylated
comment: Protein which is posttranslationally modified by the attachment of a glutathione molecule by a disulfide bond.
subclass of: PTM
category: PTM

Glycation
type: Concept
alternative label: Glycated
comment: Protein containing one or more covalently linked glucose residues, resulting from a non-enzymatic spontaneous reaction. The carbohydrate is attached to an amino-acid nitrogen atom (e.g. from a lysine side chain, or the amino-terminal group). This modification is a side effect of diabetes and aging. Glycation is the first step toward the formation of advanced glycation endproducts (AGEs). Some AGEs are benign, but others are implicated in age-related chronic diseases such as: type II diabetes mellitus, cardiovascular diseases, Alzheimer's disease, etc.
subclass of: Glycoprotein
category: PTM

Glycerol metabolism
type: Concept
alternative label: Glycerol metabolic process
comment: Protein involved in the biochemical reactions with the 3-carbon sugar alcohol glycerol. Glycerol is primarily of interest as the central structural component of the major classes of biological lipids, triglycerides and phosphatidyl phospholipids. It is also an important intermediate in carbohydrate and lipid metabolism.
subclass of: Biological process
category: Biological process

glycerol metabolic process
type: Class
database: go

Glycogen biosynthesis
type: Concept
alternative label: Glycogen anabolism
alternative label: Glycogen biosynthetic process
alternative label: Glycogen formation
alternative label: Glycogen synthesis
comment: Protein involved in the synthesis of glycogen, a branched polymer of D-glucose (mostly -(1-4) linked, but with some -(1-6) linked residues at branch points). Glycogen is the major short term storage polymer of animal cells and is particularly abundant in liver and to a lesser extent in muscles.
subclass of: Biological process
category: Biological process

glycogen biosynthetic process
type: Class
database: go

Glycogen metabolism
type: Concept
alternative label: Glycogen metabolic process
comment: Protein involved in the biochemical reactions with glycogen, a branched polymer of D-glucose (mostly -(1-4) linked, but with some - (1-6) linked residues at branch points). Glycogen is the major short term storage polymer of animal cells and is particularly abundant in liver and to a lesser extent in muscles.
subclass of: Carbohydrate metabolism
category: Biological process

glycogen metabolic process
type: Class
database: go

Glycogen storage disease
type: Concept
comment: Protein which, if defective, causes glycogen storage disease, a group of inherited metabolic disorders involving the enzymes responsible for the synthesis and degradation of glycogen. At least thirteen types of this disease have been described.
subclass of: Disease
category: Disease

Glycolate pathway
type: Concept
alternative label: C2 cycle
alternative label: Oxidative photosynthetic carbon pathway
alternative label: Photorespiration pathway
alternative label: Photosynthetic carbon oxydation cycle
comment: Protein involved in the glycolate pathway, synthesis of the amino acids serine and glycine from glycolate via a glyoxylate intermediate.
subclass of: Biological process
category: Biological process

oxidative photosynthetic carbon pathway
type: Class
database: go

Glycolysis
type: Concept
comment: Protein involved in the anaerobic enzymatic conversion of glucose to lactate or pyruvate, resulting in energy stored in the form of adenosine triphosphate (ATP), as occurs in skeletal muscle and in embryonic tissue.
subclass of: Biological process
category: Biological process

glycolytic process
type: Class
database: go

Glycoprotein
type: Concept
alternative label: Glycosylated
comment: Protein containing one or more covalently linked carbohydrates of various types, i.e. from monosaccharides to branched polysaccharides, including glycosylphosphatidylinositol (GPI), glycosaminoglycans (GAG).
subclass of: PTM
narrower: GPI-anchor
narrower: Proteoglycan
narrower: Sialic acid
narrower: Glycation
category: PTM

Glycosidase
type: Concept
comment: Hydrolases which attack glycosidic bonds in carbohydrates, glycoproteins and glycolipids. The glycosidases are not highly specific. Usually they distinguish only the type of bond, e.g. O- or N-glycosidic, and its configuration (alpha or beta).
subclass of: Hydrolase
category: Molecular function

hydrolase activity, acting on glycosyl bonds
type: Class
database: go

Glycosome
type: Concept
comment: Protein present in the glycosome, a microbody-like organelle found in all members of the protist order Kinetoplastida examined. Nine enzymes involved in glucose and glycerol metabolism are associated with these organelles. These enzymes are involved in pathways which, in other organisms, are usually located in the cytosol.
subclass of: Cellular component
category: Cellular component

glycosome
type: Class
database: go

Glycosyltransferase
type: Concept
comment: Enzymes that catalyze the transfer of glycosyl (sugar) residues to an acceptor, both during degradation (cosubstrates= water or inorganic phosphate) and during biosynthesis of polysaccharides, glycoproteins and glycolipids. In biosynthetic glycosyl transfers, the common activated monomeric sugar intermediate is a nucleoside diphosphate sugar.
subclass of: Transferase
category: Molecular function

glycosyltransferase activity
type: Class
database: go

Glyoxylate bypass
type: Concept
alternative label: Glyoxylate cycle
comment: Protein involved in the glyoxylate bypass, an alternate route in bacteria, plants, and fungi which bypasses the CO2-evolving steps of the tricarboxylic acid cycle, thus permiting the utilization of fatty acids or acetate, in the form of acetyl-CoA, as sole carbon source, particularly for the net biosynthesis of carbohydrate from fatty acids. The glyoxylate bypass is especially prominent in plant seeds.
subclass of: Biological process
category: Biological process

glyoxylate cycle
type: Class
database: go

Glyoxysome
type: Concept
comment: Protein present in the glyoxysome, a membrane-surrounded plant cell organelle, especially found in germinating seeds, and involved in the breakdown and conversion of fatty acids to acetyl-CoA for the glyoxylate bypass. Since it is also rich in catalase, the glyoxysome may be related to the microbodies or peroxisomes or derived from them.
subclass of: Cellular component
category: Cellular component

glyoxysome
type: Class
database: go

GMP biosynthesis
type: Concept
alternative label: GMP anabolism
alternative label: GMP biosynthetic process
alternative label: GMP formation
alternative label: GMP synthesis
alternative label: Guanosine 5'-monophosphate anabolism
alternative label: Guanosine 5'-monophosphate biosynthetic process
alternative label: Guanosine 5'-monophosphate formation
alternative label: Guanosine 5'-monophosphate synthesis
alternative label: Guanylic acid anabolism
alternative label: Guanylic acid biosynthetic process
alternative label: Guanylic acid formation
alternative label: Guanylic acid synthesis
comment: Protein involved in the synthesis of GMP. GMP is the abbreviation for the nucleotide guanosine 5'-monophosphate.
subclass of: Purine biosynthesis
category: Biological process

GMP biosynthetic process
type: Class
database: go

Golgi apparatus
type: Concept
alternative label: Golgi complex
alternative label: Golgi stack
comment: 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. It has four functionally distinct compartments: cis, medial and trans Golgi stacks, and the trans Golgi network (TGN). The first three are involved in posttranslational modifications of proteins (e.g., N- or O-glycosylation, sulfation, processing of acid hydrolases), while the TGN is involved in sorting the proteins to their final destination (e.g., to lysosomes, to secretory vesicles, or to plasma membrane).
subclass of: Cellular component
category: Cellular component

Golgi apparatus
type: Class
database: go

Gonadal differentiation
type: Concept
comment: Protein involved in gonadal differentiation, the progressive restriction of the developmental potential and increasing specialization of function which takes place during the embryonic development and leads to the formation of gamete-producing glands, such as ovary or testis.
subclass of: Differentiation
category: Biological process

gonadal mesoderm development
type: Class
database: go

Gout
type: Concept
comment: Protein which, if defective, causes gout, a recurrent acute arthritis of peripheral joints caused by the precipitation of monosodium urate crystals in articular cartilage. Gout is usually due to overproduction of uric acid secondary to an inherited abnormality of purine metabolism, but may be a result of urate under-excretion.
subclass of: Disease
category: Disease

GPI-anchor
type: Concept
alternative label: Glycosylphosphatidylinositol anchor
alternative label: Glycosylsphingolipidinositol anchor
comment: Protein bound to the lipid bilayer of a membrane through either a GPI-anchor (glycosylphosphatidylinositol anchor), a complex oligoglycan linked to a phosphatidylinositol group, or a GPI-like-anchor, a similar complex oligoglycan linked to a sphingolipidinositol group, resulting in the attachment of the C-terminus of the protein to the membrane.
subclass of: Glycoprotein
subclass of: Lipoprotein
subclass of: Membrane
category: PTM

obsolete anchored component of membrane
type: Class
database: go

GPI-anchor biosynthesis
type: Concept
alternative label: Glycosylphosphatidylinositol anchor anabolism
alternative label: Glycosylphosphatidylinositol anchor biosynthesis
alternative label: Glycosylphosphatidylinositol anchor biosynthetic process
alternative label: Glycosylphosphatidylinositol anchor formation
alternative label: Glycosylphosphatidylinositol anchor synthesis
alternative label: GPI-anchor anabolism
alternative label: GPI-anchor biosynthetic process
alternative label: GPI-anchor formation
alternative label: GPI-anchor synthesis
comment: Protein involved in the synthesis or the attachment to a protein of a GPI-anchor (glycosylphosphatidylinositol anchor) or a GPI-like-anchor (glycosylsphingolipidinositol anchor), both of which have complex oligoglycan linked to a phospholipidinositol molecule that serves to attach the C-terminus of some extracellular membrane proteins to the lipid bilayer of a membrane. The core glycolipid is composed of a tetraglycan: three mannose units and one glucosamine linked to a phospholipidinositol. The terminal mannose is linked to the protein via an ethanolamine attached to the C-terminal of the mature protein. The core structure is conserved from protozoa to humans. There are, however, marked differences in the glycosyl side chains attached to the core glycolipid. The phospholipid component may be either a phosphatide (two long chain fatty acids attached by ester linkage to glycerol phosphate) or a sphingolipid (a long chain fatty acid attached by amide linkage to a ceramide phosphate). Some yeast and Dictyosteliida synthesize the GPI-like anchor de novo, whereas other organisms may interconvert the lipid components by a "resculpting" process after the anchor is attached to the protein.
subclass of: Biological process
category: Biological process

GPI anchor biosynthetic process
type: Class
database: go

Growth arrest
type: Concept
alternative label: Cell cycle arrest
alternative label: Cellular quiescence
comment: Protein involved in growth arrest, a phenomenon occurring when a cell does not proceed through the cell cycle.
subclass of: Cell cycle
category: Biological process

regulation of cell cycle
type: Class
database: go

Growth factor
type: Concept
comment: Protein which, by binding to a cell-surface receptor, triggers an intracellular signal-transduction pathway leading to differentiation, proliferation, or other cellular response.
subclass of: Molecular function
category: Molecular function

growth factor activity
type: Class
database: go

Growth factor binding
type: Concept
comment: Protein other than a receptor that binds to a cell's growth factor.
subclass of: Molecular function
category: Molecular function

growth factor binding
type: Class
database: go

Growth regulation
type: Concept
alternative label: Regulation of cell growth
comment: Protein involved in growth regulation, which usually implies the control of the rate of division rather than that of the size of an individual cell.
subclass of: Biological process
category: Biological process

GTP-binding
type: Concept
alternative label: Guanosine 5'-triphosphate-binding
alternative label: Guanosine triphosphate-binding
comment: Protein which binds guanosine 5'-triphosphate (GTP), a ribonucleotide guanosine (a purine base guanine linked to the sugar D-ribofuranose) that carries three phosphate groups esterified to the sugar moiety.
subclass of: Nucleotide-binding
category: Ligand

GTP binding
type: Class
database: go

GTPase activation
type: Concept
comment: GTPase-activating protein (GAP) by itself does not hydrolyze GTP but, by binding to a GTPase, accelerates its intrinsic GTPase activity.
subclass of: Molecular function
category: Molecular function

GTPase activator activity
type: Class
database: go

Guanine-nucleotide releasing factor
type: Concept
comment: Protein which catalyzes the release of GDP (guanosine 5'-diphosphate).
subclass of: Molecular function
category: Molecular function

guanyl-nucleotide exchange factor activity
type: Class
database: go

HDL
type: Concept
comment: Protein or apolipoprotein associated with High-Density Lipoproteins (HDL), a class of proteins involved in lipid (cholesterol, phospholipids and triacylglycerol) metabolism in the body fluids. HDL are formed in the liver and are involved in reverse cholesterol transport, the transport of cholesterol from peripherical tissues to the liver. Apolipoproteins are proteins which are specifically associated with lipoproteins, which is not the case for all the proteins associated with HDL or with the other lipoprotein classes.
subclass of: Cellular component
category: Cellular component

high-density lipoprotein particle
type: Class
database: go

Hearing
type: Concept
comment: Protein involved in hearing, the special sense by which an organism is able to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
subclass of: Biological process
category: Biological process

sensory perception of sound
type: Class
database: go

Helical capsid protein
type: Concept
comment: Viral protein that forms a helical capsid to protect the viral genome. Viral helical capsids are about 7-30 nm in diameter and 200-2000 nm long.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

helical viral capsid
type: Class
database: go

Helicase
type: Concept
comment: Protein with an helicase activity. Helicases are ATPases that catalyze the unwinding of double-stranded nucleic acids. They are tightly integrated (or coupled) components of various macromolecular complexes which are involved in processes such as DNA replication, recombination, and nucleotide excision repair, as well as RNA transcription and splicing.
subclass of: ATP-binding
subclass of: Hydrolase
category: Molecular function

helicase activity
type: Class
database: go

Hemagglutinin
type: Concept
comment: Protein which causes agglutination of erythrocytes or other cell types: In viruses, a protein which is responsible for attaching the virus to cell receptors and for initiating infection.
subclass of: Molecular function
category: Molecular function

Heme
type: Concept
alternative label: Haeme
comment: Protein containing at least one heme, an iron atom coordinated to a protoporphyrin IX. In myoglobin and hemoglobin, one of the coordination positions of iron is occupied by oxygen or other ligands, such as carbon monoxide. Hemes are also found in cytochromes of the electron-transport chain where they bind electrons, in reducing peroxides (catalases and peroxidases), and act as terminal components in multienzyme systems involved in hydroxylation. Cytochrome c is the only common heme protein in which the heme is covalently bound.
subclass of: Iron
subclass of: Metal-binding
category: Ligand

Heme biosynthesis
type: Concept
alternative label: Haeme anabolism
alternative label: Haeme biosynthesis
alternative label: Haeme biosynthetic process
alternative label: Haeme formation
alternative label: Haeme synthesis
alternative label: Heme anabolism
alternative label: Heme biosynthetic process
alternative label: Heme formation
alternative label: Heme synthesis
comment: Protein involved in the synthesis of heme, an iron atom coordinated to a protoporphyrin IX.
subclass of: Biological process
category: Biological process

heme biosynthetic process
type: Class
database: go

Hemoglobin-binding
type: Concept
alternative label: Haemoglobin-binding
comment: Protein which binds hemoglobin, a gas-carrying protein found in red blood cells.
subclass of: Ligand
category: Ligand

hemoglobin binding
type: Class
database: go

Hemolymph clotting
type: Concept
alternative label: Haemolymph clotting
alternative label: Hemolymph coagulation
comment: Protein involved in the coagulation of hemolymph, the circulatory fluid of invertebrate animals which is functionally comparable to the blood and lymph of vertebrates.
subclass of: Biological process
category: Biological process

hemolymph coagulation
type: Class
database: go

Hemolysis
type: Concept
alternative label: Haemolysis
comment: Protein involved in hemolysis, the disruption of the integrity of the red cell membrane, thus causing the release of hemoglobin.
subclass of: Cytolysis
category: Biological process

Hemolytic uremic syndrome
type: Concept
alternative label: Hemolytic-uremic syndrome
alternative label: HUS
comment: Protein which, if defective, causes hemolytic uremic syndrome, a disorder characterized by non-immune hemolytic anemia, thrombocytopenia and renal failure. The vast majority of cases are sporadic, occur in young children and are associated with epidemics of diarrhea due to bacterial infections. This typical form of the disease has a good prognosis and death rate is very low. In contrast to typical hemolytic uremic syndrome, atypical forms present without a prodrome of enterocolitis and diarrhea and have a poor prognosis, with frequent development of end-stage renal disease or death.
subclass of: Disease
category: Disease

Hemophilia
type: Concept
alternative label: Haemophilia
comment: Protein which, if defective, causes hemophilia, a genetic disease characterized by uncontrollable bleeding due to a sex-linked recessive deficiency of blood-clotting factor (usually of Factor VIII).
subclass of: Blood coagulation
subclass of: Disease
category: Disease

Hemorrhagic toxin
type: Concept
alternative label: Hemorrhagin
comment: Toxin which induces the leakage of blood components into tissues by damaging endothelial cells or disturbing endothelial cell interactions with the basement membrane. Hemorrhagic toxins are mostly found in snake venoms.
subclass of: Hemostasis impairing toxin
category: Molecular function

Hemostasis
type: Concept
comment: Protein involved in the arrest of bleeding through blood clotting and contraction of blood vessels.
subclass of: Biological process
narrower: Blood coagulation
category: Biological process

hemostasis
type: Class
database: go

Hemostasis impairing toxin
type: Concept
comment: Toxin which interferes with hemostasis regrouping all mechanisms implicated in the cessation of blood loss through damaged vessels. Hence, hemostasis impairing toxins not only interfere with platelet aggregation, the coagulation cascade, fibrinogen depletion, and fibrin clot degradation (fibrinolysis), but also provoke hemorrhage by damaging endothelial cells or disturbing their interaction with the basement membrane. Numerous snake venom families have the capacity to interfere with hemostasis.
subclass of: Toxin
narrower: Hemorrhagic toxin
narrower: Platelet aggregation inhibiting toxin
narrower: Platelet aggregation activating toxin
narrower: Blood coagulation cascade inhibiting toxin
narrower: Blood coagulation cascade activating toxin
narrower: Fibrinolytic toxin
narrower: Fibrinogenolytic toxin
category: Molecular function

Heparan sulfate
type: Concept
comment: Protein containing at least one heparan sulfate, a highly sulfated glycosaminoglycan, closely related to heparin, which consists of repeating units of disaccharides composed of iduronic acid, glucosamine and N-acetylglucosamine.
subclass of: Proteoglycan
category: PTM

Heparin-binding
type: Concept
comment: Protein which binds heparin, a highly sulfated glycosaminoglycan which consists of repeating units of disaccharides composed of D-glucosamine, D-glucuronic acid or L-iduronic acid. This anticoagulant is found in the granules of mast cells.
subclass of: Molecular function
category: Molecular function

heparin binding
type: Class
database: go

Herbicide resistance
type: Concept
alternative label: Resistance to herbicide
comment: Protein that confers, on plants, bacteria or other microorganisms, the ability to withstand herbicide action. Herbicides are chemicals that selectively kill plants. Herbicide resistance occurs usually as a result of mutation or amplification of a gene, e.g. 3-phosphoshikimate 1-carboxyvinyltransferase.
subclass of: Biological process
category: Biological process

response to herbicide
type: Class
database: go

Hereditary hemolytic anemia
type: Concept
alternative label: Hereditary haemolytic anemia
comment: Protein which, if defective, causes hereditary hemolytic anemia, a hereditary disease characterized by the premature destruction of red blood cells.
subclass of: Disease
narrower: Elliptocytosis
narrower: Pyropoikilocytosis
narrower: Congenital dyserythropoietic anemia
category: Disease

Hereditary multiple exostoses
type: Concept
comment: Protein which, if defective, causes hereditary multiple exostoses (EXT). It is an autosomal dominant disease characterized by the formation of cartilage-capped benign tumors (exostoses), developing from the juxtaepiphyseal regions of the long bones and often accompanied by skeletal deformities and short stature.
subclass of: Disease
category: Disease

Hereditary nonpolyposis colorectal cancer
type: Concept
alternative label: HNPCC
alternative label: Lynch's syndrome
comment: Protein which, if defective, causes hereditary non-polyposis colorectal cancer (HNPCC), also known as Lynch's syndrome. It is an autosomal dominant syndrome which confers an increased risk for colorectal and endometrial cancers as well as others tumors. Clinically, HNPCC is often divided into two subgroups: type I, characterized by a hereditary predisposition to colorectal cancer, a young age of onset, and carcinoma observed in the proximal colon; type II, characterized by an increased risk for cancers in certain tissues such as the uterus, ovary, breast, stomach, small intestine, skin, and larynx in addition to the colon.
subclass of: Disease
category: Disease

Hereditary spastic paraplegia
type: Concept
alternative label: HSP
comment: Protein which, if defective, causes hereditary spastic paraplegias (HSPs). HSPs are a diverse class of hereditary degenerative spinal cord disorders characterized by a slow, gradual, progressive weakness and spasticity (stiffness) of the legs. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. Rate of progression and the severity of symptoms are quite variable.
subclass of: Neurodegeneration
category: Disease

Hermansky-Pudlak syndrome
type: Concept
alternative label: HPS
comment: Protein which, if defective, causes Hermansky-Pudlak syndrome, a rare autosomal recessive disorder characterized by oculocutaneous albinism and storage pool deficiency due to an absence of platelet dense bodies. Lysosomal ceroid lipofuscinosis, pulmonary fibrosis and granulomatous colitis are occasional manifestations of the disease.
subclass of: Albinism
category: Disease

Heterocyst
type: Concept
comment: Protein which is implicated in heterocyst formation. A heterocyst is a differentiated cyanobacterial cell that carries out nitrogen fixation. The heterocysts function as the sites for nitrogen fixation under aerobic conditions. They are formed in response to a lack of fixed nitrogen (NH4 or NO3). The morphological differentiation is accompanied by biochemical alterations. The mature heterocysts contain no functional photosystem II and cannot produce oxygen. Instead, they contain only photosystem I, which enables them to carry out cyclic photophosphorylation and ATP regeneration. These changes provide the appropriate conditions for the functioning of the oxygen-sensitive nitrogenase.
subclass of: Developmental stage
category: Developmental stage

heterocyst development
type: Class
database: go

Heterotaxy
type: Concept
alternative label: Heterotaxia
alternative label: Situs ambiguous
alternative label: Situs ambiguus
alternative label: Visceral heterotaxy
comment: Protein which, if defective, causes heterotaxy, a broad group of disorders caused by failure to correctly establish left-right patterning during embryogenesis with consequent abnormal segmental arrangements of cardiac chambers, vessels, lungs, and/or abdominal organs. Heterotaxy include complex cardiac malformations, situs inversus, situs ambiguus, isomerism. Situs inversus indicates complete left-right reversal of organ position and is not usually associated with structural anomalies. Situs ambiguus is an abnormal arrangement of viscera almost invariably associated with complex cardiovascular malformations as well as anomalies of the spleen and the gastrointestinal system. Isomerism is a defect in asymmetry of paired organs that usually have distinct right and left forms, but in this condition, are mirror images.
subclass of: Disease
category: Disease

Hibernation
type: Concept
comment: Protein involved in the process of hibernation. Hibernation is a state of inactivity in an animal brought about by short day lengths, cold temperatures and limitations of food.
subclass of: Biological process
category: Biological process

hibernation
type: Class
database: go

Hirschsprung disease
type: Concept
alternative label: HSCR
comment: Hirschsprung's disease (HSCR); a genetic disorder of neural crest development characterized by the absence of intramural ganglion cells in the hindgut; often resulting in intestinal obstruction.
subclass of: Disease
category: Disease

Histidine biosynthesis
type: Concept
alternative label: Histidine anabolism
alternative label: Histidine biosynthetic process
alternative label: Histidine formation
alternative label: Histidine synthesis
comment: Protein involved in the synthesis of the weakly basic amino acid histidine.
subclass of: Amino-acid biosynthesis
category: Biological process

histidine biosynthetic process
type: Class
database: go

Histidine metabolism
type: Concept
alternative label: Histidine metabolic process
comment: Protein involved in the biochemical reactions with the weakly basic amino acid histidine.
subclass of: Biological process
category: Biological process

histidine metabolic process
type: Class
database: go

Holoprosencephaly
type: Concept
comment: A clinically variable and genetically heterogeneous malformation in which the developing forebrain fails to correctly separate into right and left hemispheres. In its most severe form (alobar holoprosencephaly), the forebrain consists of a single ventricle, and midbrain structures may be malformed as well. In the most extreme cases, anophthalmia or cyclopia is evident along with a congenital absence of the mature nose. In milder forms (semilobar or lobar holoprosencephaly), rudimentary midline structures are present. The less severe form features facial dysmorphia characterized by ocular hypertelorism, defects of the upper lip and/or nose, and absence of the olfactory nerves or corpus callosum. The majority of cases are sporadic, although families with both autosomal dominant and autosomal recessive holoprosencephaly have been described.
subclass of: Disease
category: Disease

Homeobox
type: Concept
alternative label: Homeodomain
comment: 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.
subclass of: Domain
category: Domain

Hormone
type: Concept
comment: Protein which functions as a hormone, a biochemical substance secreted by specialized cells that affects the metabolism or behavior of other cells which possess functional receptors for the hormone. Hormones may be hydrophilic, like insulin, in which case the receptors are on the cell surface, or lipophilic, like the steroids, where the receptor can be intracellular.
subclass of: Molecular function
narrower: Thyroid hormone
category: Molecular function

hormone activity
type: Class
database: go

Host cell inner membrane
type: Concept
alternative label: Host inner membrane
comment: Protein found in or associated with the prokaryotic host cell inner membrane, a selectively permeable membrane which separates the host cytoplasm from the host periplasm in prokaryotes with 2 membranes.
subclass of: Host cell membrane
category: Cellular component

host cell plasma membrane
type: Class
database: go

Host cell junction
type: Concept
comment: Protein found in or associated with a host cell junction, a host cell-host cell or host cell-host extracellular matrix contact within a tissue of a host multicellular organism, especially abundant in host epithelia. In vertebrates, there are three major types of cell junctions: anchoring junctions (e.g. adherens junctions), communicating junctions (e.g. gap junctions) and occluding junctions (e.g. tight junctions).
subclass of: Cellular component
category: Cellular component

host cell junction
type: Class
database: go

Host cell lysis by virus
type: Concept
comment: Viral protein involved in the lysis of the host cell allowing the release of mature, newly formed virions. Viruses use different way to lyse their host cell. They can express viroporins as Adenoviridae or Picornaviridae do in the late phase of infection. Phycodnaviridae for their part seem to express lytic phospholipids. In dsDNA prokaryotic viruses, lysis-specific proteins are expressed: a holin, which permeabilizes the inner membrane and an endolysin which then gains access to and degrades the host peptidoglycans. Some bacterioviruses express a signal-containing endolysin and thus do not need the holin function.
subclass of: Cytolysis
subclass of: Viral release from host cell
category: Biological process

viral release from host cell by cytolysis
type: Class
database: go

Host cell membrane
type: Concept
alternative label: Host cytoplasmic membrane
alternative label: Host plasmalemma
alternative label: Host plasma membrane
comment: Protein found in or associated with the host cytoplasmic membrane, a selectively permeable membrane which separates the cytoplasm from its surroundings. Known as the host cell inner membrane in prokaryotes with 2 membranes.
subclass of: Host membrane
narrower: Host cell inner membrane
category: Cellular component

Host cell outer membrane
type: Concept
alternative label: Host outer membrane
comment: Protein found in or associated with the prokaryotic cell outer membrane, a selectively permeable membrane which separates the prokaryotic periplasm from its surroundings in prokaryotes with 2 membranes. Traditionally only Gram-negative bacteria were thought of as having an outer membrane, but recent work has shown some Actinobacteria, including Mycobacterium tuberculosis, as well as at least 1 archaea (Ignicoccus hospitalis) have a cell outer membrane.
subclass of: Host membrane
category: Cellular component

Host cell projection
type: Concept
alternative label: Host cell protrusion
comment: Protein found in or associated with a host cell projection, a host cell protrusion such as pseudopodium, filopodium, lamellipodium, growth cone, flagellum, acrosome, axon, pili or bacterial comet tail. These membrane-cytoskeleton-coupled processes are involved in many biological functions, such as host cell motility, cancer-cell invasion, endocytosis, phagocytosis, exocytosis, pathogen infection, neurite extension and cytokinesis.
subclass of: Cellular component
category: Cellular component

host cell projection
type: Class
database: go

Host cell receptor for virus entry
type: Concept
alternative label: Viral receptor activity
comment: Cell surface protein used by a virus as an attachment and entry receptor. In some cases, binding to a cellular receptor is not sufficient for infection: an additional cell surface molecule, or coreceptor, is required for entry. Some viruses are able to use different receptors depending on the target cell type. In prokaryotic viruses, cell receptor for virus entry can also be localized on host outer membrane, pilus or flagellum.
subclass of: Receptor
category: Molecular function

virus receptor activity
type: Class
database: go

Host cytoplasm
type: Concept
comment: Protein found in the host cytoplasm, the content of a host cell within the plasma membrane and, in eukaryotics cells, surrounds the host nucleus.
subclass of: Cellular component
narrower: Host cytoskeleton
category: Cellular component

host cell cytoplasm
type: Class
database: go

Host cytoplasmic vesicle
type: Concept
comment: Protein found in or associated with host cytoplasmic vesicles, which mediate vesicular transport among the organelles of host secretory and endocytic systems.
subclass of: Cellular component
category: Cellular component

host cell cytoplasmic vesicle
type: Class
database: go

Host cytoskeleton
type: Concept
comment: Protein which is a component or which is associated with the host cytoskeleton, a dynamic three-dimensional structure that fills the host cytoplasm of eukaryotic cells. It is responsible for cell movement, cytokinesis, and the organization of the organelles or organelle-like structures within the host cell.
subclass of: Host cytoplasm
category: Cellular component

host cytoskeleton
type: Class
database: go

Host endoplasmic reticulum
type: Concept
comment: Protein whose subcellular location is the host endoplasmic reticulum (ER), which is an extensive network of membrane tubules, vesicles and flattened cisternae (sac-like structures) found throughout the eukaryotic host cell, especially those responsible for the production of hormones and other secretory products.
subclass of: Cellular component
narrower: Host microsome
category: Cellular component

host cell endoplasmic reticulum
type: Class
database: go

Host endosome
type: Concept
comment: Protein found in or associated with host endosomes, which are highly dynamic membrane systems involved in transport within the host cell, they receive endocytosed host cell membrane molecules and sort them for either degradation or recycling back to the host cell surface. They also receive newly synthesised proteins destined for host vacuolar/lysosomal compartments.
subclass of: Cellular component
category: Cellular component

host cell endosome
type: Class
database: go

Host G2/M cell cycle arrest by virus
type: Concept
comment: Viral protein involved in the modulation of host cell cycle by inhibiting the G2/M transition. A variety of viruses have been associated with G2/M arrest, including some DNA viruses, some RNA viruses and retroviruses but the mechanisms by which arrest is achieved greatly differs between those viruses.
subclass of: Modulation of host cell cycle by virus
category: Biological process

suppression by virus of G2/M transition of host mitotic cell cycle
type: Class
database: go

Host gene expression shutoff by virus
type: Concept
comment: Viral protein which prevents host gene expression by blocking for example host transcription, mRNA export or translation. This gives virus transcripts a competitive edge to use the hijacked translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response.
subclass of: Host-virus interaction
narrower: Bacterial host gene expression shutoff by virus
narrower: Eukaryotic host gene expression shutoff by virus
category: Biological process

suppression by virus of host gene expression
type: Class
database: go

Host Golgi apparatus
type: Concept
alternative label: Host apparatus golgiensis
alternative label: Host complexus golgiensis
alternative label: Host Golgi
alternative label: Host Golgi complex
comment: Protein found in the host Golgi apparatus, a series of flattened, cisternal membranes and similar vesicles usually arranged in close apposition to each other to form stacks. In mammalian cells, the host Golgi apparatus is juxtanuclear, often pericentriolar. The stacks are connected laterally by tubules to create a perinuclear ribbon structure, the 'Golgi ribbon'. In plants and lower animal cells, the host Golgi exists as many copies of discrete stacks dispersed throughout the host cytoplasm. It is a polarized structure with, in most higher eukaryotic cells, a cis-face associated with a tubular reticular network of membranes facing the endoplasmic reticulum, the cis-Golgi network (CGN), a medial area of disk-shaped flattened cisternae, and a trans-face associated with another tubular reticular membrane network, the trans-Golgi network (TGN) directed toward the host plasma membrane and compartments of the host endocytic pathway.
subclass of: Cellular component
category: Cellular component

host cell Golgi apparatus
type: Class
database: go

Host lipid droplet
type: Concept
alternative label: Host adiposome
alternative label: Host lipid bodies
alternative label: Host lipid body
alternative label: Host lipid particle
alternative label: Host monolayer-surrounded lipid storage body
alternative label: Host oil bodies
alternative label: Host oil body
alternative label: Host oleosome
alternative label: Host spherosome
comment: Protein characteristic of host lipid droplet, a dynamic cytoplasmic host organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. They may play a role in host lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.
subclass of: Cellular component
category: Cellular component

host cell lipid droplet
type: Class
database: go

Host lysosome
type: Concept
comment: Protein found in the host lysosome, a membrane-limited organelle present in all eukaryotic cells, which contains a large number of hydrolytic enzymes that are used for degrading almost any kind of cellular constituent, including entire organelles. The mechanisms responsible for delivering cytoplasmic cargo to the host lysosome/vacuole are known collectively as autophagy and play an important role in the maintenance of homeostasis.
subclass of: Cellular component
category: Cellular component

host cell lysosome
type: Class
database: go

Host membrane
type: Concept
comment: Protein which is membrane-bound or membrane-associated with the host membrane, a lipid bilayer which surrounds host enclosed spaces and compartments. This selectively permeable structure is essential for effective separation of a host cell or organelle from its surroundings.
subclass of: Membrane
narrower: Host cell membrane
narrower: Host cell outer membrane
narrower: Host mitochondrion inner membrane
narrower: Host mitochondrion outer membrane
category: Cellular component

host cell membrane
type: Class
database: go

Host microsome
type: Concept
comment: Protein found in host microsomes, which are a heterogenous set of vesicles 20-200 nm in diameter and formed from the host endoplasmic reticulum when host cells are disrupted.
subclass of: Host endoplasmic reticulum
category: Cellular component

host intracellular membrane-bounded organelle
type: Class
database: go

Host mitochondrion
type: Concept
comment: Protein encoded by or localized in the host mitochondrion, a semiautonomous, self-reproducing organelle that occurs in the cytoplasm of all cells of most, but not all, host eukaryotes. Each host mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. They are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP.
subclass of: Cellular component
narrower: Host mitochondrion inner membrane
narrower: Host mitochondrion outer membrane
category: Cellular component

host cell mitochondrion
type: Class
database: go

Host mitochondrion inner membrane
type: Concept
alternative label: Host inner mitochondrial membrane
alternative label: Host mitochondrial inner membrane
comment: Protein found in or associated with the host mitochondrion inner membrane, the membrane which separates the host mitochondrial matrix from the host mitochondrial intermembrane space.
subclass of: Host membrane
subclass of: Host mitochondrion
category: Cellular component

host cell mitochondrial inner membrane
type: Class
database: go

Host mitochondrion outer membrane
type: Concept
alternative label: Host mitochondrial outer membrane
alternative label: Host outer mitochondrial membrane
comment: Protein found in or associated with the host mitochondrion outer membrane, the host mitochondrial membrane facing the host cytoplasm.
subclass of: Host membrane
subclass of: Host mitochondrion
category: Cellular component

host cell mitochondrial outer membrane
type: Class
database: go

Host mRNA suppression by virus
type: Concept
comment: Viral protein involved in suppressing host mRNAs expression to maximize expression of viral mRNAs. Decimating cellular mRNAs eventually leads to shutoff of host proteins expression and gives virus transcripts a competitive edge for access to the cellular translation machinery. Preventing the expression of host proteins is also a strategy to counteract the antiviral response. Suppression of host mRNA can be performed by interfering with host pre-mRNA processing function (splicing or polyadenylation), by degrading mRNAs or blocking their export from the nucleus to the cytoplasm.
subclass of: Eukaryotic host gene expression shutoff by virus
narrower: Inhibition of host mRNA nuclear export by virus
narrower: Inhibition of host pre-mRNA processing by virus
narrower: Decay of host mRNAs by virus
category: Biological process

Host nucleus
type: Concept
comment: Protein located in the host nucleus, which is the most obvious organelle in any host eukaryotic cell. It is a membrane-bound organelle and is surrounded by double membranes. It communicates with the surrounding cytosol via numerous nuclear pores.
subclass of: Cellular component
category: Cellular component

host cell nucleus
type: Class
database: go

Host periplasm
type: Concept
alternative label: Host periplasmic space
comment: Protein located in the host periplasm, the space between the inner and outer membrane in host Gram-negative bacteria. In Gram-positive bacteria a smaller periplasmic space is found between the inner membrane and the peptidoglycan layer. Also used for the host intermembrane spaces of host fungi and host organelles.
subclass of: Cellular component
category: Cellular component

host cell periplasmic space
type: Class
database: go

Host synapse
type: Concept
comment: Protein located in the host synapse, the communicating cell-cell junctions that allow signals to pass from a host nerve cell to a host target cell. In a chemical synapse, the signal is carried by a neurotransmitter which diffuses across a narrow synaptic cleft and activates a receptor on the postsynaptic membrane of the target cell.
subclass of: Cellular component
category: Cellular component

host cell synapse
type: Class
database: go

Host thylakoid
type: Concept
comment: Protein located in or on the host thylakoid, a membranous cellular structure containing the photosynthetic pigments, reaction centers and electron-transport chain. In host chloroplast, thylakoids stack up to form the grana or stay as single cisternae and interconnect the grana. Thylakoid, where photosynthesis occurs, are found in chloroplasts, cyanelles and in photosynthetic bacteria where they are the extensive invaginations of the plasma membrane.
subclass of: Cellular component
category: Cellular component

host thylakoid
type: Class
database: go

Host-virus interaction
type: Concept
comment: Viral or cellular protein involved in a host-virus interaction. Viruses interact with many cellular pathways to achieve their replication cycle. Entry into the host cell, transport to the viral replication sites or viral exit from the host cell are all steps that require specific interactions between the virus and its host. Additionally, the evasion from the host immune response requires a lot of viral proteins to associate with and inhibit cellular proteins with antiviral functions.
subclass of: Biological process
narrower: Viral immunoevasion
narrower: Activation of host autophagy by virus
narrower: Activation of host NF-kappa-B by virus
narrower: Inhibition of host autophagy by virus
narrower: Inhibition of host NF-kappa-B by virus
narrower: Modulation of host cell apoptosis by virus
narrower: Modulation of host cell cycle by virus
narrower: Modulation of host chromatin by virus
narrower: Modulation of host ubiquitin pathway by virus
narrower: Viral attachment to host cell
narrower: Microtubular inwards viral transport
narrower: Viral budding via the host ESCRT complexes
narrower: Microtubular outwards viral transport
narrower: Host gene expression shutoff by virus
narrower: DNA end degradation evasion by virus
narrower: CRISPR-cas system evasion by virus
narrower: Restriction-modification system evasion by virus
narrower: Evasion of bacteria-mediated translation shutoff by virus
narrower: Superinfection exclusion
category: Biological process

Hyaluronic acid
type: Concept
comment: Protein which binds hyaluronic acic, an acidic glycosaminoglycan which consists of repeating units of the disaccharide composed of D-glucuronic acid and N-acetyl-D-glucosamine. This linear polymer is present in cell coats and in the extracellular ground substance of the connective tissues of vertebrates; it also occurs in the synovial fluid in joints and in the vitreous humor of the eye.
subclass of: Ligand
category: Ligand

hyaluronic acid binding
type: Class
database: go

Hybridoma
type: Concept
comment: Protein sequenced from a hybridoma, an artificially produced hybrid cell line created by fusion of a lymphocyte and a myeloma cell. These cells can multiply indefinitely in culture and produce monoclonal antibodies.
subclass of: Technical term
category: Technical term

Hydrogen ion transport
type: Concept
alternative label: Hydrogen cation transport
alternative label: Proton transport
comment: Protein involved in the transport of hydrogen ions across a membrane. Used to power processes such as ATP synthesis and bacterial flagellar rotation.
subclass of: Ion transport
narrower: CF(0)
category: Biological process

proton transmembrane transport
type: Class
database: go

Hydrogen peroxide
type: Concept
comment: Protein involved in hydrogen peroxide (H(2)O(2)) decomposition, e.g., catalase. H(2)O(2) is generated by the body as a byproduct of aerobic cellular respiration.
subclass of: Peroxidase
subclass of: Biological process
category: Biological process

hydrogen peroxide catabolic process
type: Class
database: go

Hydrogenosome
type: Concept
comment: Protein characteristic of the hydrogenosome, a redox organelle of anaerobic unicellular eukaryotes which contains hydrogenase and produces hydrogen and ATP by glycolysis. They are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Most hydrogenosomes lack a genome, but some like that of the anaerobic ciliate Nyctotherus ovalis, have retained a rudimentary genome.
subclass of: Cellular component
category: Cellular component

hydrogenosome
type: Class
database: go

Hydrolase
type: Concept
comment: Enzyme which catalyzes hydrolysis reaction, i.e. the addition of the hydrogen and hydroxyl ions of water to a molecule with its consequent splitting into two or more simpler molecules.
subclass of: Molecular function
narrower: Aspartyl esterase
narrower: Glycosidase
narrower: Helicase
narrower: Nuclease
narrower: Protease
narrower: Serine esterase
narrower: Protein phosphatase
category: Molecular function

hydrolase activity
type: Class
database: go

Hydroxylation
type: Concept
alternative label: Hydroxylated
comment: Protein which is posttranslationally modified by the attachment of at least one hydroxyl (-OH) group.
subclass of: PTM
category: PTM

Hyperlipidemia
type: Concept
comment: Protein which, if defective, causes hyperlipidemia, a condition characterized by the elevation of lipids in the bloodstream. There are different types of hyperlipidemias: type I (lipoprotein lipase deficiency), IIa (hypercholesterolemia; LDL receptor deficiency), IIb (combined hyperlipidemia), III (dysbetalipoproteinemia), IV (hypertriglyceridemia) and V (mixed hyperlipidemia).
subclass of: Disease
category: Disease

Hypersensitive response
type: Concept
alternative label: HR
comment: Protein involved in hypersensitive response, a complex and early defense response that causes necrosis and cell death to restrict the growth of a pathogen. Local and systemic biochemical changes include generation of active oxygen species (oxidative burst), cell death, overproduction of lignin-related materials, and the induction of certain proteins such as pathogen related (PR) proteins.
subclass of: Plant defense
category: Biological process

plant-type hypersensitive response
type: Class
database: go

Hypersensitive response elicitation
type: Concept
comment: Proteins involved in hypersensitive response (HR) elicitation. HR is a rapid defense-associated programmed cell death of plant cells at the site of invasion.
subclass of: Biological process
category: Biological process

modulation by symbiont of host defense-related programmed cell death
type: Class
database: go

Hypogonadotropic hypogonadism
type: Concept
alternative label: HH
alternative label: Idiopathic hypogonadotropic hypogonadism
alternative label: IHH
alternative label: Isolated hypogonadotropic hypogonadism
comment: Protein which, if defective, causes hypogonadotropic hypogonadism, a disorder characterized by a deficiency of the pituitary secretion of follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Affected individuals present with absent or impaired sexual development due to sex-steroid-hormone deficiency, low serum levels of the pituitary gonadotropins FSH and LH, and infertility.
subclass of: Disease
category: Disease

Hypotensive agent
type: Concept
alternative label: Antihypertensive agents
comment: Protein which can cause hypotension, i.e. low blood pressure or a sudden drop in blood pressure.
subclass of: Molecular function
category: Molecular function

regulation of blood pressure
type: Class
database: go

Hypotrichosis
type: Concept
comment: Protein which, if defective, causes hypotrichosis, a condition characterized by reduced pilosity over the body and scalp (with sparse, thin, and short hair).
subclass of: Disease
category: Disease

Hypusine
type: Concept
comment: Protein which is posttranslationally modified on at least one lysine residue to form hypusine (N-epsilon-(4-aminobutyl)lysine). This spermidine-dependent reaction is catalyzed by deoxyhypusine synthase and deoxyhypusine hydroxylase. eIF-5A is the only protein in eukaryotes and archaebacteria known to contain hypusine.
subclass of: PTM
category: PTM

Hypusine biosynthesis
type: Concept
alternative label: Hypusine anabolism
alternative label: Hypusine biosynthetic process
alternative label: Hypusine formation
alternative label: Hypusine synthesis
comment: Protein involved in the synthesis of hypusine, an amino acid formed by the two posttranslational steps in the modification of a lysine: (i) deoxyhypusine synthase catalyzes the transfer of a 4-aminobutyl moiety from spermidine to a specific lysine residue to form a deoxyhypusine residue, N-epsilon-(4-aminobutyl)lysine, and (ii) deoxyhypusine hydroxylase catalyzes the hydroxylation of the deoxyhypusine residue to form hypusine (N-epsilon-(4-amino-2-hydroxybutyl)lysine).
subclass of: Biological process
category: Biological process

peptidyl-lysine modification to peptidyl-hypusine
type: Class
database: go

Ice nucleation
type: Concept
comment: Protein which promotes the nucleation of ice. The proteins catalyzes the formation of ice crystals in extracellular fluid at relatively high temperatures (up to -2 degrees Celsius) to protect the organism from damage by intracellular ice formation.
subclass of: Molecular function
category: Molecular function

ice binding
type: Class
database: go

Ichthyosis
type: Concept
comment: Protein which, if defective, causes ichthyosis, any of a group of cutaneous disorders characterized by increased or aberrant keratinization and resulting in non-inflammatory scaling of the skin. Most ichthyoses are genetically determined, while some may be acquired and develop in association with various systemic diseases or be a prominent feature in certain genetic syndromes.
subclass of: Disease
category: Disease

IFIT mRNA restriction evasion by virus
type: Concept
comment: Viral protein allowing host innate defense evasion by methylating the first and second ribonucleotide of viral mRNAs (cap1 and cap2). These methylations allow viral RNA to escape cellular antiviral process mediated by host IFIT proteins which degrade non cap1-methylated mRNAs. Also prevents IFIH1/MDA5 sensor activation by cap0 mRNAs, which would trigger interferon beta synthesis.
subclass of: Viral transcription
category: Biological process

viral mRNA cap methylation
type: Class
database: go

IgA-binding protein
type: Concept
comment: Protein binding to immunoglobulin A, the major class of antibodies found in external secretions such as saliva, tears, gastric fluid, milk and mucosal secretions.
subclass of: Molecular function
category: Molecular function

IgA binding
type: Class
database: go

IgE-binding protein
type: Concept
comment: Protein binding to immunoglobulin E, the antibody class involved in local inflammatory reactions, reactions to parasites, and also in allergic responses.
subclass of: Molecular function
category: Molecular function

IgE binding
type: Class
database: go

IgG-binding protein
type: Concept
comment: Protein binding to immunoglobulin G, the main type of immunoglobulin produced towards the end of a primary immune response and in a secondary response.
subclass of: Molecular function
category: Molecular function

IgG binding
type: Class
database: go

Immunity
type: Concept
alternative label: Immune response
comment: Protein involved in immunity, any immune system process that functions in the response of an organism to a potential internal or invasive threat. The vertebrate immune system is formed by the innate immune system (composed of phagocytes, complement, antimicrobial peptides, etc) and by the adaptive immune system which consists of T- and B-lymphocytes.
subclass of: Biological process
narrower: Innate immunity
narrower: MHC I
narrower: Adaptive immunity
category: Biological process

immune system process
type: Class
database: go

Immunoglobulin
type: Concept
alternative label: Antibody
comment: A glycoprotein produced in membrane-bound or secreted form by B lymphocytes. The basic structural unit of an immunoglobulin (Ig) is composed of two identical covalently linked heavy chains and two identical light chains. Both the heavy chains and light chains contain a series of repeating homologous structural units called Ig domains. The N-terminal variable regions of the heavy and light chains form the antigen binding sites, whereas the C-terminal constant regions of the heavy chains interact with other molecules in the immune system. The membrane-bound antibodies serve as receptors that mediate the antigen-triggered activation of B cells. Secreted antibodies function as mediators of specific humoral immunity by engaging various effector mechanisms that serve to eliminate the bound antigen.
subclass of: Adaptive immunity
subclass of: Cellular component
category: Cellular component

immunoglobulin complex
type: Class
database: go

Immunoglobulin domain
type: Concept
alternative label: Immunoglobulin fold
comment: A globular structural motif found in many proteins of the immune system, including immunoglobulins (Igs), T cell receptors (TCRs) and major histocompatibility complex (MHC) molecules. Ig domains are approximately 110 amino acid residues in length, include an internal disulfide bond, and contain two layers of beta-pleated sheets, each layer composed of three to five strands of antiparallel polypeptide chains. Ig domains are classified as V-like or C-like on the basis of closest homology to either Ig V or C domains.
subclass of: Domain
category: Domain

Inflammasome
type: Concept
alternative label: ASC focus
alternative label: ASC speck
comment: Component of the inflammasome complex involved in innate immunity and inflammation. Inflammasomes are supramolecular micron-sized complexes that assemble in the cytosol adjacent to the nucleus in response to pathogens and other damage-associated signals. The core of inflammasomes consists of at least 2 components: a signal sensor and an effector inflammatory caspase (mostly CASP1). However, most inflammasomes contain a third element, an adaptor (often ASC/PYCARD). In response to a danger signal, the sensor homooligomerizes and interacts with the adaptor that polymerizes and forms a platform to recruit caspase precursors. This results in increased local concentration of the enzyme, leading to trans-autocleavage and activation. Active caspases process proinflammatory IL1B and IL18 cytokine precursors, which are then secreted in the extracellular milieu and induce inflammatory responses. In adaptor-independent inflammasomes, the sensor directly recruits the caspase. Additional proteins may interaction with the core complex. Inflammasomes also induce pyroptosis, an inflammatory form of programmed cell death.
subclass of: Cytoplasm
category: Cellular component

inflammasome complex
type: Class
database: go

Inflammatory response
type: Concept
alternative label: Response to inflammation
comment: 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.
subclass of: Biological process
narrower: Pyrogen
category: Biological process

inflammatory response
type: Class
database: go

Inhibition of eukaryotic host transcription initiation by virus
type: Concept
comment: Viral protein involved in the disruption of the host transcriptional machinery. Viruses have evolved ways of interacting with the cellular preinitiation complex (PIC) to shutoff host transcription initiation. For example, the TATA binding protein and TFIIH are targeted by some viral proteins and thus cannot assemble properly to form a functional PIC.
subclass of: Eukaryotic host transcription shutoff by virus
category: Biological process

suppression by virus of host transcription initiation from RNA polymerase II promoter
type: Class
database: go

Inhibition of eukaryotic host translation factors by virus
type: Concept
comment: Viral protein that inhibits or degrades host translation initiation factor(s). Viruses have evolved ways of interacting with the cellular translational machinery to shutoff host gene expression. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. Some viruses are known to cleave host translation initiation factors like EIF3 or EIF4G, while others achieve translation inhibition by promoting dephosphorylation of some host translation initiation factors or their binding partners.
subclass of: Eukaryotic host translation shutoff by virus
category: Biological process

suppression by virus of host translation initiation
type: Class
database: go

Inhibition of host adaptive immune response by virus
type: Concept
comment: Viral protein involved in the evasion of host adaptive immune response. Upon infection, the innate immune system provides mechanisms for the rapid sensing and elimination of viruses. Adaptive immunity has evolved to provide a broader and more finely tuned repertoire of recognition for both self- and nonself-antigens. A lot of viruses escape the adaptive immune response by different mechanisms including interference with the presentation of antigenic peptides at the surface of infected cells.
subclass of: Viral immunoevasion
narrower: Inhibition of host TAP by virus
narrower: Inhibition of host tapasin by virus
narrower: Inhibition of host MHC class I molecule presentation by virus
narrower: Inhibition of host MHC class II molecule presentation by virus
narrower: Inhibition of host proteasome antigen processing by virus
category: Biological process

suppression by virus of host adaptive immune response
type: Class
database: go

Inhibition of host apoptosis by viral BCL2-like protein
type: Concept
comment: Viral protein sharing sequence similarity with host BCL2 protein. Cellular BCL2 family members are divided in two groups, some having anti-apoptotic activity (such as BCL2 itself) while others have pro-apoptotic function (such as BAX). If the level of proapoptotic members are higher than inhibitors, then the cell undergoes apoptosis. So far, all viral homologues display anti-apoptotic activity.
subclass of: Modulation of host cell apoptosis by virus
category: Biological process

suppression by virus of host apoptotic process
type: Class
database: go

Inhibition of host apoptosis by viral FLIP-like protein
type: Concept
comment: Viral protein sharing sequence similarity with host FLIPs (FLICE-inhibitory proteins). Cellular FLIPs play an essential role in apoptosis functioning as a link between cell survival and cell death pathways . Viral FLIPs inhibit apoptosis by interfering with death receptor signaling.
subclass of: Modulation of host cell apoptosis by virus
category: Biological process

Inhibition of host autophagy by virus
type: Concept
comment: Viral protein involved in the inhibition of host autophagy. Autophagy is a major intracellular pathway in the delivery of cytoplasmic material to lysosomes for degradation. It is also essential for the removal of pathogenic protein aggregates from the cell during infection. Several viruses including influenza and HIV-1 block autophagosome maturation by interacting with and inhibiting host Beclin-1, an essential protein playing a central role in autophagy.
subclass of: Host-virus interaction
category: Biological process

suppression by virus of host autophagy
type: Class
database: go

Inhibition of host caspases by virus
type: Concept
comment: Viral protein involved in the evasion of host cell apoptosis by inhibiting host caspases. Many viruses from diverse families have evolved mechanisms to evade or delay cell death by suppressing the activity of cytoplasmic proteases termed caspases which have a central role in apoptosis induction.
subclass of: Modulation of host cell apoptosis by virus
category: Biological process

Inhibition of host chemokines by virus
type: Concept
comment: Viral protein involved in the evasion of host immune response by inhibiting chemokines. Chemokines have several roles including Th1/Th2 differentiation, T_cell costimulation, or promotion of leukocyte migration. Due to the importance of chemokines in immunity, viruses have evolved mechanisms to counter the chemokine network. They encode chemokine-like proteins, chemokine receptors, or chemokine-binding proteins to inhibit cellular chemokines.
subclass of: Viral immunoevasion
category: Biological process

evasion of host immune response via modulation of host cytokine network
type: Class
database: go

Inhibition of host complement factors by virus
type: Concept
comment: Viral protein involved in the evasion of host humoral response by inhibiting the complement factors. The activation of complement involves the sequential proteolyis of proteins to generate enzymes with catalytic activities. The biological functions of the complement include opsonization, inflammation, lysis of immune complexes, or enhancement of the humoral immune response. Some herpesviruses, poxviruses and retroviruses mimic or interact with complement regulatory proteins to block complement activation and neutralization of virus particles.
subclass of: Viral immunoevasion
category: Biological process

suppression by virus of host complement activation
type: Class
database: go

Inhibition of host DNA replication by virus
type: Concept
comment: Viral protein that blocks host DNA replication without inhibiting host transcription or translation. Inhibiting host replication provides an advantage during the virus life cycle by reducing or eliminating competing host macromolecular synthesis. Bacteriophage N4 for example is known to shut off the host DNA replication while the host genome remains structurally intact. Bacteriophage lambda prevents host DNA replication initiation and Staphylococcus bacteriophages target the replicative DNA polymerase processivity clamp and the helicase.
subclass of: Modulation of host cell cycle by virus
category: Biological process

inhibition of host DNA replication by virus
type: Class
database: go

Inhibition of host IKBKE by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defenses by inhibiting the IKBKE/IKK-epsilon kinase. Upon viral infection, the DDX58/RIG-I or IFIH1/MDA5 receptors recognize foreign material and transmit the signal to downstream components MAVS and IKBKE. In turn, the IKBKE kinase phosphorylates and activates IRF3 and/or IRF7. Once phosphorylated, IRF3 and IRF7 translocate into the nucleus to drive transcription of interferons. Several viruses including arenaviruses or ebola virus interact directly with and inhibit IKBKE/IKK-epsilon to prevent IRFs activation.
subclass of: Inhibition of host RLR pathway by virus
category: Biological process

suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity
type: Class
database: go

Inhibition of host innate immune response by virus
type: Concept
comment: Viral protein involved in the evasion of host innate immune response. Upon viral infection, the innate immune system initially defends the host in a non-specific manner. Many viral proteins interact with and inhibit components the host innate system to replicate more efficiently.
subclass of: Viral immunoevasion
narrower: Inhibition of host RLR pathway by virus
narrower: Inhibition of host interferon signaling pathway by virus
narrower: Inhibition of host TLR pathway by virus
category: Biological process

suppression by virus of host innate immune response
type: Class
database: go

Inhibition of host interferon receptors by virus
type: Concept
comment: Viral protein involved in the evasion of the interferon pathway by inhibiting interferon receptors. Interferon signaling exerts antiviral effects through cell surface receptors termed interferon receptors. In response to binding of extracellular interferons, they activate the JAK/STAT pathway causing transcriptional activation of IFN-regulated genes. To avoid this antiviral response, several viruses target the interferon receptors and send them to degradation via the proteasome.
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

obsolete suppression by virus of host interferon receptor activity
type: Class
database: go

Inhibition of host interferon signaling pathway by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defense by inhibiting the interferon signaling pathway leading to the production of interferon-induced genes. Interferons bind to the IFN receptors (IFNAR) on the cell surface and activate Jak/Tyk kinases. These kinases phosphorylate STAT1 and STAT2 that translocate to the nucleus and induce the expression of interferon stimulated genes (ISGs). Many viruses interact with components of this pathway to prevent expression of ISGs and inhibit the host immune response.
subclass of: Inhibition of host innate immune response by virus
narrower: Inhibition of host tetherin by virus
narrower: Inhibition of host interferon receptors by virus
narrower: Inhibition of host IRF9 by virus
narrower: Inhibition of host ISG15 by virus
narrower: Inhibition of host JAK1 by virus
narrower: Inhibition of host PKR by virus
narrower: Inhibition of host STAT1 by virus
narrower: Inhibition of host STAT2 by virus
narrower: Inhibition of host TYK2 by virus
narrower: Modulation of host PP1 activity by virus
category: Biological process

suppression by virus of host type I interferon-mediated signaling pathway
type: Class
database: go

Inhibition of host IRF3 by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defense by inhibiting the interferon regulatory factor-3 (IRF3) protein. Viral infection triggers the phosphorylation and activation of IRF3. The activated IRF3 migrates to the nucleus, where it complexes with the transcription coactivator CREBBP/EP300, leading to the transcriptional activation of the IFN-alpha and IFN-beta genes. Several viral proteins directly bind to IRF3 and inhibit its transcriptional activity while others target it to the proteasome for degradation.
subclass of: Inhibition of host RLR pathway by virus
category: Biological process

suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity
type: Class
database: go

Inhibition of host IRF7 by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defense by inhibiting the interferon regulatory factor-7 (IRF7) protein. Viral infection triggers the phosphorylation and activation of IRF7. The activated IRF7 migrates to the nucleus leading to the transcriptional activation of the IFN-alpha and IFN-beta genes. Some viral proteins prevent IRF7 phosphorylation and nuclear activation. Ebola virus VP35 interacts with IRF7 and hijacks the cellular SUMOylation machinery for its advantage to increase IRF7 SUMOylation thereby disabling its activity.
subclass of: Inhibition of host RLR pathway by virus
category: Biological process

suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity
type: Class
database: go

Inhibition of host IRF9 by virus
type: Concept
comment: Viral protein involved in the evasion of the type I and III interferon pathway by inhibiting the interferon regulatory factor-9 (IRF9) protein. Viral infection triggers the phosphorylation and activation of IRF9. The activated IRF9 migrates to the nucleus leading to the transcriptional activation of several hundred IFN-responsive genes. Some viral proteins inhibit IRF9 activation by preventing its nuclear localization upon infection or by sending it to the nucleus in an inactive state.
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

suppression by virus of host JAK-STAT cascade via inhibition of host IRF9 activity
type: Class
database: go

Inhibition of host ISG15 by virus
type: Concept
comment: Viral protein involved in the evasion of host immune defense by inhibiting the ISG15 protein, an ubiquitin-like modifier playing important roles in the innate immune response. Like ubiquitin, ISG15 is conjugated to lysines on numerous target proteins through its conserved C-terminal region. Viruses escape from the antiviral activity of ISG15 by direct interaction or by cleavage of ISG15 derivatives.
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

suppression by virus of host ISG15-protein conjugation
type: Class
database: go

Inhibition of host JAK1 by virus
type: Concept
comment: Viral protein involved in the evasion of the type I, II and III interferon pathways by inhibiting the JAK1 protein. Upon viral infection, JAK1 is activated by the interferon-alpha/beta, -gamma, and -lambda signal transduction pathways. Several viral proteins can directly interact with JAK1 to prevent its ability to phosphorylate the downstream partners STAT1 or STAT2.
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

suppression by virus of host JAK-STAT cascade via inhibition of JAK1 activity
type: Class
database: go

Inhibition of host MAVS by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defense by inhibiting the MAVS protein. During viral replication, dsRNA is produced and detected by DDX58/RIG-I or IFIH1/MDA5 that will activate MAVS to coordinate pathways leading to induction of antiviral cytokines. Several viral proteins including NS3/4A from Hepatitis C, or protease 3C from hepatitis A virus, cleave MAVS to abrogate its activity.
subclass of: Inhibition of host RLR pathway by virus
category: Biological process

suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity
type: Class
database: go

Inhibition of host MDA5 by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defense by inhibiting the IFIH1/MDA5 protein. Upon recognition of long viral dsRNAs, IFIH1/MDA5 initiates an antiviral signaling cascade by interacting with downstream partners. Some viral proteins including paramyxovirus V proteins interact with IFIH1/MDA5 and blocks its binding with its downstream partner MAVS.
subclass of: Inhibition of host RLR pathway by virus
category: Biological process

suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of host MDA-5 activity
type: Class
database: go

Inhibition of host MHC class I molecule presentation by virus
type: Concept
comment: Viral protein involved in the evasion of host adaptive immune response by inhibiting the presentation of loaded MHC class I molecules at the cell surface. Many viruses 'intercept' the loaded MHC class I molecules and retain them in the endoplasmic reticulum or target them to degradation in order to prevent presentation of the peptides at the cell surface.
subclass of: Inhibition of host adaptive immune response by virus
category: Biological process

suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I
type: Class
database: go

Inhibition of host MHC class II molecule presentation by virus
type: Concept
comment: Viral protein involved in the evasion of host adaptive immune response by inhibiting the presentation of loaded MHC class II molecules at the cell surface. MHC class II molecules are found only on a few specialized cells termed professional antigen-presenting cells (APCs). This group includes macrophages, dendritic cells and B-cells. Many viruses 'intercept' the loaded MHC class II molecules and retain them in the endoplasmic reticulum or target them to degradation in order to prevent presentation of the peptides at the cell surface.
subclass of: Inhibition of host adaptive immune response by virus
category: Biological process

suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II
type: Class
database: go

Inhibition of host mitotic exit by virus
type: Concept
comment: Viral protein involved in the inhibition of host cell cycle progression by preventing cells to exit mitosis.
subclass of: Modulation of host cell cycle by virus
category: Biological process

suppression by virus of host exit from mitosis
type: Class
database: go

Inhibition of host mRNA nuclear export by virus
type: Concept
comment: Viral protein involved in the disruption of the mRNA nuclear export machinery. Viruses have evolved ways of interacting with the nuclear export machinery to inhibit cellular translation and maximize the expression of their own mRNAs. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response.
subclass of: Host mRNA suppression by virus
category: Biological process

suppression by virus of host mRNA export from nucleus
type: Class
database: go

Inhibition of host NF-kappa-B by virus
type: Concept
comment: Viral protein involved in the inhibition of host NF-kappa-B. This protein is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. Many viruses have developed strategies to inhibit the NF-kappa-B pathway in order to evade host immunity and inhibit production of proinflammatory cytokines.
subclass of: Host-virus interaction
category: Biological process

suppression by virus of host NF-kappaB cascade
type: Class
database: go

Inhibition of host PKR by virus
type: Concept
comment: Viral protein involved in the evasion of the interferon pathway by inhibiting the interferon induced PKR/EIF2AK2 protein. During viral replication of RNA viruses, dsRNA is produced leading to the activation of the PKR/EIF2AK2 kinase. Once activated, PKR/EIF2AK2 autophosphorylates and catalyzes the phosphorylation of many substrates including the translation initiation factor EIF2S1, leading to the inhibition of the initiation of protein synthesis. Several viral proteins prevent PKR/EIF2AK2 activation by direct interaction while others target PKR/EIF2AK2 to degradation.
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

protein serine/threonine kinase inhibitor activity
type: Class
database: go

suppression by virus of host PKR signaling
type: Class
database: go

Inhibition of host poly(A)-binding protein by virus
type: Concept
comment: Viral protein involved in the inhibition of host translation by inhibiting the poly(A)-binding protein PABPC1. Viruses have evolved ways of interacting with the host translational machinery to shutoff host gene expression. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response. One common target is the translation initiation factor PABPC1. Some viruses proteolytically cleave PABPC1, while others displace PABPC1 from EIF4G1.
subclass of: Eukaryotic host translation shutoff by virus
category: Biological process

Inhibition of host pre-mRNA processing by virus
type: Concept
comment: Viral protein involved in the disruption of host pre-mRNA processing. Viruses have evolved ways of interacting with the cellular RNA splicing machinery and regulate splicing of cellular pre-mRNAs as a part of the mechanism for shutting down the synthesis of host proteins. This global inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response.
subclass of: Host mRNA suppression by virus
category: Biological process

suppression by virus of host mRNA processing
type: Class
database: go

Inhibition of host proteasome antigen processing by virus
type: Concept
comment: Viral protein involved in the evasion of host adaptive immune response by inhibiting MHC class I peptide antigen generation by the proteasome. The processing of foreign proteins leads to the presentation of viral peptides by MHC class I molecules to cytotoxic T lymphocytes and triggers immune response. Several viral proteins have evolved mechanisms to avoid synthesis of antigenic peptide by the proteasome. Epstein-Barr virus EBNA-1 for example contains an internal repeat exclusively composed of glycines and alanines that inhibits its proteasomal degradation.
subclass of: Inhibition of host adaptive immune response by virus
category: Biological process

suppression by virus of host antigen processing and presentation
type: Class
database: go

Inhibition of host RIG-I by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defense by inhibiting the DDX58/RIG-I protein. Upon recognition of viral RNA, the cytosolic receptor DDX58/RIG-I initiates an antiviral signaling cascade by interacting with downstream partners. Several viral proteins inhibit DDX58/RIG-I via direct interaction while others via proteolytic cleavage.
subclass of: Inhibition of host RLR pathway by virus
category: Biological process

suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of host RIG-I activity
type: Class
database: go

Inhibition of host RLR pathway by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defense by inhibiting the DDX58/RIG-I-like receptor (RLR) pathway leading to the triggering of interferon-mediated response. This pathway starts with the recognition of viral RNA by host proteins including DDX58/RIG-I or IFIH1. Then, the signal is transmitted through MAVS and TRAFs leading to the activation and nuclear localization of transcription factors IRF3 and IRF7 to induce IFNalpha/beta transcription and protein production. Many viruses interact with components of this pathway to inhibit production of interferons and establishment of the antiviral state.
subclass of: Inhibition of host innate immune response by virus
narrower: Inhibition of host RIG-I by virus
narrower: Inhibition of host MDA5 by virus
narrower: Inhibition of host IRF3 by virus
narrower: Inhibition of host IRF7 by virus
narrower: Inhibition of host MAVS by virus
narrower: Inhibition of host TRAFs by virus
narrower: Inhibition of host IKBKE by virus
category: Biological process

negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway
type: Class
database: go

Inhibition of host RNA polymerase II by virus
type: Concept
comment: Viral protein involved in the disruption of the host RNA polymerase II. Many viruses induce alterations in the cellular gene expression. Among these, shutoff of host transcription by targeting RNA polymerase II is commonly used. Indeed, many viruses are able to modify RNAP II CTD including Herpes virus, HIV, Epstein-Barr virus or Bunyamwera virus.
subclass of: Eukaryotic host transcription shutoff by virus
category: Biological process

suppression by virus of host mRNA transcription via inhibition of RNA polymerase II activity
type: Class
database: go

Inhibition of host STAT1 by virus
type: Concept
comment: Viral protein involved in the evasion of the type I, II and III interferon pathways by inhibiting the STAT1 protein. Upon viral infection, STAT1 is activated by IFN-gamma, IFN-alpha/beta, or IFN-lambda that bind to specific cell surface receptors. While IFN-gamma induces STAT1 homodimerization, IFN-alpha/beta and IFN-lambda stimulate heterodimerization of STAT1 and STAT2, both leading to STAT1 nuclear localization and subsequent induction of IFN-stimulated genes. Many viruses interfere with STAT1 activation, often by preventing STAT1 phosphorylation and nuclear localization.
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

suppression by virus of host JAK-STAT cascade via inhibition of STAT1 activity
type: Class
database: go

Inhibition of host STAT2 by virus
type: Concept
comment: Viral protein involved in the evasion of type I and III interferon pathways by inhibiting STAT2 protein. Upon viral infection, STAT2 is activated by IFN-alpha/beta or IFN-lambda that bind to specific cell surface receptors. In turn, IFN-alpha/beta (or IFN-lambda) induces heterodimerization of STAT1 and STAT2 by phosphorylation, leading to STAT2 nuclear localization and subsequent induction of IFN-stimulated genes. Many viruses interfere with STAT2 activation, often by preventing STAT2 phosphorylation and nuclear localization.
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

suppression by virus of host JAK-STAT cascade via inhibition of STAT2 activity
type: Class
database: go

Inhibition of host TAP by virus
type: Concept
comment: Viral protein involved in the evasion of host adaptive immune response by inhibiting the TAP complex. Transporter associated with antigen (TAP), composed of two subunits TAP1 and TAP2, is required for the translocation of peptides into the ER, where they are loaded onto MHC class I. Thereafter, the viral peptides are presented to cytotoxic T lymphocytes at the cell surface and trigger immune response. The loading of peptide on MHC by TAP is targeted by several viruses including herpesviruses and retroviruses.
subclass of: Inhibition of host adaptive immune response by virus
category: Biological process

Inhibition of host tapasin by virus
type: Concept
comment: Viral protein involved in the evasion of host adaptive immune response by inhibiting the tapasin/TAPBP protein. tapasin/TAPBP is a type I transmembrane protein essential for the optimal expression of stable MHC class I molecules on host cell surface. Its helps the MHC class I molecules to remain in a peptide receptive state, avoiding irreversible denaturation. Several retroviruses and DNA viruses encode proteins interacting with tapasin/TAPBP and inhibiting its activity.
subclass of: Inhibition of host adaptive immune response by virus
category: Biological process

Inhibition of host TBK1 by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defenses by inhibiting the TBK1 kinase. Upon viral infection, Toll-like receptors (TLRs) or DNA recognition receptors recognize foreign material and transmit the signal to TBK1 that in turn phosphorylates and activates IRF3 and IRF7. Once phosphorylated, IRF3 and/or IRF7 translocate into the nucleus to drive transcription of interferons. Several viruses including herpes simplex virus 1 or vaccinia virus interact directly with and inhibit TBK1 to prevent IRFs activation.
subclass of: Inhibition of host TLR pathway by virus
category: Biological process

suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity
type: Class
database: go

Inhibition of host tetherin by virus
type: Concept
comment: Viral protein involved in the evasion of host immune defense by inhibiting the BST2/tetherin protein. BST2/tetherin is an alpha interferon-inducible cellular factor that impairs the release of many enveloped viruses, including human immunodeficiency virus type 1 (HIV-1), HIV-2, as well as other retroviruses. Several viruses manage to circumvent the antiviral activity of BST2/tetherin either by sending BST2/tetherin to degradation (HIV-1) or by lowering the presence of BST2 on cell surfaces (HIV-2).
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

suppression by virus of host tetherin activity
type: Class
database: go

Inhibition of host TLR pathway by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defenses by inhibiting the Toll-like recognition receptor (TLR) pathway. This pathway usually starts with the recognition of viruses by host TLRs including TLR3 or TLR4. Then, the signal is transmitted through MYD88 (or TRIF) and then to TBK1 leading to the activation and nuclear localization of transcription factors IRF3 and/or IRF7 to induce IFNalpha/beta transcription and production of proinflammatory cytokines through activation of the NF-kappaB signaling pathway. Many viruses interact with components of this pathway to inhibit production of interferons and establishment of the antiviral state.
subclass of: Inhibition of host innate immune response by virus
narrower: Inhibition of host TBK1 by virus
category: Biological process

suppression by virus of host toll-like receptor signaling pathway
type: Class
database: go

Inhibition of host TRAFs by virus
type: Concept
comment: Viral protein involved in the evasion of host innate defense by inhibiting TRAF proteins. After viral infection, the cellular signaling pathway leading to production of interferons is activated and several TRAF family members including TRAF2, TRAF3, and TRAF5 participate in this cascade. Many viruses encode protein able to interact with TRAF members to inhibit their antiviral activity.
subclass of: Inhibition of host RLR pathway by virus
category: Biological process

suppression by virus of host TRAF-mediated signal transduction
type: Class
database: go

Inhibition of host TYK2 by virus
type: Concept
comment: Viral protein involved in the evasion of the type I and III interferon pathways by inhibiting the host TYK2 protein. Upon viral infection, the TYK2 protein is activated by IFNalpha/beta or IFN-lambda stimulation leading to a series of phosphorylation events that induce transcription of several hundred IFN-responsive genes. Several viruses have evolved mechanisms to inhibit TYK2 activity thereby preventing the subsequent activation of downstream partners STAT1 and STAT2.
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

suppression by virus of host JAK-STAT cascade via inhibition of host TYK2 activity
type: Class
database: go

Initiation factor
type: Concept
alternative label: Translation initiation factor
comment: Protein which plays an important role in initiating the translation of a mRNA molecule into a polypeptide. Initiation factors help to form the complex between the mRNA and a ribosome.
subclass of: Protein biosynthesis
subclass of: Molecular function
category: Molecular function

translation initiation factor activity
type: Class
database: go

translational initiation
type: Class
database: go

Innate immunity
type: Concept
comment: Protein involved in innate immunity, an inborn defense mechanism used by organisms to defend themselves against invasion by pathogens (bacteria, fungi, viruses, etc.). Initially discovered in insects which are devoid of an adaptive immune system and rely only on innate immune reactions for their defense, this immediate response accomplishes many activities including recognition and effector functions. Recognition is mediated by broad specificity, pattern recognition, receptors which recognize many related molecular structures (e.g. polysaccharides, polynucleotides) present in microorganisms but not found in the host. The innate responses include the release of antimicrobial peptides, production of cytokines, acute-phase proteins, complement. Although many different innate immune mechanisms are deployed for host defence, a unifying theme of innate immunity is the use of germline-encoded pattern recognition receptors for pathogens or damaged self components, such as the Toll-like receptors, nucleotide-binding domain leucine-rich repeat (LRR)-containing receptors, retinoic acid-inducible gene I-like RNA helicases and C-type lectin receptors.
subclass of: Immunity
narrower: Complement alternate pathway
narrower: Complement pathway
narrower: Complement activation lectin pathway
category: Biological process

innate immune response
type: Class
database: go

Inner capsid protein
type: Concept
comment: Viral protein that is a component of the inner layer of a double or triple concentric icosahedral capsid. Inner capsids are part of reoviridae and cystoviridae virions.
subclass of: Capsid protein
category: Cellular component

viral inner capsid
type: Class
database: go

Inositol biosynthesis
type: Concept
alternative label: Inositol anabolism
alternative label: Inositol biosynthetic process
alternative label: Inositol formation
alternative label: Inositol synthesis
comment: Protein involved in the synthesis of inositol, a cyclic hexahydric alcohol. It occurs in various forms, of which myo-inositol, a constituent of phospholipids, is the most important.
subclass of: Biological process
category: Biological process

inositol biosynthetic process
type: Class
database: go

Insecticide resistance
type: Concept
alternative label: Resistance to insecticide
comment: Protein that confers, on insect vectors and pests, the ability to withstand insecticide action. Insecticides are chemicals that selectively kill insects. Insecticide resistance usually occurs by two broad mechanisms. The first is where the insect may produce large amounts of enzymes, such as esterases which either break down the insecticide molecule or bind to it so tightly that it cannot function (a process known as sequestration). The second mechanism involves mutation of the insecticide target site, such as the acetylcholinesterase enzyme in the nervous system. This effectively blocks the action of the insecticide.
subclass of: Biological process
category: Biological process

Integrin
type: Concept
comment: Protein of the integrin family of cell surface heterodimeric receptors that mediates dynamic cell-to-cell as well as cell-to-matrix adhesion. Integrins function as mechanochemical sensors and transducers able to change rapidly and reversibly their adhesive functions by modulating their ligand-binding affinity. Each subunit has a large N-terminal extracellular domain followed by a transmembrane domain and a short C-terminal cytoplasmic region. Some subclasses of integrins share a common beta chain while having different alpha chains.
subclass of: Molecular function
category: Molecular function

integrin-mediated signaling pathway
type: Class
database: go

Intellectual disability
type: Concept
alternative label: Mental deficiency
alternative label: Mental retardation
alternative label: Mental subnormality
comment: Protein which, if defective, is involved in intellectual disability, a disorder appearing during development and characterized by subnormal intellectual functioning and impaired adaptive behavior.
subclass of: Disease
category: Disease

Interferon antiviral system evasion
type: Concept
alternative label: Antiviral state evasion
alternative label: Interferon response evasion
comment: Viral protein which prevents the activation of the antiviral state induced by interferon (IFN) in the host cell, thereby allowing the virus to replicate optimally. The antiviral state is the result of a signaling pathway induced by IFN-alpha or IFN-beta following viral infection. It leads to the transcription of various cellular antiviral genes coding for host defense proteins.
subclass of: Biological process
category: Biological process

Intermediate capsid protein
type: Concept
comment: Viral protein that is a component of the intermediate layer of a triple concentric icosahedral capsid. Intermediate capsids are part of reoviridae virions.
subclass of: Capsid protein
category: Cellular component

viral intermediate capsid
type: Class
database: go

Intermediate filament
type: Concept
comment: Intermediate filaments (IF) are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide and intermediate in size between microtubules and microfilaments. This family of protein includes cytokeratins, vimentin, desmin, glial fibrillary acidic protein, neurofilament proteins and nestin. All IF proteins are structurally similar in that they consist of: a central rod domain which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; an N-terminal non-helical domain (head) of variable length; and an C-terminal domain (tail) which is also non-helical and shows extreme length variation between different IF proteins.
subclass of: Cellular component
category: Cellular component

intermediate filament
type: Class
database: go

Intrahepatic cholestasis
type: Concept
comment: Protein which, if defective, causes intrahepatic cholestasis, a condition characterized by stoppage or suppression of the bile flow from the liver to the duodenum without extrahepatic bile duct obstruction.
subclass of: Disease
category: Disease

Intron homing
type: Concept
alternative label: Intron transposition
comment: Endonucleases involved in intron homing, a genetic event leading to the transfer of an intron DNA sequence. This type of intron mobility depends on site-specific restriction endonucleases encoded by the mobile introns.
subclass of: Endonuclease
subclass of: Biological process
category: Biological process

intron homing
type: Class
database: go

Iodination
type: Concept
alternative label: Iodinated
comment: Protein which is posttranslationally modified by the replacement of at least one hydrogen by iodine.
subclass of: PTM
category: PTM

Ion channel
type: Concept
comment: Protein which is part of a transmembrane protein complex that forms a hydrophilic channel across the lipid bilayer through which specific inorganic ions can diffuse down their electrochemical gradients. The channels are usually gated and only open in response to a specific stimulus, such as a change in membrane potential (voltage-gated) or the binding of a ligand (ligand-gated channel).
subclass of: Ion transport
subclass of: Molecular function
narrower: Calcium channel
narrower: Potassium channel
narrower: Voltage-gated channel
narrower: Chloride channel
narrower: Sodium channel
narrower: Ligand-gated ion channel
narrower: Viral ion channel
category: Molecular function

monoatomic ion channel activity
type: Class
database: go

Ion channel impairing toxin
type: Concept
comment: Protein which interferes with the function of ion channels, which are hydrophilic channels across the lipid bilayer through which specific inorganic ions can diffuse down their electrochemical gradients.
subclass of: Toxin
narrower: Calcium channel impairing toxin
narrower: Potassium channel impairing toxin
narrower: Voltage-gated sodium channel impairing toxin
narrower: Ionotropic glutamate receptor inhibitor
narrower: Chloride channel impairing toxin
narrower: Proton-gated sodium channel impairing toxin
category: Molecular function

ion channel regulator activity
type: Class
database: go

Ion transport
type: Concept
comment: Protein involved in the transport of ions. Such proteins are usually transmembrane and mediate a movement of ions across cell membranes. Transport may be passive (facilitated diffusion; down the electrochemical gradient), or active (against the electrochemical gradient). Active transport requires energy which may come from light, oxidation reactions, ATP hydrolysis, or cotransport of other ions or molecules.
subclass of: Transport
narrower: Anion exchange
narrower: Calcium transport
narrower: Cobalt transport
narrower: Copper transport
narrower: Hydrogen ion transport
narrower: Ion channel
narrower: Iron transport
narrower: Porin
narrower: Potassium transport
narrower: Sodium transport
narrower: Voltage-gated channel
narrower: Zinc transport
narrower: Chloride channel
narrower: Nickel transport
narrower: Ligand-gated ion channel
narrower: Viral ion channel
category: Biological process

monoatomic ion transport
type: Class
database: go

Ionotropic glutamate receptor inhibitor
type: Concept
comment: Protein that inhibits ionotropic glutamate receptor (iGluR). iGluRs are glutamate-gated ion channels that mediate excitatory neurotransmission in the central nervous system. Based on both molecular and pharmacological criteria, iGluRs have been divided into two major classes, the non-NMDA class, which includes both AMPA and kainate subtypes of receptors, and the NMDA class.
subclass of: Postsynaptic neurotoxin
subclass of: Ion channel impairing toxin
category: Molecular function

Iron
type: Concept
alternative label: Fe
alternative label: Fe cation
alternative label: Fe ion
alternative label: Iron cation
alternative label: Iron ion
comment: Protein which binds at least one iron atom, or protein whose function is iron-dependent. Iron is a metal, chemical symbol Fe.
subclass of: Ligand
narrower: Heme
narrower: Iron storage
narrower: Iron transport
narrower: Iron-sulfur
category: Ligand

Iron storage
type: Concept
comment: Protein involved in the storage of iron.
subclass of: Iron
subclass of: Biological process
category: Biological process

intracellular iron ion homeostasis
type: Class
database: go

Iron transport
type: Concept
alternative label: Fe transport
alternative label: Iron cation transport
alternative label: Iron ion transport
comment: Protein involved in the transport of iron.
subclass of: Ion transport
subclass of: Iron
category: Biological process

iron ion transmembrane transport
type: Class
database: go

Iron-sulfur
type: Concept
alternative label: Iron-sulfur cluster
comment: Protein which binds at least one iron-sulfur cluster, e.g. 2Fe-2S, 3Fe-4S, 4Fe-4S.
subclass of: Iron
subclass of: Metal-binding
narrower: 2Fe-2S
narrower: 3Fe-4S
narrower: 4Fe-4S
category: Ligand

iron-sulfur cluster binding
type: Class
database: go

Isoleucine biosynthesis
type: Concept
alternative label: Isoleucine anabolism
alternative label: Isoleucine biosynthetic process
alternative label: Isoleucine formation
alternative label: Isoleucine synthesis
comment: Protein involved in the synthesis of the hydrophobic amino acid isoleucine.
subclass of: Branched-chain amino acid biosynthesis
category: Biological process

isoleucine biosynthetic process
type: Class
database: go

Isomerase
type: Concept
comment: Enzyme that catalyzes the 1,1-, 1,2- or 1,3-hydrogen shift. The 1,1-hydrogen shift is an inversion at an asymmetric carbon center (racemases, epimerases). The 1,2-hydrogen shift involved a hydrogen transfer between two adjacent carbon atoms, one undergoing oxidation, the other reduction (aldose-ketose isomerases). The 1,3-hydrogen shifts are allylic or azaallylic (when nitrogen is one of the three atoms) isomerizations.
subclass of: Molecular function
narrower: Rotamase
narrower: Topoisomerase
category: Molecular function

isomerase activity
type: Class
database: go

Isopeptide bond
type: Concept
comment: Protein which is posttranslationally modified by the formation of an amide bond between an amino-group and a carboxyl-group at least one of which is not an alpha group. An isopeptide bond involves the side chain of one or two amino acid residues. Because there are few enzymes that hydrolyze isopeptide bonds, the formation of interchain isopeptide bonds can produce stably linked protein dimers, multimers or complexes, such as blood clots.
subclass of: PTM
category: PTM

Isoprene biosynthesis
type: Concept
alternative label: Isoprene anabolism
alternative label: Isoprene biosynthetic process
alternative label: Isoprene formation
alternative label: Isoprene synthesis
comment: Protein involved in the synthesis of isoprene, an important organic unit of 5 carbons in plants. It is used to build up isoprenoids, including carotenoids, terpenes and natural rubber.
subclass of: Biological process
category: Biological process

isoprenoid biosynthetic process
type: Class
database: go

Jasmonic acid signaling pathway
type: Concept
alternative label: JA mediated signaling
alternative label: JA signaling pathway
alternative label: Jasmonate mediated signaling
alternative label: Jasmonate signaling pathway
alternative label: Jasmonic acid mediated signaling
comment: Protein involved in the jasmonic acid (jasmonate, JA) signaling pathway (e.g. transport and signal transduction) that regulates many aspects of plant growth, development and cellular signaling (e.g. growth inhibition, senescence, tuber formation, response to wounding, plant defense, and leaf abscission). This phytohormone and its derivatives such as methyl jasmonate (MeJA) can be synthesized from the fatty acid linolenic acid in the oxylipin octadecanoid pathway.
subclass of: Biological process
category: Biological process

Joubert syndrome
type: Concept
alternative label: Cerebellar vermis agenesis
alternative label: Cerebelloparenchymal disorder IV
alternative label: CPD IV
alternative label: JBTS
alternative label: Joubert-Boltshauser syndrome
alternative label: JS
comment: Protein which, if defective, causes Joubert syndrome, an autosomal recessive multisystem disorder characterized by cerebellar ataxia, developmental delay, hypotonia, neonatal breathing abnormalities and oculomotor apraxia. Neuroradiologically, it is characterized by cerebellar vermis hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of the 'molar tooth sign' on transaxial slices. A wide clinical variability with a marked variation in severity and inconsistent presence of the following features is observed: episodic apnea-hyperpnea, abnormal eye movements, occipital meningoencephalocele, polydactyly, nephronophthisis or cystic dysplasia of the kidney, chorioretinal coloboma and retinal dysplasia. The variable association of ocular and renal abnormalities with cerebellar features typical of Joubert syndrome defines the cerebello-oculo-renal syndromes (CORSs).
subclass of: Ciliopathy
category: Disease

Kallmann syndrome
type: Concept
alternative label: Dysplasia olfactogenitalis of De Morsier
alternative label: HHA
alternative label: Hypogonadotropic hypogonadism and anosmia
alternative label: Kallmann's syndrome
alternative label: Kallmann de Morsier syndrome
alternative label: KMS
comment: Protein which, if defective, causes Kallmann syndrome, a disorder characterized by the association of hypogonadotropic hypogonadism with anosmia or hyposmia. Kallmann syndrome is caused by impaired embryonic development of the olfactory system and the GnRH-synthesizing neurons. The main clinical features consist of the association of micropenis and cryptorchidism in young boys, the absence of spontaneous puberty, and a partial or total loss of the sense of smell (anosmia). In some patients other developmental anomalies can be present such as renal agenesis, cleft lip/palate, selective tooth agenesis and bimanual synkinesis.
subclass of: Disease
category: Disease

Kartagener syndrome
type: Concept
alternative label: Dextrocardia-bronchiectasis-sinusitis syndrome
alternative label: KTGS
alternative label: Siewert syndrome
comment: Protein which, if defective, causes Kartagener syndrome, a rare and genetically heterogeneous disorder characterized by the combination of primary ciliary dyskinesia and situs inversus viscerum.
subclass of: Primary ciliary dyskinesia
category: Disease

Karyogamy
type: Concept
comment: Protein involved in the fusion of the nuclei of two gametes after cytoplasmic fusion.
subclass of: Biological process
category: Biological process

karyogamy
type: Class
database: go

Kelch repeat
type: Concept
comment: Protein containing at least one Kelch repeat.
subclass of: Domain
category: Domain

Keratin
type: Concept
comment: Fibrous proteins rich in cysteine and the chief constituent of horn, nails, hair, epidermis and feathers. Two major conformational groups have been characterized, alpha-keratin, whose peptide backbone forms an alpha-helix, and beta-keratin, whose backbone forms a zigzag or pleated sheet structure.
subclass of: Cellular component
category: Cellular component

Keratinization
type: Concept
comment: Protein involved in keratinization, the process in which the cytoplasm of the outermost cells of the vertebrate epidermis is replaced by keratin. Keratinization occurs in the stratum corneum, feathers, hair, claws, nails, hooves, and horns.
subclass of: Biological process
category: Biological process

keratinization
type: Class
database: go

Kinase
type: Concept
alternative label: Phosphotransferase
comment: Enzyme that catalyzes the transfer of phosphate (phosphoryl or pyrophosphoryl transfer) usually from ATP to a second substrate.
subclass of: Transferase
narrower: Serine/threonine-protein kinase
narrower: Tyrosine-protein kinase
category: Molecular function

kinase activity
type: Class
database: go

phosphorylation
type: Class
database: go

Kinetochore
type: Concept
comment: The kinetochore is a complex assembled at centromeric region of DNA, which provides the major attachment point for the spindle microtubules. In monocentric chromosomes, the kinetochores of point centromeres bind a single microtubule and the larger kinetochores of regional centromeres interact with a number of microtubules. In holocentric chromosomes, the kinetochores bind the diffuse centromere along the length of the chromosomes.
subclass of: Cellular component
category: Cellular component

kinetochore
type: Class
database: go

Kinetoplast
type: Concept
comment: Protein associated with the kinetoplast DNA (kDNA), the mitochondrial DNA of trypanosomatid protozoa. kDNA is a massive network, composed of thousands of topologically interlocked DNA circles. Each cell contains one network condensed into a disk-shaped structure within the matrix of its single mitochondrion. The kDNA circles are of two types, maxicircles present in a few dozen copies and minicircles present in several thousand copies.
subclass of: Mitochondrion
category: Cellular component

kinetoplast
type: Class
database: go

Knottin
type: Concept
alternative label: ICK
alternative label: Inhibitor Cystine Knot
comment: Small disulfide-rich protein characterized by a special 'disulfide through disulfide knot'. This knot is obtained when one disulfide bridge crosses the macrocycle formed by two other disulfides and the interconnecting backbone (disulfide III-VI goes through disulfides I-IV and II-V). The knottin structure is found in some plant protease inhibitors, cyclotides, toxins from cone snails, spiders, insects, horseshoe crabs and scorpions, gurmarin-like peptides, agouti-related proteins, and some antimicrobial peptides.
subclass of: Domain
category: Domain

Kringle
type: Concept
comment: Protein containing at least one kringle domain, a triple-looped, disulfide cross-linked domain of approximately 80 amino acids in length and involved in protein-protein interactions.
subclass of: Domain
category: Domain

Lacrimo-auriculo-dento-digital syndrome
type: Concept
alternative label: Lacrimoauriculodentodigital syndrome
alternative label: LADD syndrome
alternative label: Levy-Hollister syndrome
comment: Protein which, if defective, causes lacrimo-auriculo-dento-digital syndrome. Lacrimo-auriculo-dento-digital syndrome, a form of ectodermal dysplasia, is an autosomal dominant multiple congenital anomaly. It is characterized by aplastic/hypoplastic lacrimal and salivary glands and ducts, cup-shaped ears, hearing loss, hypodontia and enamel hypoplasia, and distal limb segments anomalies. In addition to these cardinal features, facial dysmorphism, malformations of the kidney and respiratory system and abnormal genitalia have been reported. Craniosynostosis and severe syndactyly are not observed.
subclass of: Ectodermal dysplasia
category: Disease

Lactation
type: Concept
comment: Protein involved in lactation, the secretion of milk by mammary glands.
subclass of: Biological process
category: Biological process

lactation
type: Class
database: go

Lactose biosynthesis
type: Concept
alternative label: Lactose anabolism
alternative label: Lactose biosynthetic process
alternative label: Lactose formation
alternative label: Lactose synthesis
comment: Protein involved in the synthesis of lactose, a disaccharide of glucose and galactose present in milk.
subclass of: Biological process
category: Biological process

lactose biosynthetic process
type: Class
database: go

Lactose metabolism
type: Concept
alternative label: Lactose metabolic process
comment: Protein involved in the biochemical reactions with lactose, a disaccharide of glucose and galactose, found in milk.
subclass of: Biological process
category: Biological process

lactose metabolic process
type: Class
database: go

Laminin EGF-like domain
type: Concept
comment: 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). The tertiary structure of this domain is remotely similar, in its N-terminal, to that of the EGF-like module.
subclass of: Domain
category: Domain

Lantibiotic
type: Concept
comment: Lanthionine-containing peptide antibiotics are peptides produced by Gram-positive bacteria which cause cell death of other Gram-positive bacteria.
subclass of: Bacteriocin
category: Molecular function

signaling receptor binding
type: Class
database: go

Late protein
type: Concept
comment: Bacteriophage or viral protein expressed in a later phase of the infectious cycle.
subclass of: Developmental stage
category: Developmental stage

Latency-replication decision
type: Concept
comment: Viral protein part of a genetic system that takes part in the decision of the outcome of the infection: latency or replication. Expression of genetic switch proteins control the expression of viral genes that act as effectors in either the establishment of latency (lysogeny) or in promoting productive replication (lytic cycle). Interactions between proteins involved in switch regulatory processes and host proteins often influence the decision.
subclass of: Biological process
category: Biological process

latency-replication decision
type: Class
database: go

LDL
type: Concept
comment: Protein constituent of the low-density lipoproteins or protein which binds LDLs. LDLs are plasma lipoproteins rich in cholesterol esters, synthesized from the very low-density lipoprotein (VLDL), and which transport cholesterol to peripheral tissue and regulate de novo cholesterol synthesis.
subclass of: Cellular component
category: Cellular component

low-density lipoprotein particle
type: Class
database: go

Lead
type: Concept
alternative label: Lead cation
alternative label: Lead ion
alternative label: Pb
alternative label: Pb cation
alternative label: Pb ion
comment: Protein which binds at least one lead atom, or protein whose function is lead-dependent. Lead is a metal, chemical symbol Pb.
subclass of: Ligand
category: Ligand

Leader peptide
type: Concept
comment: Short peptide sequences translated from bacterial leader RNA sequences which are involved in transcriptional or translation attenuation, mechanisms that modulate mRNA transcription or translation.
subclass of: Molecular function
category: Molecular function

Leber congenital amaurosis
type: Concept
comment: Protein which, if defective, causes Leber congenital amaurosis, a clinically and genetically heterogeneous type of blindness transmitted as an autosomal recessive trait and occurring at or shortly after birth. It is associated with an atypical form of diffuse pigmentation and commonly with optic atrophy and attenuation of the retinal vessels.
subclass of: Disease
category: Disease

Leber hereditary optic neuropathy
type: Concept
comment: Protein which, if defective, causes Leber hereditary optic neuropathy, a mitochondrial disease leading to bilateral, painless loss of central vision due to selective degeneration of the retinal ganglion cells and their axons. The disease arises during young adult life and displays sex-dependent incomplete penetrance and male predominance.
subclass of: Primary mitochondrial disease
category: Disease

Lectin
type: Concept
comment: Protein which specifically binds carbohydrates. Lectins are obtained particularly from seeds of leguminous plants but also from other plant and animal sources. They contain binding sites for specific mono-and oligosaccharides. They agglutinate cells by binding to specific sugar residues in membrane glycoproteins.
subclass of: Ligand
narrower: Mannose-binding
category: Ligand

carbohydrate binding
type: Class
database: go

Leigh syndrome
type: Concept
comment: Protein which, if defective, causes Leigh syndrome, a neurodegenerative disorder characterized by the subacute onset of psychomotor retardation, hypotonia, ataxia, weakness, vision loss, eye movement abnormalities, seizures, dysphagia, and lactic acidosis. Pathological features include spongy degeneration of the neuropile of the basal ganglia, thalamus, brain stem, and spinal cord. The syndrome is caused by a variety of defects of enzymes involved in energy metabolism, including cytochrome c oxidase (COX), the mitochondrial encoded ATP6 subunit of ATP synthase, and the X-linked E1-alpha subunit of pyruvate dehydrogenase.
subclass of: Primary mitochondrial disease
category: Disease

Leucine biosynthesis
type: Concept
alternative label: Leucine anabolism
alternative label: Leucine biosynthetic process
alternative label: Leucine formation
alternative label: Leucine synthesis
comment: Protein involved in the synthesis of the hydrophobic amino acid leucine.
subclass of: Branched-chain amino acid biosynthesis
category: Biological process

leucine biosynthetic process
type: Class
database: go

Leucine-rich repeat
type: Concept
alternative label: LRR
comment: Protein containing at least one leucine-rich repeat (LRR).
subclass of: Domain
category: Domain

Leukodystrophy
type: Concept
comment: Protein which, if defective, causes leukodystrophy, any of a group of diseases that affect the formation or maintenance of myelin in the central nervous system.
subclass of: Disease
narrower: Metachromatic leukodystrophy
category: Disease

Leukotriene biosynthesis
type: Concept
alternative label: Leukotriene anabolism
alternative label: Leukotriene biosynthetic process
alternative label: Leukotriene formation
alternative label: Leukotriene synthesis
comment: Protein involved in the synthesis of leukotrienes, eicosanoid hormones first isolated from leukocytes. They are thought to mediate the allergic response that causes lung constriction and muscle contraction in asthma.
subclass of: Biological process
category: Biological process

leukotriene biosynthetic process
type: Class
database: go

Li-Fraumeni syndrome
type: Concept
alternative label: LFS
alternative label: Sarcoma family syndrome of Li and Fraumeni
alternative label: SBLA syndrome
comment: Protein which, if defective, causes Li-Fraumeni syndrome (LFS), an autosomal dominant familial cancer predisposition syndrome associated with soft-tissue sarcoma, breast cancer, leukemia, osteosarcoma, melanoma, and cancer of the colon, pancreas, adrenal cortex and brain. Individuals with LFS are at increased risk for developing multiple primary cancers.
subclass of: Disease
category: Disease

Ligand
type: Concept
comment: Keywords assigned to proteins because they bind, are associated with, or whose activity is dependent of some molecule.
narrower: Biotin
narrower: Cadmium
narrower: Calcium
narrower: cAMP
narrower: cGMP
narrower: Chitin-binding
narrower: Chromophore
narrower: Cobalt
narrower: Copper
narrower: Flavoprotein
narrower: Folate-binding
narrower: Hemoglobin-binding
narrower: Hyaluronic acid
narrower: Iron
narrower: Lectin
narrower: Lipid-binding
narrower: Lithium
narrower: Magnesium
narrower: Manganese
narrower: Mercury
narrower: Metal-binding
narrower: Molybdenum
narrower: NAD
narrower: NADP
narrower: Nickel
narrower: Nucleotide-binding
narrower: Pheromone-binding
narrower: Pigment
narrower: Plastoquinone
narrower: Potassium
narrower: PQQ
narrower: Pyridoxal phosphate
narrower: Pyruvate
narrower: Retinol-binding
narrower: Schiff base
narrower: Selenium
narrower: Sialic acid
narrower: Thiamine pyrophosphate
narrower: Tungsten
narrower: Ubiquinone
narrower: Vanadium
narrower: Vitamin A
narrower: Vitamin C
narrower: Vitamin D
narrower: Zinc
narrower: Chloride
narrower: Sodium
narrower: S-adenosyl-L-methionine
narrower: c-di-GMP
narrower: Lead
subclass of: Concept

Ligand-gated ion channel
type: Concept
alternative label: LGIC
alternative label: Ligand-gated channel
comment: Protein which forms or is a component of a ligand-gated channel. Ligand-gated channels are transmembrane ion channels whose permeability is increased by the binding of a specific ligand, such as neurotransmitters, ionositol triphosphates, and cyclic nucleotides.
subclass of: Ion transport
subclass of: Ion channel
category: Molecular function

Ligase
type: Concept
comment: Enzyme that catalyzes the joining of two molecules coupled with the breakdown of a pyrophosphate bond in ATP or a similar triphosphate. Sometimes the terms "synthase", "synthetase" or "carboxylase" are also used for this class of enzymes.
subclass of: Molecular function
narrower: Aminoacyl-tRNA synthetase
category: Molecular function

ligase activity
type: Class
database: go

Light-harvesting polypeptide
type: Concept
comment: Proteins which form part of the antenna complex, a light-harvesting system found in photosynthetic bacteria which absorb light radiation and transfer the excitation energy to the reaction centres.
subclass of: Molecular function
category: Molecular function

Lignin biosynthesis
type: Concept
alternative label: Lignin anabolism
alternative label: Lignin biosynthetic process
alternative label: Lignin formation
alternative label: Lignin synthesis
comment: Protein involved in the synthesis of lignin, a polymer of phenylpropanoid subunits found in the walls of plant cells such as xylem and sclerenchyma fibres. Lignin imparts strength to the wall and protects against degradation by microorganisms.
subclass of: Biological process
category: Biological process

lignin biosynthetic process
type: Class
database: go

Lignin degradation
type: Concept
alternative label: Lignin breakdown
alternative label: Lignin catabolic process
alternative label: Lignin catabolism
comment: 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.
subclass of: Biological process
category: Biological process

lignin catabolic process
type: Class
database: go

LIM domain
type: Concept
alternative label: LIM motif
comment: Protein which contains at least one LIM domain, a conserved cysteine-rich domain of approximately 60 amino acids with seven conserved cysteines and a histidine. The LIM domain binds two zinc ions and seems to be involved in protein-protein interactions.
subclass of: Metal-binding
subclass of: Zinc
subclass of: Domain
category: Domain

Limb-girdle muscular dystrophy
type: Concept
alternative label: LGMD
alternative label: Muscular dystrophy limb-girdle type
comment: Protein which, if defective, causes limb-girdle muscular dystrophy, a degenerative myopathy without nervous system involvement. The disease is characterized by slowly progressive wasting and weakness of the proximal muscles of arms and legs around the pelvic or shoulder girdles, elevated creatine kinase levels and dystrophic features on muscle biopsy. Onset of symptoms is in late childhood, adolescence or even adult life. Limb-girdle muscular dystrophy is a genetically heterogeneous disorder. Inheritance can be autosomal dominant or autosomal recessive.
subclass of: Disease
category: Disease

Lipid A biosynthesis
type: Concept
alternative label: Lipid A anabolism
alternative label: Lipid A biosynthetic process
alternative label: Lipid A formation
alternative label: Lipid A synthesis
comment: Protein involved in the synthesis of lipid A (endotoxin), the hydrophobic anchor of lipopolysaccharide (LPS). Lipid A is a glucosamine-based phospholipid that makes up the outer monolayer of the outer membranes of most Gram-negative bacteria.
subclass of: Lipid biosynthesis
category: Biological process

lipid A biosynthetic process
type: Class
database: go

Lipid biosynthesis
type: Concept
alternative label: Lipid anabolism
alternative label: Lipid biosynthetic process
alternative label: Lipid formation
comment: Protein involved in the synthesis 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.
subclass of: Lipid metabolism
narrower: Fatty acid biosynthesis
narrower: Lipid A biosynthesis
narrower: Phospholipid biosynthesis
narrower: Steroid biosynthesis
category: Biological process

lipid biosynthetic process
type: Class
database: go

Lipid degradation
type: Concept
alternative label: Lipid breakdown
alternative label: Lipid catabolic process
alternative label: Lipid catabolism
comment: Protein involved in the breakdown of lipids, a diverse class of compounds, insoluble in water but soluble in organic solvents, and which include fats, oils, triacylglycerols, fatty acids, glycolipids, phospholipids and steroids.
subclass of: Lipid metabolism
narrower: Bile acid catabolism
narrower: Phospholipid degradation
category: Biological process

lipid catabolic process
type: Class
database: go

Lipid droplet
type: Concept
alternative label: Adiposome
alternative label: Lipid bodies
alternative label: Lipid body
alternative label: Lipid particle
alternative label: Monolayer-surrounded lipid storage body
alternative label: Oil bodies
alternative label: Oil body
alternative label: Oleosome
alternative label: Spherosome
comment: Protein characteristic of a lipid droplet, a dynamic cytoplasmic organelle which consists of an heterogeneous macromolecular assembly of lipids and proteins covered by a unique phospholipid monolayer. Lipid droplets may play a role in lipid metabolism and storage, and they may be involved in the regulation of intracellular trafficking and signal transduction.
subclass of: Cellular component
category: Cellular component

lipid droplet
type: Class
database: go

Lipid metabolism
type: Concept
alternative label: Lipid metabolic process
comment: Protein involved in the biochemical reactions of lipids. Lipids are 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.
subclass of: Biological process
narrower: Fatty acid metabolism
narrower: Lipid degradation
narrower: Lipid biosynthesis
narrower: Sphingolipid metabolism
narrower: Steroid metabolism
narrower: Phospholipid metabolism
category: Biological process

lipid metabolic process
type: Class
database: go

Lipid transport
type: Concept
comment: 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.
subclass of: Transport
category: Biological process

lipid transport
type: Class
database: go

Lipid-binding
type: Concept
comment: Protein which binds one or more lipids.
subclass of: Ligand
narrower: Steroid-binding
category: Ligand

lipid binding
type: Class
database: go

Lipopolysaccharide biosynthesis
type: Concept
alternative label: Lipopolysaccharide anabolism
alternative label: Lipopolysaccharide biosynthetic process
alternative label: Lipopolysaccharide formation
alternative label: Lipopolysaccharide synthesis
comment: Protein involved in the synthesis of lipopolysaccharides (LPS), the main constituents of the outer cell wall of Gram-negative bacteria. LPS are composed of lipid molecules joined to polysaccharides and are highly immunogenic.
subclass of: Biological process
category: Biological process

lipopolysaccharide biosynthetic process
type: Class
database: go

Lipoprotein
type: Concept
alternative label: Lipidated
comment: Protein which is posttranslationally modified by the attachment of at least one lipid or fatty acid, e.g. farnesyl, palmitate and myristate.
subclass of: PTM
narrower: GPI-anchor
narrower: Myristate
narrower: Palmitate
narrower: Prenylation
category: PTM

Lipoyl
type: Concept
comment: Protein which contains at least one lipoyl-binding domain. Lipoic acid is an essential cofactor for E2 acyltransferases and some other proteins.
subclass of: Domain
category: Domain

Lissencephaly
type: Concept
comment: Protein which, if defective, causes lissencephaly, a brain malformation characterized by the absence (agyria) or reduction (pachygyria) of brain surface convolutions (gyri), in association with abnormal organisation of the cortical layers. It results from neuronal migration defects during embryogenesis. Two large groups can be distinguished: classical lissencephaly (and its variants) and cobblestone lissencephaly. Lissencephaly means "smooth brain".
subclass of: Disease
category: Disease

Lithium
type: Concept
alternative label: Li
alternative label: Li cation
alternative label: Li ion
alternative label: Lithium cation
alternative label: Lithium ion
comment: Protein whose function is lithium-dependent. Lithium is an alkali metal, chemical symbol Li.
subclass of: Ligand
category: Ligand

Long QT syndrome
type: Concept
alternative label: LQTS
comment: Protein which, if defective, causes the long QT syndrome, a heart disease which manifests itself by a prolonged QT interval on the ECG and, clinically, by a propensity for tachyarrhythmias, causing syncopes and sudden cardiac death. LQTS may be drug-induced, but mutations in genes coding for cardiac ion-channels are the cause of the hereditary forms: Romano-Ward syndrome (RWS), and Jervell and Lange-Nielsen Syndrome (JLNS).
subclass of: Disease
category: Disease

LTQ
type: Concept
alternative label: Lysine topaquinone
alternative label: Lysine tyrosylquinone
comment: Protein which contains at least one lysine tyrosylquinone (LTQ) cross-link modification. LTQ is formed by oxidation of the phenol ring of a tyrosine to form tyrosylquinone (topaquinone) followed by covalent cross-linking with a lysine residue.
subclass of: PTM
category: PTM

Luminescence
type: Concept
alternative label: Bioluminescence
comment: Protein involved in luminescence, the property of giving off light without emitting a corresponding degree of heat.
subclass of: Biological process
narrower: Photoprotein
category: Biological process

bioluminescence
type: Class
database: go

Lyase
type: Concept
comment: Enzyme that catalyzes the cleavage of C-C, C-O, C-S, C-N or other bonds by other means than by hydrolysis or oxidation, with two substrates in one reaction direction, and one in the other. In the latter direction, a molecule (of carbon dioxide, water, etc) is eliminated, thus creating a new double bond or a new ring.
subclass of: Molecular function
narrower: Decarboxylase
category: Molecular function

lyase activity
type: Class
database: go

Lysine biosynthesis
type: Concept
alternative label: Lysine anabolism
alternative label: Lysine biosynthetic process
alternative label: Lysine formation
alternative label: Lysine synthesis
comment: Protein involved in the synthesis of the essential basic amino acid lysine.
subclass of: Amino-acid biosynthesis
category: Biological process

lysine biosynthetic process
type: Class
database: go

Lysosome
type: Concept
comment: 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.
subclass of: Cellular component
category: Cellular component

lysosome
type: Class
database: go

Magnesium
type: Concept
alternative label: Magnesium cation
alternative label: Magnesium ion
alternative label: Mg
alternative label: Mg cation
alternative label: Mg ion
comment: Protein which binds at least one magnesium atom, or protein whose function is magnesium-dependent. Magnesium is a metallic element, chemical symbol Mg.
subclass of: Ligand
category: Ligand

Magnetosome
type: Concept
comment: Protein located in or on the magnetosome, a membrane-bound bacterial organelle that envelops crystals of magnetic iron minerals in magnetotactic bacteria. Magnetosomes form linear chains that align along the cellular motility axis at midcell and function in bacterial navigation along the Earth's magnetic field. They are formed by invagination of the cell inner membrane; in some species they remain connected to the inner membrane, in others they pinch off to form independent intracellular vesicles.
subclass of: Cellular component
category: Cellular component

magnetosome
type: Class
database: go

Malaria
type: Concept
comment: Protein involved in malaria, a human disease caused by Plasmodium, a parasitic protozoan that grows by sexual reproduction in the Anopheles mosquito.
subclass of: Disease
category: Disease

Maltose metabolism
type: Concept
alternative label: Maltose metabolic process
comment: Protein involved in the biochemical reactions with maltose, a disaccharide of glucose. Maltose is produced by the hydrolysis of starch.
subclass of: Biological process
category: Biological process

maltose metabolic process
type: Class
database: go

Mandelate pathway
type: Concept
comment: Enzyme involved in the mandelate pathway. These enzymes enable various microorganisms to grow using D(-)-, L(+)- or DL-mandelate (2-hydroxy-2-phenylacetate) as the sole source of carbon and energy.
subclass of: Biological process
category: Biological process

mandelate metabolic process
type: Class
database: go

Manganese
type: Concept
alternative label: Manganese cation
alternative label: Manganese ion
alternative label: Mn
alternative label: Mn cation
alternative label: Mn ion
comment: Protein which binds at least one manganese atom, or protein whose function is manganese-dependent. Manganese is a metallic element, chemical symbol Mn.
subclass of: Ligand
category: Ligand

Mannose-binding
type: Concept
comment: Protein which binds mannose, a 6-carbon aldose sugar, that is found in many glycoproteins and polysaccharides.
subclass of: Lectin
category: Ligand

mannose binding
type: Class
database: go

Maple syrup urine disease
type: Concept
comment: Protein which, if defective, causes maple syrup urine disease, an autosomal recessive disorder characterized by mental and physical retardation, feeding problems and a maple syrup odour to the urine.
subclass of: Disease
category: Disease

Mast cell degranulation
type: Concept
comment: Protein involved in mast cell degranulation. Mast cell is a large, ovoid cell of hematopoietic lineage, with a centrally located nucleus and numerous large, intensely basophilic granules. The binding of an antigen to its specific immunoglobulin-E antibody on the mast cell surface triggers the release of the MC granules. Mast cells are involved in hypersensitivity reactions.
subclass of: Biological process
category: Biological process

mast cell degranulation
type: Class
database: go

Meckel syndrome
type: Concept
alternative label: Dysencephalia splanchnocystica
alternative label: Gruber syndrome
alternative label: Meckel-Gruber syndrome
alternative label: MKS
comment: Protein which, if defective, causes Meckel syndrome, an autosomal recessive disorder characterized by a combination of renal cysts and variably associated features, including developmental anomalies of the central nervous system (usually occipital encephalocele), hepatic ductal dysplasia and cysts, and polydactyly.
subclass of: Ciliopathy
category: Disease

Meiosis
type: Concept
comment: Protein involved in meiotic processes or in regulation of meiosis. Meiosis is the nuclear division which results in the daughter nuclei each containing half the number of chromosomes of the parent. It comprises two distinct nuclear divisions, the first and second meiotic divisions (which may be separated by cell division), the actual reduction in chromosome number takes place during the first division.
subclass of: Biological process
category: Biological process

meiotic cell cycle
type: Class
database: go

Melanin biosynthesis
type: Concept
alternative label: Melanin anabolism
alternative label: Melanin biosynthetic process
alternative label: Melanin formation
alternative label: Melanin synthesis
comment: Protein involved in the synthesis of melanin. Melanins are brown or black pigments found in skin, hair, feathers, etc. They are irregular polymeric structures produced from tyrosine. Melanins can be divided into 3 groups: allomelanins in the plant kingdom, and eumelanins and phaeomelanins in the animal kingdom.
subclass of: Biological process
category: Biological process

melanin biosynthetic process
type: Class
database: go

MELAS syndrome
type: Concept
comment: Protein which, if defective, causes mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) syndrome, a genetically heterogeneous disorder, characterized by episodic vomiting, seizures, and recurrent cerebral insults resembling strokes and causing hemiparesis, hemianopsia, or cortical blindness.
subclass of: Primary mitochondrial disease
category: Disease

Melatonin biosynthesis
type: Concept
alternative label: Melatonin anabolism
alternative label: Melatonin biosynthetic process
alternative label: Melatonin formation
alternative label: Melatonin synthesis
comment: Protein involved in the synthesis of melatonin (N-acetyl 5-methoxytryptamine), a neurohormone synthesized by lower plants and in the pineal gland in animals. In humans, it is involved in the regulation of sleep, mood, puberty, ovarian cycles and in the establishment of circadian rhythms. In lower vertebrates, it causes aggregation of pigment in melanophores, and thus lightens skin.
subclass of: Biological process
category: Biological process

melatonin biosynthetic process
type: Class
database: go

Membrane
type: Concept
comment: Protein which is membrane-bound or membrane-associated. A membrane is the layer which forms the boundary of cells and intracellular organelles. It is composed of two oriented lipid layers in which proteins are embedded and acts as a selective permeability barrier.
subclass of: Cellular component
narrower: Coated pit
narrower: GPI-anchor
narrower: Postsynaptic cell membrane
narrower: Transmembrane
narrower: Cell outer membrane
narrower: Mitochondrion inner membrane
narrower: Mitochondrion outer membrane
narrower: Plastid inner membrane
narrower: Plastid outer membrane
narrower: Cell membrane
narrower: Host membrane
narrower: Target membrane
narrower: Transmembrane helix
narrower: Transmembrane beta strand
category: Cellular component

membrane
type: Class
database: go

Membrane attack complex
type: Concept
comment: Component of the membrane attack complex which groups the complement plasma glycoproteins C5b, C6, C7, C8 and polymeric C9 on biological membranes. The complex forms transmembrane channels which displace lipid molecules and other constituents, thus disrupting the phospholipid bilayer of target cells leading to cell lysis by osmotic leakage. The formation of the membrane attack complex is the terminal step in the complement cascade.
subclass of: Complement pathway
subclass of: Cytolysis
subclass of: Cellular component
category: Cellular component

membrane attack complex
type: Class
database: go

Menaquinone biosynthesis
type: Concept
alternative label: Menaquinone anabolism
alternative label: Menaquinone biosynthetic process
alternative label: Menaquinone formation
alternative label: Menaquinone synthesis
alternative label: Vitamin K2 anabolism
alternative label: Vitamin K2 biosynthesis
alternative label: Vitamin K2 biosynthetic process
alternative label: Vitamin K2 formation
alternative label: Vitamin K2 synthesis
comment: Protein involved in the synthesis of menaquinone, a derivative of 2-methyl-1,4-naphthoquinone in which the 3-position is substituted with a variable-length polyisoprene chain. In mammals, menaquinone is an important component of the blood coagulation system. Mammals need to obtain this vitamin by their diet or from the bacterial flora of the gut.
subclass of: Biological process
category: Biological process

menaquinone biosynthetic process
type: Class
database: go

Mercuric resistance
type: Concept
alternative label: Mercuric cation resistance
alternative label: Mercuric ion resistance
alternative label: Resistance to mercury ion
comment: Protein that confers bacteria or other microorganisms the ability to withstand mercury salts.
subclass of: Biological process
category: Biological process

response to mercury ion
type: Class
database: go

Mercury
type: Concept
alternative label: Hg
alternative label: Hg cation
alternative label: Hg ion
alternative label: Mercury cation
alternative label: Mercury ion
comment: Protein which binds mercury and/or is involved in the cleavage of carbon-mercury bonds. Mercury is the only liquid metallic element, chemical symbol is Hg.
subclass of: Ligand
category: Ligand

Merozoite
type: Concept
comment: Protein expressed in the merozoite stage of sporozoite parasites, an invasive stage in the life cycle produced by schizogony or asexual reproduction in which the nucleus of a cell undergoes division several times. This results in a multinucleate schizont which subsequently gives rise to a number of uninucleate cells called merozoites.
subclass of: Developmental stage
category: Developmental stage

Metachromatic leukodystrophy
type: Concept
alternative label: Metachromatic leucodystrophy
comment: Protein which, if defective, causes metachromatic leukodystrophy, a disease characterized by intralysosomal or myelin membrane storage of cerebroside-3-sulfate. Whereas storage occurs in many cells, the disease almost exclusively affects oligodendrocytes. Patients suffer from a progressive demyelination, which causes a variety of neurological symptoms, including gait disturbances, ataxias, optical atrophy, dementia, seizures and spastic tetraparesis.
subclass of: Leukodystrophy
category: Disease

Metal-binding
type: Concept
comment: Protein which binds metals.
subclass of: Ligand
narrower: 2Fe-2S
narrower: 3Fe-4S
narrower: 4Fe-4S
narrower: Heme
narrower: Iron-sulfur
narrower: LIM domain
narrower: Metal-thiolate cluster
narrower: Zinc-finger
category: Ligand

metal ion binding
type: Class
database: go

Metal-thiolate cluster
type: Concept
comment: Protein which binds at least a cluster composed of metal coordinated via cysteinyl thiolate bridges to cysteine ligands.
subclass of: Metal-binding
category: Ligand

Metalloenzyme inhibitor
type: Concept
comment: Protein that inhibits metalloenzymes, enzymes which contains metal ions.
subclass of: Molecular function
narrower: Metalloprotease inhibitor
category: Molecular function

enzyme inhibitor activity
type: Class
database: go

Metalloprotease
type: Concept
alternative label: Metallopeptidase
comment: Proteolytic enzyme which use a metal for its catalytic mechanism. Most metalloproteases are zinc-dependent, some use cobalt.
subclass of: Protease
category: Molecular function

metallopeptidase activity
type: Class
database: go

Metalloprotease inhibitor
type: Concept
alternative label: Metallopeptidase inhibitor
comment: Protein that inhibits metalloproteases, which are peptide hydrolases that use a metal in the catalytic mechanism.
subclass of: Metalloenzyme inhibitor
subclass of: Protease inhibitor
category: Molecular function

metalloendopeptidase inhibitor activity
type: Class
database: go

Methanogenesis
type: Concept
alternative label: Methane biosynthesis
alternative label: Methane biosynthetic process
alternative label: Methane synthesis
comment: Protein involved in methanogenesis, the energy yielding formation of methane by methanogenic bacteria.
subclass of: Biological process
category: Biological process

methanogenesis
type: Class
database: go

Methanol utilization
type: Concept
comment: Protein involved in the utilization of methanol.
subclass of: Biological process
category: Biological process

methanol metabolic process
type: Class
database: go

Methionine biosynthesis
type: Concept
alternative label: Methionine anabolism
alternative label: Methionine biosynthetic process
alternative label: Methionine formation
alternative label: Methionine synthesis
comment: Protein involved in the synthesis of the hydrophobic amino acid methionine, an essential amino acid in human diets which contains a thioether linkage.
subclass of: Amino-acid biosynthesis
category: Biological process

methionine biosynthetic process
type: Class
database: go

Methotrexate resistance
type: Concept
alternative label: Resistance to methotrexate
comment: Protein that confers the ability to withstand methotrexate, an inhibitor of dehydrofolate reductase (DHFR). Methotrexate resistance occurs usually as a result of mutation or amplification of the DHFR gene.
subclass of: Biological process
category: Biological process

response to methotrexate
type: Class
database: go

Methylation
type: Concept
alternative label: Methylated
comment: Protein which is posttranslationally modified by the attachment of at least one methyl group.
subclass of: PTM
category: PTM

Methyltransferase
type: Concept
comment: Enzyme that transfers methyl groups from one compound to another.
subclass of: Transferase
category: Molecular function

methyltransferase activity
type: Class
database: go

methylation
type: Class
database: go

MHC I
type: Concept
comment: A heterodimeric membrane protein composed of two non-covalently linked polypeptide chains, a major histocompatibility complex (MHC)-encoded alpha chain and a non-MHC-encoded subunit B2M/beta2-microglobulin. Each MHC molecule consists of an extracellular peptide-binding cleft, followed by an immunoglobulin (Ig)-like domain and transmembrane and cytoplasmic domains. The amino-terminal alpha-1 and alpha-2 segments of the alpha chain form the peptide-binding cleft. Expressed on all nucleated cells, displays peptides derived from cytosolic proteins for recognition by CD8-positive T cells. By scanning MHC I molecules, CD8-positive T cells can detect infected or tumor cells and eliminate them.
subclass of: Immunity
subclass of: Cellular component
category: Cellular component

antigen processing and presentation of peptide antigen via MHC class I
type: Class
database: go

MHC class I protein complex
type: Class
database: go

MHC II
type: Concept
comment: A heterodimeric membrane protein composed of two non-covalently linked alpha and beta polypeptide chains, both major histocompatibility complex (MHC)-encoded. Each MHC molecule consists of an extracellular peptide-binding cleft followed by an immunoglobulin (Ig)-like domain and transmembrane and cytoplasmic domains. The amino-terminal alpha-1 and beta-1 segments interact to form the peptide-binding cleft. Expressed on professional antigen presenting cells, displays peptides derived from endocytosed proteins for recognition by CD4-positive helper T cells. By scanning MHC II molecules, CD4-positive T cells activate effector mechanisms that eliminate extracellular microbes.
subclass of: Adaptive immunity
subclass of: Cellular component
category: Cellular component

antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
type: Class
database: go

MHC class II protein complex
type: Class
database: go

Microphthalmia
type: Concept
alternative label: Microphthalmos
comment: Protein which, if defective, causes microphthalmia, a developmental anomaly in which the eyeballs are abnormally small. Disease severity ranges from moderate reduction of the size of a single eye to complete bilateral absence of ocular tissues. Microphthalmia can occur in isolation or as part of a syndrome.
subclass of: Disease
category: Disease

Microsome
type: Concept
comment: Protein found in microsomes, a heterogenous set of vesicles 20-200 nm in diameter and formed from the endoplasmic reticulum when cells are disrupted. The vesicles are isolated by differential centrifugation and are composed of three structural features: rough vesicles, smooth vesicles and ribosomes. Numerous enzyme activities are associated with the microsomal fraction.
subclass of: Endoplasmic reticulum
category: Cellular component

intracellular membrane-bounded organelle
type: Class
database: go

Microtubular inwards viral transport
type: Concept
comment: Viral protein that allows the active transport of complete particles and viral components along microtubules toward the intracellular replication sites during virus entry. This transport, which usually involves motor proteins like dynein or polymerization/depolymerization reactions as a driving force, is mostly used by viruses that replicate their genome near or in the nucleus. Neurotropic viruses for example, often enter neurons at the terminal axon and their viral genome must be moved retrogradely to cell bodies. Viruses such as adenovirus, Adeno-associated virus, rabies virus, canine parvovirus, vaccinia, foamy virus, human papillomavirus 16 and herpes virus utilize this type of intracellular transport.
subclass of: Host-virus interaction
subclass of: Cytoplasmic inwards viral transport
category: Biological process

microtubule-dependent intracellular transport of viral material towards nucleus
type: Class
database: go

Microtubular outwards viral transport
type: Concept
comment: Viral protein that allows the active transport of viral components and assembled, complete particles along microtubules toward the cell periphery during virus egress. This transport, which usually involves interaction with motor proteins like kinesin or polymerization/depolymerization reactions as a driving force, is mostly used by viruses that replicate their genome near or in the nucleus and allows newly assembled viral progeny to reach the plasma membrane. Herpes simplex virus for example is transported anterogradely along the axon.
subclass of: Host-virus interaction
subclass of: Viral release from host cell
category: Biological process

microtubule-dependent intracellular transport of viral material towards cell periphery
type: Class
database: go

Microtubule
type: Concept
comment: Protein associated with or component of the microtubule. The microtubule is formed by the arrangement of 13 parallel protofilaments arising from end-to-end aggregation of the tubulin alpha/beta-dimers. Microtubules are associated with various other proteins (MAPs, dynein, kinesin) and are involved in structures responsible for cellular movement such as flagella or cilia. Microtubules of the ciliary axoneme are more permanent than cytoplasmic and spindle microtubules. Microtubule formation is inhibited by agents such as colchicine, vinblastine or vincristine.
subclass of: Cellular component
category: Cellular component

microtubule
type: Class
database: go

Milk protein
type: Concept
comment: 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.
subclass of: Molecular function
category: Molecular function

Mineral balance
type: Concept
alternative label: Regulation of bone mineralization
comment: Protein that influences the equilibrium of minerals present in bone, e.g., fetuin.
subclass of: Biological process
category: Biological process

regulation of bone mineralization
type: Class
database: go

Mitochondrion
type: Concept
comment: 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. Each mitochondrion is surrounded by a double limiting membrane. The inner membrane is highly invaginated, and its projections are called cristae. Mitochondria are the sites of the reactions of oxidative phosphorylation, which result in the formation of ATP. The size and coding capacity of the mitochondrial DNA varies considerably in different organisms, and encodes rRNAs, tRNAs and essential mitochondrial proteins.
subclass of: Cellular component
narrower: Kinetoplast
narrower: Mitochondrion inner membrane
narrower: Mitochondrion outer membrane
narrower: Mitochondrion nucleoid
category: Cellular component

mitochondrion
type: Class
database: go

Mitochondrion inner membrane
type: Concept
alternative label: Inner mitochondrial membrane
alternative label: Mitochondrial inner membrane
comment: Protein found in or associated with the inner membrane of a mitochondrion, the membrane which separates the mitochondrial matrix from the intermembrane space.
subclass of: Membrane
subclass of: Mitochondrion
category: Cellular component

mitochondrial inner membrane
type: Class
database: go

Mitochondrion nucleoid
type: Concept
alternative label: Mitochondrial nucleoid
alternative label: Mitochromosome
comment: Protein found associated with the mitochondrial nucleoid, the mitochondrial pseudocompartment formed by the chromatin-dense area. This region, which is functionally equivalent to the eukaryotic nucleus, is not surrounded by a membrane.
subclass of: Mitochondrion
category: Cellular component

mitochondrial nucleoid
type: Class
database: go

Mitochondrion outer membrane
type: Concept
alternative label: Mitochondrial outer membrane
alternative label: Outer mitochondrial membrane
comment: Protein found in or associated with the outer membrane of a mitochondrion, the mitochondrial membrane facing the cytoplasm.
subclass of: Membrane
subclass of: Mitochondrion
category: Cellular component

mitochondrial outer membrane
type: Class
database: go

Mitogen
type: Concept
comment: Protein which can induce mitosis of certain eukaryotic cells, i.e. it stimulates cellular proliferation.
subclass of: Molecular function
category: Molecular function

positive regulation of cell division
type: Class
database: go

Mitosis
type: Concept
comment: Protein involved in mitosis, the nuclear division in eukaryotic cells involving the exact duplication and separation of the chromosome threads so that each daughter nucleus carries a chromosome complement identical to that of the parent nucleus. Mitosis is divided into four substages: prophase, metaphase, anaphase and telophase.
subclass of: Cell division
category: Biological process

Mitosome
type: Concept
comment: Protein localized in the mitosome, an organelle found in "amitochondrial" unicellular organisms which do not have the capability of gaining energy from oxidative phosphorylation. Mitosomes are almost certainly derived from mitochondria, they have a double membrane and most proteins are delivered to them by a targeting sequence. Unlike mitochondria, mitosomes do not contain any DNA. The mitosome functions in iron-sulphur cluster assembly.
subclass of: Cellular component
category: Cellular component

mitosome
type: Class
database: go

Mobility protein
type: Concept
comment: Protein involved in the conjugative transfer of plasmid DNA. These proteins provide the function of nicking the DNA at a certain point, guiding the 5' end of the nicked strand into the recipient cell, recircularization, and perhaps the priming of complementary strand synthesis in the recipient.
subclass of: Conjugation
subclass of: Molecular function
category: Molecular function

Modulation of host cell apoptosis by virus
type: Concept
comment: Viral protein involved in the modulation of host cell apoptosis by acting different steps of the process. Several viruses encode proteins that inhibit apoptosis while other viruses use apoptosis to their advantage to suppress immune response or to disseminate.
subclass of: Host-virus interaction
narrower: Activation of host caspases by virus
narrower: Inhibition of host apoptosis by viral BCL2-like protein
narrower: Inhibition of host apoptosis by viral FLIP-like protein
narrower: Inhibition of host caspases by virus
category: Biological process

modulation by virus of host apoptotic process
type: Class
database: go

Modulation of host cell cycle by viral cyclin-like protein
type: Concept
comment: Viral protein sharing sequence homology with cellular cyclins. Most viral cyclin homologues are closely related in sequence to the cellular D-type cyclins, which are implicated in regulating the transit of cells from G1 into S and are thought to operate via the inactivation of the retinoblastoma tumour suppressor protein.
subclass of: Modulation of host cell cycle by virus
category: Biological process

modulation by virus of host cell cycle
type: Class
database: go

Modulation of host cell cycle by virus
type: Concept
comment: Viral protein involved in the modulation of host cell cycle. The cell cycle can be divided into four stages: G1, S, G2 and mitosis, while cells resting are termed quiescent cells (G0). Viruses have evolved strategies to modulate cell cycle progression including stimulation of S phase entry from G1 or G0 or cell cycle arrest at G2/M for example. This regulation allows viruses to maximize their own replication.
subclass of: Host-virus interaction
narrower: G0/G1 host cell cycle checkpoint dysregulation by virus
narrower: G1/S host cell cycle checkpoint dysregulation by virus
narrower: Host G2/M cell cycle arrest by virus
narrower: Inhibition of host mitotic exit by virus
narrower: Modulation of host cell cycle by viral cyclin-like protein
narrower: Inhibition of host DNA replication by virus
category: Biological process

Modulation of host chromatin by virus
type: Concept
comment: Viral protein involved in the regulation of host chromatin structure. Chromatin has a major role in life cycle of many viruses, and a lot of them have evolved mechanisms to modulate chromatin-related processes. For example, histone acetyltransferases, histone deacetylases or histones are common targets of viruses.
subclass of: Host-virus interaction
category: Biological process

modulation by virus of host chromatin organization
type: Class
database: go

Modulation of host dendritic cell activity by virus
type: Concept
comment: Viral protein involved in the modulation of host dendritic cell activity. Dendritic cells operate at the interface between the innate and adaptive immune response by their ability to sample their environment for pathogenic products, to process them, and to present viral antigens to T-cells. This results in T cell proliferation and the induction of virus-specific adaptive immune responses. Therefore impairing dendritic cell function by viruses is an effective strategy to disrupt the host immune response.
subclass of: Viral immunoevasion
category: Biological process

evasion by virus of host dendritic cell activity
type: Class
database: go

Modulation of host E3 ubiquitin ligases by virus
type: Concept
comment: Viral protein involved in the modulation of cellular E3 ubiquitin ligases. In general, viral proteins redirect cellular E3 ubiquitin ligases to select specific host proteins for proteasomal degradation. The aim of this subversion is the creation of a favorable environment for virus replication and dissemination.
subclass of: Modulation of host ubiquitin pathway by virus
category: Biological process

modulation by symbiont of host protein ubiquitination
type: Class
database: go

Modulation of host immunity by viral IgG Fc receptor-like protein
type: Concept
comment: Viral protein acting as an IgG Fc receptors, able to bind IgG and inhibit host Fc-dependent immune activation. Fc receptors are proteins found at the surface of certain cells of the immune system including macrophages, monocytes, natural killer cells or B-cells. They allow these cells to bind to antibodies that are attached to the surface of infected cells or pathogens, helping these cells to identify and eliminate pathogens.
subclass of: Viral immunoevasion
category: Biological process

modulation by virus of host immune response
type: Class
database: go

Modulation of host NK-cell activity by virus
type: Concept
comment: Viral protein involved in the modulation of host NK-cell activity. Natural killer (NK) cells are critical in defense against viral infections, since they provide host protection by releasing cytokines such as IFN-gamma or by direct lysis of infected targets. Therefore, during viral infections, viruses and NK cells are in a constant battle and many viruses have developed a variety of strategies to modulate NK cell activity.
subclass of: Viral immunoevasion
category: Biological process

evasion by virus of host natural killer cell activity
type: Class
database: go

Modulation of host PP1 activity by virus
type: Concept
comment: Protein phosphatase-1 (PP1) is a member of the Serine/Threonine phosphatases. The enzyme regulates many important physiological processes, including gene transcription, translation, metabolism, cell growth and division. Different viruses including asfivirus, herpes simplex virus or papillomavirus interact with and modulate PPP1 phosphatase activity to dephosphorylate specific cellular substrates including EIF2S1. Upon viral infection, the host PKR/EIF2AK2 triggers the phosphorylation of EIF2S1 leading to a complete translational shut-off. By dephosphroylating EIF2S1 with PPP1CA, viruses manage to circumvent this antiviral response and prevent translational shut-off.
subclass of: Inhibition of host interferon signaling pathway by virus
category: Biological process

protein serine/threonine phosphatase inhibitor activity
type: Class
database: go

Modulation of host ubiquitin pathway by viral deubiquitinase
type: Concept
comment: Viral protein possessing deubiquitinating activity. Hijacking the ubiquitin system plays an essential role during viral replication. Therefore, several viruses including EBV or HCMV encode for proteins able to remove ubiquitin or ubiquitin-like proteins from their substrate.
subclass of: Modulation of host ubiquitin pathway by virus
category: Biological process

Modulation of host ubiquitin pathway by viral E3 ligase
type: Concept
comment: Viral protein functioning as a cellular E3 ubiquitin ligase. These viral proteins usually target several host proteins for proteasomal degradation.
subclass of: Modulation of host ubiquitin pathway by virus
category: Biological process

Modulation of host ubiquitin pathway by viral ubl
type: Concept
comment: Viral protein sharing sequence similarity with host ubiquitin. Several of these homologues are present in large DNA viruses such as entomopoxvirus or canarypoxvirus and are thought to modulate host ubiquitin pathway.
subclass of: Modulation of host ubiquitin pathway by virus
category: Biological process

Modulation of host ubiquitin pathway by virus
type: Concept
comment: Viral protein involved in the modulation of the host ubiquitin pathway. The ubiquitination pathway comprises E1, E2, and E3 ligases that conjugate ubiquitin to protein substrate. Usually, the host E3 ligase determines the substrate specificity. Some viruses encode E3 ligases that modulate the substrate specificity of host E3 ligases. Alternatively, some viruses encode deubiquitinases able to remove ubiquitin or ubiquitin-like proteins from their substrate.
subclass of: Host-virus interaction
narrower: Modulation of host E3 ubiquitin ligases by virus
narrower: Modulation of host ubiquitin pathway by viral deubiquitinase
narrower: Modulation of host ubiquitin pathway by viral E3 ligase
narrower: Modulation of host ubiquitin pathway by viral ubl
category: Biological process

Modulation of host virulence by virus
type: Concept
comment: Viral factor that modulates its bacterial host's virulence against a third organism. These virulence factors are mostly expressed from integrated viral genomes and have diverse functions. Bacterial host, and populations, and the encoding (pro)virus probably benefit from the expression of such factors. For example, Bor and Lom outer membrane proteins encoded by bacteriophage lambda modify the virulence of the host bacteria against a eukaryotic target. Some enteric bacterioviruses direct alterations in lipopolysaccharide biosynthesis, resulting in bacterial immune evasion of its eukaryotic target. Other prokaryotic viruses encode exotoxins changing their host bacteria into serious pathogens. A well-known bacterial exotoxin encoded by a provirus is the diphtheria toxin.
subclass of: Virulence
narrower: Viral exotoxin
category: Biological process

modulation of host virulence by virus
type: Class
database: go

Molecular function
type: Concept
comment: Keywords assigned to proteins due to their particular molecular function.
narrower: Actin-binding
narrower: Activator
narrower: Allosteric enzyme
narrower: Alpha-amylase inhibitor
narrower: Antifreeze protein
narrower: Antioxidant
narrower: Bence-Jones protein
narrower: Blood group antigen
narrower: Calmodulin-binding
narrower: Actin capping
narrower: Chaperone
narrower: Chromatin regulator
narrower: Cyclin
narrower: Cytokine
narrower: Developmental protein
narrower: DNA invertase
narrower: DNA replication inhibitor
narrower: DNA-binding
narrower: Elongation factor
narrower: Endorphin
narrower: Excision nuclease
narrower: Eye lens protein
narrower: Growth factor
narrower: Growth factor binding
narrower: GTPase activation
narrower: Guanine-nucleotide releasing factor
narrower: Hemagglutinin
narrower: Heparin-binding
narrower: Hormone
narrower: Hydrolase
narrower: Hypotensive agent
narrower: Ice nucleation
narrower: IgA-binding protein
narrower: IgE-binding protein
narrower: IgG-binding protein
narrower: Initiation factor
narrower: Integrin
narrower: Ion channel
narrower: Isomerase
narrower: Leader peptide
narrower: Ligase
narrower: Light-harvesting polypeptide
narrower: Lyase
narrower: Metalloenzyme inhibitor
narrower: Milk protein
narrower: Mitogen
narrower: Mobility protein
narrower: Monoclonal antibody
narrower: Morphogen
narrower: Motor protein
narrower: Multifunctional enzyme
narrower: Muscle protein
narrower: Mutator protein
narrower: Neuropeptide
narrower: Neurotransmitter
narrower: Viral nucleoprotein
narrower: Opioid peptide
narrower: Oxidoreductase
narrower: Pathogenesis-related protein
narrower: Pheromone
narrower: Phospholipase A2 inhibitor
narrower: Photoprotein
narrower: Porin
narrower: Prion
narrower: Protease inhibitor
narrower: Protein kinase inhibitor
narrower: Protein phosphatase inhibitor
narrower: Protein synthesis inhibitor
narrower: Prothrombin activator
narrower: Pyrogen
narrower: Receptor
narrower: Repressor
narrower: Ribonucleoprotein
narrower: RNA-binding
narrower: Serine protease homolog
narrower: Sigma factor
narrower: Signal transduction inhibitor

Molybdenum
type: Concept
alternative label: Mo
alternative label: Mo cation
alternative label: Mo ion
alternative label: Molybdenum cation
alternative label: Molybdenum ion
comment: Protein which binds molybdenum (or molybdopterin) or protein involved in the transport of molybdenum, a metallic element, chemical symbol Mo. It plays an essential role in the active site of all eukaryotic Mo-containing enzymes. In plants, Mo enzymes are important for nitrate assimilation, phytohormone synthesis, and purine catabolism. Mo is often coordinated to the sulfur atoms of a pterin derivative (molybdopterin [MPT]), thereby forming the active Molybdenum cofactor (Moco), which is highly conserved in eukaryotes, eubacteria, and archaebacteria.
subclass of: Ligand
category: Ligand

Molybdenum cofactor biosynthesis
type: Concept
alternative label: Moco anabolism
alternative label: Moco biosynthesis
alternative label: Moco biosynthetic process
alternative label: Moco formation
alternative label: Moco synthesis
alternative label: Molybdenum cofactor anabolism
alternative label: Molybdenum cofactor biosynthetic process
alternative label: Molybdenum cofactor formation
alternative label: Molybdenum cofactor synthesis
alternative label: Molybdopterin anabolism
alternative label: Molybdopterin biosynthesis
alternative label: Molybdopterin biosynthetic process
alternative label: Molybdopterin formation
alternative label: Molybdopterin synthesis
comment: Protein involved in the synthesis of the molybdenum cofactor (Moco), a molybdenum atom coordinated to the sulfur atoms of a pterin derivative (molybdopterin [MPT]). It is highly conserved in eukaryotes, eubacteria, and archaebacteria. In prokaryotes, two operons are directly associated with biosynthesis of the pterin moiety and its side chain while additional loci play a role in the acquisition of molybdenum and/or activation of the cofactor.
subclass of: Biological process
category: Biological process

Mo-molybdopterin cofactor biosynthetic process
type: Class
database: go

Monoclonal antibody
type: Concept
comment: Antibody produced by a single clone of B cells and thus consisting of a population of identical antibody molecules all specicfic for a single antigenic determinant. They are produced from cultured hybridoma cell lines for research and commercial purposes.
subclass of: Molecular function
category: Molecular function

antigen binding
type: Class
database: go

Monooxygenase
type: Concept
comment: Enzymes that reduce molecular oxygen by incorporating one oxygen atom into its substrate and the other one in water.
subclass of: Oxidoreductase
category: Molecular function

monooxygenase activity
type: Class
database: go

Morphogen
type: Concept
comment: Diffusible protein that influence morphogenesis or embryonic development. These proteins carry information relating, for example, to a position in the embryo, and thus, determine the differentiation that cells perceiving this information will undergo. They are thought to act as a function of a threshold of their concentration.
subclass of: Molecular function
category: Molecular function

anatomical structure morphogenesis
type: Class
database: go

morphogen activity
type: Class
database: go

Motor protein
type: Concept
comment: Protein that walks or slides along microtubules or microfilaments using the energy provided by ATP or GTP hydrolysis, e.g. dyneins, myosins and kinesins. Or protein which mediates motility by other non enzymatic processes, e.g. prestin, a bidirectional voltage-to-force converter.
subclass of: Molecular function
narrower: Myosin
category: Molecular function

mRNA capping
type: Concept
alternative label: Messenger RNA capping
comment: Protein involved in the modification (capping) of the 5' end of eukaryotic mRNAs. This modification occurs after the beginning of transcription in the nucleus, and consists of adding a guanosine nucleotide to the 5'-end of mRNAs and then, methylating the guanosine. Capping protects mRNAs at their termini against attack by phosphatases and other nucleases and promotes mRNA function at the level of initiation of translation.
subclass of: mRNA processing
category: Biological process

7-methylguanosine mRNA capping
type: Class
database: go

mRNA processing
type: Concept
alternative label: Messenger RNA processing
comment: Protein involved in the processing of the primary mRNA transcript to yield a functional mRNA. This includes 5' capping, 3' cleavage and polyadenylation, as well as mRNA splicing and RNA editing.
subclass of: Biological process
narrower: mRNA capping
narrower: mRNA splicing
category: Biological process

mRNA processing
type: Class
database: go

mRNA splicing
type: Concept
alternative label: Messenger RNA splicing
comment: 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.
subclass of: mRNA processing
narrower: Spliceosome
category: Biological process

RNA splicing
type: Class
database: go

mRNA transport
type: Concept
alternative label: Messenger RNA transport
comment: Protein which is involved in the mechanism of export of mRNAs from the nucleus to the cytoplasm.
subclass of: Transport
narrower: Nuclear pore complex
category: Biological process

mRNA transport
type: Class
database: go

Mucolipidosis
type: Concept
comment: Protein which, if defective, causes mucolipidosis, a group of inherited metabolic diseases characterised by the accumulation of excessive amounts of acid mucopolysaccharides, sphingolipids, and/or glycolipids in visceral and mesenchymal cells. Abnormal amounts of sphingolipids or glycolipids are present in neural tissue. Mental retardation and skeletal changes are common. All mucolipidosis are lysosomal disorders and are inherited in an autosomal recessive manner.
subclass of: Disease
category: Disease

Mucopolysaccharidosis
type: Concept
comment: Protein which, if defective, causes mucopolysaccharidosis. These inherited diseases are characterized by excessive accumulation and secretion of oligomucopoloysaccharide due to the deficiency of enzymes involved in the degradation of glycosaminoglycans (mucopolysaccharides). They are progressive and often display a wide spectrum of clinical severity within one enzyme deficiency.
subclass of: Disease
category: Disease

Multifunctional enzyme
type: Concept
comment: Protein that contains at least two distinct enzymatic activities and two distinct active sites.
subclass of: Molecular function
category: Molecular function

Muscle protein
type: Concept
comment: Characteristic protein of a muscle cell. The major ones are myosin and actin, which are responsible for the contraction and relaxation of muscles.
subclass of: Molecular function
narrower: Thick filament
category: Molecular function

Mutator protein
type: Concept
comment: Protein which is encoded by a mutator gene (mutator). Generally, these are genes within which certain mutations cause an increase in frequency of spontaneous mutations in other genes. Mutator proteins are therefore thought to be responsible for inaccurate DNA replication.
subclass of: Molecular function
category: Molecular function

Myofibrillar myopathy
type: Concept
comment: Protein which, if defective, causes myofibrillar myopathy, a group of morphologically homogeneous, but genetically heterogeneous neuromuscular disorders. The morphologic changes in skeletal muscle result from disintegration of the sarcomeric Z disc and the myofibrils, followed by abnormal ectopic accumulation of multiple proteins involved in the structure of the Z disc. Clinical manifestations are variable and can involve the skeletal, cardiac and smooth muscle.
subclass of: Disease
narrower: Desmin-related myopathy
category: Disease

Myogenesis
type: Concept
alternative label: Muscle development
alternative label: Muscle formation
comment: 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.
subclass of: Biological process
category: Biological process

muscle organ development
type: Class
database: go

Myosin
type: Concept
comment: A motor protein which uses the energy provided by the hydrolysis of ATP to drive movements along actin filaments. Different types of myosin are found in eukaryotic cells.
subclass of: Motor protein
category: Molecular function

myosin complex
type: Class
database: go

Myotoxin
type: Concept
comment: Protein which causes muscle necrosis. Myotoxins are principally found in snake venoms. The myotoxic activity can be monitored by morphological analysis and by the increase of plasma creatine kinase (CK) activity. The increase in plasma CK levels results from sarcolemmal damage due to myotoxic components of the venom.
subclass of: Toxin
category: Molecular function

Myristate
type: Concept
alternative label: Myristylated
alternative label: n-tetradecanoate
comment: Protein which is posttranslationally modified by the attachment of at least one myristate group. The myristate (14-carbon saturated fatty acid) group is attached through an amide bond to the N-terminal glycine residue of the mature form of a protein or to an internal lysine residue. Myristoylproteins may be cytoplasmic or membrane-associated.
subclass of: Lipoprotein
category: PTM

NAD
type: Concept
alternative label: Nicotinamide adenine dinucleotide
alternative label: Nicotinic adenine dinucleotide
comment: Enzymes which use NAD(H) as an electron acceptor or as a cofactor. Nicotinamide adenine dinucleotide, an important redox coenzyme that participates in a variety of enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). NAD also functions as an ADP-ribose donor in ADP-ribosylation reactions.
subclass of: Ligand
category: Ligand

NADP
type: Concept
alternative label: Nicotinamide adenine dinucleotide phosphate
alternative label: Nicotinic adenine dinucleotide phosphate
comment: Enzymes which use NADP(H) as an electron acceptor or as a cofactor. Nicotinamide adenine dinucleotide phosphate, a redox coenzyme that participates in a variety of enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NADP+) and reduced (NADPH). Analogue of NAD, but NADPH is used extensively in biosynthetic, rather than catabolic pathways as well as in photosynthesis.
subclass of: Ligand
category: Ligand

Necrosis
type: Concept
alternative label: Necroptosis
alternative label: Necrotic cell death
alternative label: Necrotic programmed cell death
comment: Protein involved in necrotic programmed cell death. Necrosis is a form of traumatic cell death that results from acute cellular injury due infection, toxins, trauma, etc. Necrosis is characterized by blebbing, mitochondrial fission, loss of cell membrane integrity and an uncontrolled release of products of cell death into the intracellular space. This initiates an inflammatory response in the surrounding tissue often resulting is a build-up of dead tissue and cell debris at, or near, the site of the cell death.
subclass of: Biological process
category: Biological process

programmed cell death
type: Class
database: go

Nemaline myopathy
type: Concept
alternative label: NEM
alternative label: NM
alternative label: Rod body myopathy
alternative label: Rod myopathy
comment: Protein which, if defective, causes nemaline myopathy, a hereditary neuromuscular disorder characterized by generally non-progressive muscle weakness of varying severity, and abnormal thread- or rod-like structures in muscle fibers on histologic examination. The age of onset varies from birth to adulthood. The main clinical manifestations include weakness (usually most severe in the face, the neck flexors, and the proximal limb muscles), hypotonia, and depressed or absent deep tendon reflexes. Nemaline myopathy is divided into several broad groups classified by onset and severity of motor and respiratory involvement.
subclass of: Disease
category: Disease

Nematocyst
type: Concept
alternative label: Cnidocyst
comment: Protein localized in the nematocyst, an organelle found in nematoblast (cnidoblast) cells. When matured, these stinging organelles store toxins and can deliver them when the cnidocil (a short extension of the nematocyst) is stimulated by a prey or another stimulus. These proteins are principally found in anemones and jellyfishes.
subclass of: Cellular component
category: Cellular component

nematocyst
type: Class
database: go

Nephronophthisis
type: Concept
alternative label: NPHP
comment: Protein which, if defective, causes nephronophthisis, a chronic tubulo-interstitial nephritis that progresses to end-stage renal failure. Clinical features include anemia, polyuria, polydipsia, isosthenuria, and death in uremia. Some children present with extrarenal symptoms such as tapeto-retinal degeneration, mental retardation, cerebellar ataxia, bone anomalies or liver involvement.
subclass of: Disease
category: Disease

Neurodegeneration
type: Concept
comment: Protein which, if defective, causes neurodegeneration.
subclass of: Disease
narrower: Amyotrophic lateral sclerosis
narrower: Neuronal ceroid lipofuscinosis
narrower: Hereditary spastic paraplegia
narrower: Spinocerebellar ataxia
category: Disease

Neurogenesis
type: Concept
alternative label: Nervous system development
alternative label: Nervous system formation
comment: Protein involved in neurogenesis, which involves the differentiation and development of the nervous system.
subclass of: Biological process
category: Biological process

nervous system development
type: Class
database: go

Neuronal ceroid lipofuscinosis
type: Concept
alternative label: CLN
alternative label: NCL
comment: Protein which, if defective, causes neuronal ceroid lipofuscinosis, a group of neurodegenerative, lysosome storage disorders characterized by intracellular accumulation of autofluorescent wax-like lipid materials in brain and other tissues. Neuronal ceroid lipofuscinoses are associated with variable yet progressive symptoms including seizures, dementia, visual loss, and/or cerebral atrophy.
subclass of: Neurodegeneration
category: Disease

Neuropathy
type: Concept
comment: Protein which, if defective, causes neuropathy, a functional disturbance or pathological change in the peripheral nervous system, sometimes limited to non-inflammatory lesions as opposed to those of neuritis. Neuropathies affecting a specific nerve may be named for the nerve. The terms mononeuropathy and polyneuropathy may be used to denote whether one or several nerves are involved.
subclass of: Disease
narrower: Charcot-Marie-Tooth disease
narrower: Dejerine-Sottas syndrome
category: Disease

Neuropeptide
type: Concept
comment: Peptides released by neurons as intercellular messengers. Many neuropeptides are also hormones released by non-neuronal cells. They have direct synaptic effects (peptide neurotransmitters) or indirect modulatory effects on the nervous system (peptide neuromodulators).
subclass of: Molecular function
category: Molecular function

Neurotoxin
type: Concept
comment: 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.
subclass of: Toxin
narrower: Postsynaptic neurotoxin
narrower: Presynaptic neurotoxin
category: Molecular function

Neurotransmitter
type: Concept
comment: Protein, released by the axon terminal in response to an electrical impulse, which travels across the synapse to either excite or inhibit the target cell.
subclass of: Molecular function
category: Molecular function

chemical synaptic transmission
type: Class
database: go

Neurotransmitter biosynthesis
type: Concept
alternative label: Neurotransmitter anabolism
alternative label: Neurotransmitter biosynthetic process
alternative label: Neurotransmitter formation
alternative label: Neurotransmitter synthesis
comment: Protein involved in the synthesis of neurotransmitters. The proteins are released by the axon terminal in response to an electrical impulse and travel across the synapse to either excite or inhibit the target cell.
subclass of: Biological process
category: Biological process

neurotransmitter biosynthetic process
type: Class
database: go

Neurotransmitter degradation
type: Concept
alternative label: Neurotransmitter breakdown
alternative label: Neurotransmitter catabolic process
alternative label: Neurotransmitter catabolism
comment: Protein involved in the breakdown of neurotransmitters. The proteins are released by the axon terminal in response to an electrical impulse and travel across the synapse to either excite or inhibit the target cell.
subclass of: Biological process
category: Biological process

neurotransmitter catabolic process
type: Class
database: go

Neurotransmitter transport
type: Concept
comment: Protein involved in the transport of neurotransmitters. The proteins are released by the axon terminal in response to an electrical impulse and travel across the synapse to either excite or inhibit the target cell.
subclass of: Transport
category: Biological process

neurotransmitter transport
type: Class
database: go

Nickel
type: Concept
alternative label: Ni
alternative label: Ni cation
alternative label: Nickel cation
alternative label: Nickel ion
alternative label: Ni ion
comment: Protein which binds at least one nickel atom, or protein whose function is nickel-dependent. Nickel is a metal, chemical symbol Ni.
subclass of: Ligand
narrower: Nickel transport
category: Ligand

Nickel insertion
type: Concept
alternative label: Ni insertion
comment: Protein which is involved in the creation and/or insertion of a nickel metallocenter into another protein, without necessarily binding the metal itself.
subclass of: Biological process
category: Biological process

Nickel transport
type: Concept
alternative label: Nickel cation transport
alternative label: Nickel ion transport
alternative label: Ni transport
comment: Protein involved in the transport of nickel.
subclass of: Ion transport
subclass of: Nickel
category: Biological process

nickel cation transport
type: Class
database: go

Niemann-Pick disease
type: Concept
alternative label: Niemann's disease
alternative label: NPD
comment: Protein which, if defective, causes Niemann-Pick disease. Niemann-Pick disease comprises an inherited group of congenital lipidoses in which sphingolipids accumulate in cells, especially in the reticuloendothelial system, due to defective lysosomal storage. The disease is clinically characterized by progressive degeneration of the central nervous system with visceral accumulation of cholesterol and sphingomyelin. The clinical phenotype is highly variable and different types are distinguished by age of onset, degree of central nervous system involvement and by the amount of sphingomyelin phosphodiesterase activity.
subclass of: Disease
category: Disease

Nitrate assimilation
type: Concept
comment: Protein involved in the uptake, from the environment, of nitrates, inorganic or organic salts and esters of nitric acid. This includes the uptake and transport into cells by nitrate transporters, with the sequential reduction to nitrite and ammonium, catalyzed by the enzymes nitrate reductase and nitrite reductase, respectively.
subclass of: Biological process
category: Biological process

nitrate assimilation
type: Class
database: go

Nitration
type: Concept
alternative label: Nitrated
comment: Protein which is posttranslationally modified by replacement of a hydrogen on an aromatic ring of one or more tyrosine or tryptophan residues by a nitro (NO2) group.
subclass of: PTM
category: PTM

Nitrogen fixation
type: Concept
comment: Protein involved in nitrogen fixation, the reduction of gaseous nitrogen to ammonia. This process is carried out only by prokaryotes who are either free-living or form symbiotic associations with plants or other organisms (e.g. termites, protozoa).
subclass of: Biological process
category: Biological process

nitrogen fixation
type: Class
database: go

Nodulation
type: Concept
comment: Protein involved in nodulation, the formation of nitrogen-fixing nodules on roots of both leguminous plants and the Parasponia genus.
subclass of: Biological process
category: Biological process

nodulation
type: Class
database: go

Non-syndromic deafness
type: Concept
alternative label: Isolated deafness
comment: Protein which, if defective, causes inability to hear in the absence of other clinical signs and symptoms. Most forms of non-syndromic deafness are associated with permanent hearing loss caused by damage to structures in the inner ear.
subclass of: Deafness
category: Disease

Nonsense-mediated mRNA decay
type: Concept
alternative label: NMD
comment: Protein involved in nonsense-mediated messenger RNA (mRNA) decay, a critical process of selective degradation of mRNAs that contain premature stop codons.
subclass of: Biological process
category: Biological process

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
type: Class
database: go

Notch signaling pathway
type: Concept
comment: Protein involved in the Notch signaling, a signaling pathway involved in cell-cell communications that regulates a broad spectrum of cell-fate determinations. Notch proteins are transmembrane receptors, which are cleaved by the gamma-secretase complex upon activation and released from the cell membrane and turn into transcriptional activators after their association with SU(H) proteins.
subclass of: Biological process
category: Biological process

Notch signaling pathway
type: Class
database: go

Nuclear pore complex
type: Concept
alternative label: NPC
alternative label: Nuclear pore
comment: Protein associated predominantly with the nuclear pore complex (NPC). NPCs constitute the exclusive means of nucleocytoplasmic transport in eukaryotes during interphase. NPCs allow the passive diffusion of ions and small molecules (up to about 20 kDa or 5 nm) and the active, nuclear transport receptor (karyopherin: importin and exportin)-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoprotein (RNPs), and ribosomal subunits (up to about 10 MDa) across the double-membrane nuclear envelope. NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. The NPC is composed of at least 30 distinct subunits, shows 8-fold rotational symmetry with specialized structures on the cyto- and nucleoplasmic side and in the nuclear envelope embedded core. The MW varies from about 44-60 MDa in S. cerevisiae to 60-120 MDa in vertebrates, yet the overall architecture is conserved.
subclass of: mRNA transport
subclass of: Nucleus
subclass of: Translocation
category: Cellular component

nuclear pore
type: Class
database: go

Nuclease
type: Concept
comment: Enzyme that degrades nucleic acids into shorter oligonucleotides or single nucleotide subunits by hydrolyzing sugar-phosphate bonds in the nucleic acid backbone.
subclass of: Hydrolase
narrower: Endonuclease
narrower: Exonuclease
category: Molecular function

Nucleomorph
type: Concept
comment: Protein associated with the nucleomorph. A nucleomorph is a remnant nucleus found between the outer two and inner two membranes of the plastid in cryptomonads and chlorarachniophyte algae.
subclass of: Cellular component
category: Cellular component

nucleomorph
type: Class
database: go

Nucleosome core
type: Concept
comment: Protein characteristic of the nucleosome, a repeating structural unit in chromatin that packages DNA to give the chromatin a 'beads-on-a-string' appearance. Each repeat consists of approximately 146 base pairs of DNA wound around a disk-shaped protein core which is composed of two of each of the nucleosomal histones H2A, H2B, H3 and H4.
subclass of: Chromosome
subclass of: DNA-binding
category: Cellular component

nucleosome
type: Class
database: go

Nucleotide biosynthesis
type: Concept
alternative label: Nucleotide anabolism
alternative label: Nucleotide biosynthetic process
alternative label: Nucleotide formation
alternative label: Nucleotide synthesis
comment: Protein involved in the synthesis of a nucleotide, a phosphate ester of a nucleoside consisting of a purine or pyrimidine base linked to ribose or deoxyribose phosphates.
subclass of: Biological process
category: Biological process

nucleotide biosynthetic process
type: Class
database: go

Nucleotide metabolism
type: Concept
alternative label: Nucleotide metabolic process
comment: Protein involved in the biochemical reactions of nucleotides. Nucleotides are phosphate esters of a nucleoside consisting of a purine or pyrimidine base linked to ribose or deoxyribose phosphates.
subclass of: Biological process
category: Biological process

nucleotide metabolic process
type: Class
database: go

Nucleotide-binding
type: Concept
comment: Protein which binds a nucleotide, a phosphate ester of a nucleoside consisting of a purine or pyrimidine base linked to ribose or deoxyribose phosphates.
subclass of: Ligand
narrower: ATP-binding
narrower: cAMP-binding
narrower: cGMP-binding
narrower: GTP-binding
category: Ligand

nucleotide binding
type: Class
database: go

Nucleotidyltransferase
type: Concept
comment: Enzyme which transfers a nucleotide from one compound to another.
subclass of: Transferase
narrower: DNA-directed DNA polymerase
narrower: RNA-directed DNA polymerase
narrower: RNA-directed RNA polymerase
narrower: Terminal addition
category: Molecular function

nucleotidyltransferase activity
type: Class
database: go

Nucleus
type: Concept
comment: Protein located in the nucleus of a cell.
subclass of: Cellular component
narrower: Nuclear pore complex
category: Cellular component

nucleus
type: Class
database: go

Nylon degradation
type: Concept
alternative label: Nylon breakdown
alternative label: Nylon catabolic process
alternative label: Nylon catabolism
comment: Protein involved in the degradation of nylon, a polymer whose main chain comprises recurrent amide groups. These compounds are generally formed from combinations of diamines, diacids and amino acids.
subclass of: Biological process
category: Biological process

nylon catabolic process
type: Class
database: go

Obesity
type: Concept
comment: Protein which, if defective, causes obesity, a disorder characterized by excessive deposition of fat.
subclass of: Disease
category: Disease

Olfaction
type: Concept
comment: Protein involved in olfaction, the process of smelling.
subclass of: Sensory transduction
category: Biological process

sensory perception of smell
type: Class
database: go

Oncogene
type: Concept
alternative label: Oncoprotein
comment: Protein encoded by an oncogene, which promotes cell transformation. Examples include viral homologs of cellular proto-oncogenes such as the transcription factors v-myc and v-jun, the growth factor v-fgr, the regulatory GTPase v-ras, and papillomavirus protein E6.
subclass of: Disease
category: Disease

One-carbon metabolism
type: Concept
alternative label: One-carbon compound metabolic process
comment: Protein involved in the biochemical reactions with one-carbon groups, e.g., methyl and formyl groups.
subclass of: Biological process
category: Biological process

one-carbon metabolic process
type: Class
database: go

Oogenesis
type: Concept
comment: Protein involved in egg development and maturation. A process whereby primordial germ cells form mature ova.
subclass of: Differentiation
category: Biological process

oogenesis
type: Class
database: go

Opioid peptide
type: Concept
comment: Endogenous peptides with opiate-like activity.
subclass of: Molecular function
category: Molecular function

opioid peptide activity
type: Class
database: go

Organellar chromatophore
type: Concept
comment: Protein encoded by the organellar chromatophore genome or a protein targeted to the organellar chromatophore. The organellar chromatophore is the photosynthetic inclusion found in Paulinella species, which are photosynthetic thecate amoeba. It probably derives from a different endosymbiotic event than that which led to all other plastids. Houses the machinery necessary for photosynthesis and CO(2) fixation; it also has the genetic capacity to synthesize some amino acids, some fatty acids and a few cofactors. It contains thylakoid membranes, and a residual peptidoglycan wall between the 2 envelope membranes. There are 1 or 2 chromatophores per cell.
subclass of: Plastid
category: Cellular component

organellar chromatophore
type: Class
database: go

Organic radical
type: Concept
comment: Protein which is posttranslationally modified by the formation of a stable radical. E.g., P09373 is posttranslationally interconverted, under anaerobic conditions, from an inactive to an active form that carries a stable radical localized to a specific glycine at the C-terminal region of the polypeptidic chain.
subclass of: PTM
category: PTM

Osteogenesis
type: Concept
alternative label: Bone formation
alternative label: Ossification
comment: Protein involved in osteogenesis, the mechanism of bone formation wether intramembranous or endochondral. In intramembranous ossification, bone is formed by differentiation of mesenchymal cells into osteoblasts with absence of a cartilaginous model. The flat bones of the skull, the sternum, and the scapula are examples of bones that develop by intramembranous ossification. The term endochondral refers to the close association of the developing bone with the pre-existing hyaline cartilage model of that bone. The long bones of the limbs (including the phalanges) and the ribs develop by endochondral ossification.
subclass of: Biological process
category: Biological process

ossification
type: Class
database: go

Osteogenesis imperfecta
type: Concept
alternative label: Brittle bone disease
alternative label: Fragilitas ostium
alternative label: Glass bone disease
alternative label: Lobstein's disease
alternative label: Lobstein disease
comment: Protein which, if defective, causes osteogenesis imperfecta, a bone disorder characterized by low bone mass, and brittle, osteoporotic and easily fractured bones. It may also present with blue sclerae, loose joints, and imperfect dentin formation.
subclass of: Disease
category: Disease

Osteopetrosis
type: Concept
comment: Protein which, if defective, causes osteopetrosis, an hereditary disorder characterized by abnormally dense bone due to reduced bone resorption, and by the common occurrence of fractures of affected bones.
subclass of: Disease
category: Disease

Outer capsid protein
type: Concept
comment: Viral protein that is a component of the outer layer of a double or triple concentric icosahedral capsid. Outer capsids are part of reoviridae and cystoviridae virions.
subclass of: Capsid protein
category: Cellular component

viral outer capsid
type: Class
database: go

Oxidation
type: Concept
comment: Protein which is posttranslationally modified by oxidation of a residue.
subclass of: PTM
category: PTM

Oxidoreductase
type: Concept
comment: Enzyme that catalyzes the oxidation of one compound with the reduction of another.
subclass of: Molecular function
narrower: Dioxygenase
narrower: Monooxygenase
narrower: Peroxidase
category: Molecular function

oxidoreductase activity
type: Class
database: go

Oxygen transport
type: Concept
comment: Protein involved in the transport of oxygen (e.g. hemoglobin and myoglobin).
subclass of: Transport
category: Biological process

oxygen carrier activity
type: Class
database: go

oxygen transport
type: Class
database: go

Oxylipin biosynthesis
type: Concept
alternative label: Oxylipin anabolism
alternative label: Oxylipin biosynthetic process
alternative label: Oxylipin formation
alternative label: Oxylipin synthesis
comment: Protein involved in the synthesis of oxygenated fatty acids (oxylipins), including jasmonic acid (jasmonate) (JA) and its derivatives. Oxylipins regulate many defense and developmental pathways in plants. JA is involved in wound-mediated signaling pathways, plant defense, and reproductive development. It acts as a growth inhibitor and promotes senescence.
subclass of: Fatty acid biosynthesis
category: Biological process

oxylipin biosynthetic process
type: Class
database: go

Pair-rule protein
type: Concept
comment: 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.
subclass of: Developmental protein
category: Molecular function

periodic partitioning by pair rule gene
type: Class
database: go

Paired box
type: Concept
comment: 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.
subclass of: Domain
category: Domain

Palmitate
type: Concept
alternative label: n-hexadecanoate
alternative label: Palmitoylated
comment: Protein which is posttranslationally modified by the attachment of at least one palmitate group. The palmitate (16-carbon saturated fatty acid) group is usually attached to cysteine via a thioester bond. Lysine, serine and threonine may also serve as palmitate acceptors. Many palmitoylproteins are membrane associated either directly through the palmitate moiety or as transmembrane proteins anchored by the fatty acid. However, a few are actually secreted from cells.
subclass of: Lipoprotein
category: PTM

Palmoplantar keratoderma
type: Concept
alternative label: Hyperkeratosis palmaris et plantaris
alternative label: Keratoderma palmaris et plantaris
alternative label: Keratosis palmoplantaris
alternative label: Palmoplantar keratosis
alternative label: PPK
comment: Protein which, if defective, causes hereditary palmoplantar keratoderma (PPK), a genetically and clinically diverse group of cutaneous disorders characterized by abnormal thickening of the skin on the palms and soles. It results from excessive keratin formation leading to hypertrophy of the stratum corneum (hyperkeratosis). PPKs are distinguished from each other on the basis of mode of inheritance, presence of transgrediens (defined as contiguous extension of hyperkeratosis beyond the palmar and/or plantar skin), association with other skin findings and/or abnormalities of other organs, and extent of epidermal involvement (diffuse, focal, punctate). Diffuse PPK is characterized by uniform involvement of the palmoplantar surface; focal PPK consists of localized areas of hyperkeratosis located mainly on pressure points and sites of recurrent friction; punctate PPK shows multiple small, hyperkeratotic papules or nodules on the palms and soles.
subclass of: Disease
category: Disease

Pantothenate biosynthesis
type: Concept
alternative label: Pantothenate anabolism
alternative label: Pantothenate biosynthetic process
alternative label: Pantothenate formation
alternative label: Pantothenate synthesis
comment: Protein involved in the synthesis of pantothenate.
subclass of: Biological process
category: Biological process

pantothenate biosynthetic process
type: Class
database: go

Parkinson disease
type: Concept
alternative label: Paralysis agitans
alternative label: Parkinson's disease
alternative label: PD
comment: Protein which, if defective, causes classic Parkinson disease. Parkinson disease is a complex multifactorial neurodegenerative disorder, usually occurring in late life, although an early onset and a juvenile form are known. Typical features are masklike facies, tremor of resting muscles, a slowing of voluntary movements (bradykinesia), festinating gait and postural instability. The signs and symptoms of the disease are the consequence of a striatal deficiency of dopamine, resulting from neuronal death in the substantia nigra. Parkinson disease is characterized by the presence of Lewy bodies, intraneuronal inclusions found in many brain regions which are not entirely specific to, but are a highly sensitive marker for, Parkinson disease.
subclass of: Disease
category: Disease

Parkinsonism
type: Concept
comment: Protein which, if defective, causes parkinsonism. Parkinsonism refers to disorders, both genetic and non-genetic, characterized by four primary parkinsonian symptoms: tremor, rigidity, postural instability and bradykinesia, resulting from the loss or dysfunction of dopamine-producing neurons in the substantia nigra. Lewy bodies, intraneuronal accumulations of aggregated proteins, may or may not be present in the brain of the patients.
subclass of: Disease
category: Disease

Pathogenesis-related protein
type: Concept
alternative label: PR protein
comment: Protein induced in several plant species when they are infected by viruses, viroids, fungi or bacteria. The occurrence of these proteins is not pathogen-specific, but determined by the type of reaction of the host plant. They form a protective barrier against pathogens by collecting at infection sites and act to decrease susceptibility of plants. They may have anti-fungal or anti-bacterial activity.
subclass of: Plant defense
subclass of: Molecular function
category: Molecular function

response to biotic stimulus
type: Class
database: go

Pentose shunt
type: Concept
alternative label: Hexose monophosphate pathway
alternative label: Pentose phosphate pathway
alternative label: Phosphogluconate oxidative pathway
comment: Protein involved in the pentose shunt, the biochemical pathway in which glucose-6-phosphate is oxidized to 6-phosphogluconate with the production of NADPH. Then 6-phosphogluconate is converted to ribulose-5-phosphate and CO2 and a second molecule of NADH. This pathway is an important source of NADPH and ribose-5-phosphate.
subclass of: Biological process
category: Biological process

pentose-phosphate shunt
type: Class
database: go

Peptide transport
type: Concept
comment: Protein involved in the transport of peptides.
subclass of: Protein transport
category: Biological process

peptide transport
type: Class
database: go

Peptidoglycan synthesis
type: Concept
alternative label: Murein anabolism
alternative label: Murein biosynthesis
alternative label: Murein biosynthetic process
alternative label: Murein formation
alternative label: Murein synthesis
alternative label: Peptidoglycan anabolism
alternative label: Peptidoglycan biosynthesis
alternative label: Peptidoglycan biosynthetic process
alternative label: Peptidoglycan formation
alternative label: Pseudomurein anabolism
alternative label: Pseudomurein biosynthesis
alternative label: Pseudomurein biosynthetic process
alternative label: Pseudomurein formation
alternative label: Pseudomurein synthesis
comment: Protein involved in the synthesis of peptidoglycan which consists of a glycosaminoglycan formed by alternating residues of D-glucosamine and either muramic acid {2-amino-3-O-[(R)-1-carboxyethyl]-2-deoxy-D-glucose} or L-talosaminuronic acid (2-amino-2-deoxy-L-taluronic acid), which are usually N-acetylated or N-glycoloylated. The carboxyl group of the muramic acid is commonly substituted by a peptide containing residues of both L- and D-amino acids, whereas that of L-talosaminuronic acid is substituted by a peptide consisting of L-amino acids only. These peptide units may be cross-linked by a peptide bond, thereby giving rise to a giant macromolecule that forms the rigid cell wall (sacculus or murein sacculus). This macromolecule is known to occur as a monomolecular layer between the inner and outer membrane in Gram-negative bacteria and as a multimolecular layer, often associated covalently or non-covalently with various additional compounds (teichoic acids, neutral polysaccharides. etc.) in Gram-positive bacteria. In the archaebacteria, several organisms contain a peptidoglycan, also called pseudomurein, which differs in certain respects from those of the eubacteria.
subclass of: Cell shape
subclass of: Biological process
category: Biological process

peptidoglycan biosynthetic process
type: Class
database: go

Peptidoglycan-anchor
type: Concept
comment: Protein that is covalently anchored to the peptidoglycan of a cell wall envelope. In Gram-positive bacteria, binding proceeds through a transpeptidation mechanism which requires a C-terminal sorting signal with a conserved LPXTG or LPXAG motif; an amide bond is created between the alpha-carboxyl group of the conserved threonine, alternatively alanine, and the amino group of peptidoglycan cross-bridges. In Gram-negative bacteria, binding proceeds through the formation of an isopeptide bond between the epsilon-amino group of a lysine and the alpha-carboxyl group of a peptidoglycan diaminopimelic acid.
subclass of: PTM
category: PTM

Periplasm
type: Concept
comment: Protein located in the space between the inner membrane and the outer membrane (cell wall) of Gram negative bacteria and some eukaryotic algae. Also used for proteins located in the region between the plasma membrane and the cell wall in fungi.
subclass of: Cellular component
category: Cellular component

periplasmic space
type: Class
database: go

Peroxidase
type: Concept
comment: Enzyme that catalyzes the oxidation of a substrate by reducing peroxide to water. These enzymes are often located in peroxisomes.
subclass of: Oxidoreductase
narrower: Hydrogen peroxide
category: Molecular function

peroxidase activity
type: Class
database: go

Peroxisome
type: Concept
comment: Protein found in or associated with the peroxisome, a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions. Contains mainly peroxidases, several other oxidases and catalase. The catalase regulates the contents of the produced toxic hydrogen peroxide thus protecting the cell. Beta-oxidation of fatty acids is another major function of peroxisomes. In plants and fungi this degradation occurs only in this cellular compartment.
subclass of: Cellular component
category: Cellular component

peroxisome
type: Class
database: go

Peroxisome biogenesis
type: Concept
alternative label: Peroxisome assembly
alternative label: Peroxisome formation
comment: Protein which is involved in the formation, organization and maintenance of the peroxisome. The peroxisome is a small eukaryotic organelle limited by a single membrane, specialized for carrying out oxidative reactions.
subclass of: Biological process
category: Biological process

peroxisome organization
type: Class
database: go

Peroxisome biogenesis disorder
type: Concept
alternative label: PBD
alternative label: Peroxisome-biogenesis disorder
comment: Protein which, if defective, causes peroxisome biogenesis disorder, a group of peroxisomal disorders arising from a failure of protein import into the peroxisomal membrane or matrix. The PBD group is comprised of four disorders: Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata type 1 (RCDP1). ZWS, NALD and IRD are distinct from RCDP1 and constitute a clinical continuum of overlapping phenotypes known as Zellweger spectrum. The PBD group is genetically heterogeneous with at least 12 distinct genetic groups as concluded from complementation studies.
subclass of: Disease
narrower: Zellweger syndrome
category: Disease

Peters anomaly
type: Concept
comment: Protein which, if defective, causes Peters anomaly, an ocular disorder characterized by congenital central corneal leukoma, absence of the posterior corneal stroma and Descemet membrane, and a variable degree of iris and lenticular attachments to the central aspect of the posterior cornea.
subclass of: Disease
category: Disease

PHA biosynthesis
type: Concept
alternative label: PHA anabolism
alternative label: PHA biosynthetic process
alternative label: PHA formation
alternative label: PHA synthesis
alternative label: Poly(3-hydroxyalkanoate) anabolism
alternative label: Poly(3-hydroxyalkanoate) biosynthesis
alternative label: Poly(3-hydroxyalkanoate) biosynthetic process
alternative label: Poly(3-hydroxyalkanoate) formation
alternative label: Poly(3-hydroxyalkanoate) synthesis
comment: Protein involved in the synthesis of poly(3-hydroxyalkanoates) (PHA). In Pseudomonas oleovorans large amounts of this polyester are synthesized when cells are grown under nitrogen-limiting conditions. When nitrogen is further supplied in the medium, the accumulated PHA is degraded.
subclass of: Biological process
category: Biological process

poly(3-hydroxyalkanoate) biosynthetic process
type: Class
database: go

Phagocytosis
type: Concept
comment: Protein that is involved in phagocytosis or that renders the organism resistant to phagocytosis, the process by which a cell is engulfed and broken down by another for purposes of defense or sustenance.
subclass of: Biological process
category: Biological process

phagocytosis
type: Class
database: go

Pharmaceutical
type: Concept
comment: Protein which is used or may be used as a pharmaceutical drug, e.g. to treat specific diseases.
subclass of: Technical term
category: Technical term

PHB biosynthesis
type: Concept
alternative label: PHB anabolism
alternative label: PHB biosynthetic process
alternative label: PHB formation
alternative label: PHB synthesis
alternative label: Poly-(3-hydroxybutyrate) anabolism
alternative label: Poly-(3-hydroxybutyrate) biosynthesis
alternative label: Poly-(3-hydroxybutyrate) biosynthetic process
alternative label: Poly-(3-hydroxybutyrate) formation
alternative label: Poly-(3-hydroxybutyrate) synthesis
alternative label: Poly-beta-hydroxybutyrate anabolism
alternative label: Poly-beta-hydroxybutyrate biosynthesis
alternative label: Poly-beta-hydroxybutyrate biosynthetic process
alternative label: Poly-beta-hydroxybutyrate formation
alternative label: Poly-beta-hydroxybutyrate synthesis
alternative label: Poly-hydroxybutyrate anabolism
alternative label: Poly-hydroxybutyrate biosynthesis
alternative label: Poly-hydroxybutyrate biosynthetic process
alternative label: Poly-hydroxybutyrate formation
alternative label: Poly-hydroxybutyrate synthesis
comment: Protein involved in the synthesis of poly-hydroxybutyrate (PHB). It accumulates in a variety of bacteria as an energy source. This polyester is thermoplastic with biodegradable properties.
subclass of: Biological process
category: Biological process

poly-hydroxybutyrate biosynthetic process
type: Class
database: go

Phenylalanine biosynthesis
type: Concept
alternative label: Phenylalanine anabolism
alternative label: Phenylalanine biosynthetic process
alternative label: Phenylalanine formation
alternative label: Phenylalanine synthesis
comment: Protein involved in the biosynthesis of the aromatic amino acid phenylalanine.
subclass of: Aromatic amino acid biosynthesis
category: Biological process

L-phenylalanine biosynthetic process
type: Class
database: go

Phenylalanine catabolism
type: Concept
alternative label: Phenylalanine breakdown
alternative label: Phenylalanine catabolic process
alternative label: Phenylalanine degradation
comment: Protein involved in the degradation of the aromatic amino acid phenylalanine.
subclass of: Biological process
category: Biological process

L-phenylalanine catabolic process
type: Class
database: go

Phenylketonuria
type: Concept
comment: Protein which, if defective, causes phenylketonuria, an autosomal recessive disorder in which the body is unable to break down the amino acid phenylalanine. The resulting buildup of phenylalanine in the body causes intellectual disability, mental disturbances, eczema and skin pigmentation.
subclass of: Disease
category: Disease

Phenylpropanoid metabolism
type: Concept
alternative label: Phenylpropanoid metabolic process
comment: Protein involved in the biochemical reactions with phenylpropanoids.
subclass of: Biological process
category: Biological process

phenylpropanoid metabolic process
type: Class
database: go

Pheromone
type: Concept
comment: Proteins which acts as a pheromone. Pheromones are odours of conspecifics which elicit an adaptive behavioral response, e.g. insect sex pheromones. Generally, they are comprised of mixtures of compounds and behavioral responsiveness to them is largely instinctual, sexually-dimorphic, and attributable to a specialized component(s) of the olfactory system.
subclass of: Molecular function
category: Molecular function

pheromone activity
type: Class
database: go

Pheromone response
type: Concept
alternative label: Pheromone response pathway
alternative label: Response to pheromone
comment: Protein involved in the pheromone response.
subclass of: Biological process
category: Biological process

response to pheromone
type: Class
database: go

Pheromone-binding
type: Concept
comment: Protein which binds pheromones, the odours of conspecifics which elicit an adaptive behavioral response, e.g. insect sex pheromones.
subclass of: Ligand
category: Ligand

pheromone binding
type: Class
database: go

Phosphate transport
type: Concept
comment: Protein involved in the transport of phosphate.
subclass of: Transport
category: Biological process

phosphate ion transport
type: Class
database: go

Phospholipase A2 inhibitor
type: Concept
comment: Protein which inhibits phospholipase A2 (EC 3.1.1.4) (PA2), an enzyme which releases fatty acids from the second carbon group of glycerol. Phospholipase A2 inhibitors are widely distributed in venoms and digestive secretions.
subclass of: Molecular function
category: Molecular function

phospholipase A2 inhibitor activity
type: Class
database: go

Phospholipid biosynthesis
type: Concept
alternative label: Phospholipid anabolism
alternative label: Phospholipid biosynthetic process
alternative label: Phospholipid formation
alternative label: Phospholipid synthesis
comment: Protein involved in the synthesis of phospholipids, the major lipid component of most cellular membranes. Phospholipids are usually composed of two fatty acid chains esterified to two of the carbons of glycerol phosphate, the phosphate being esterified to a hydroxyl group of another hydrophilic compound, such as choline, ethanolamine or serine.
subclass of: Lipid biosynthesis
subclass of: Phospholipid metabolism
category: Biological process

phospholipid biosynthetic process
type: Class
database: go

Phospholipid degradation
type: Concept
alternative label: Phospholipid breakdown
alternative label: Phospholipid catabolic process
alternative label: Phospholipid catabolism
comment: Protein involved in the breakdown of phospholipids, the major lipid component of most cellular membranes. Phospholipids are usually composed of two fatty acid chains esterified to two of the carbons of glycerol phosphate, the phosphate being esterified to a hydroxyl group of another hydrophilic compound, such as choline, ethanolamine or serine.
subclass of: Lipid degradation
subclass of: Phospholipid metabolism
category: Biological process

phospholipid catabolic process
type: Class
database: go

Phospholipid metabolism
type: Concept
alternative label: Phospholipid metabolic process
comment: Protein involved in the metabolism of phospholipids, the major lipid component of most cellular membranes. Phospholipids are usually composed of two fatty acid chains esterified to two of the carbons of glycerol phosphate, the phosphate being esterified to a hydroxyl group of another hydrophilic compound, such as choline, ethanolamine or serine.
subclass of: Lipid metabolism
narrower: Phospholipid biosynthesis
narrower: Phospholipid degradation
category: Biological process

Phosphonate transport
type: Concept
comment: Protein involved in the transport of phosphonates. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only prokaryotic microorganisms are able to cleave this bond. Certain bacteria such as Escherichia coli can use alkylphosphonates as a phosphorus source.
subclass of: Transport
category: Biological process

Phosphopantetheine
type: Concept
alternative label: Pantetheine 4'phosphate
comment: Protein which contains at least one phosphopantetheine as the prosthetic group. In acyl carrier proteins (ACP) for example, it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups.
subclass of: PTM
category: PTM

Phosphoprotein
type: Concept
alternative label: Phosphorylation
comment: Protein which is posttranslationally modified by the attachment of either a single phosphate group, or of a complex molecule, such as 5'-phospho-DNA, through a phosphate group. Target amino acid is usually serine, threonine or tyrosine residues (mostly in eukaryotes), aspartic acid or histidine residues (mostly in prokaryotes).
subclass of: PTM
category: PTM

Phosphotransferase system
type: Concept
alternative label: Phosphoenolpyruvate-dependent sugar phosphotransferase system
alternative label: PTS
alternative label: Sugar phosphotransferase system
comment: Protein involved in the phosphotransferase system, the major carbohydrate transport system in bacteria. This phosphotransferase system catalyzes the transfer of the phosphoryl group from phosphoenolpyruvate to incoming sugar substrates concomitant with their translocation across the cell membrane.
subclass of: Biological process
category: Biological process

phosphoenolpyruvate-dependent sugar phosphotransferase system
type: Class
database: go

Photoprotein
type: Concept
comment: Luminescent proteins, which are involved in the phenomenon of light emission in certain living organisms. E.g., green fluorescent protein which is unique among fluorescent proteins in that its chromophore is not a separately synthesized prostethic group but is composed of modified amino acid residues within its polypeptide chain.
subclass of: Luminescence
subclass of: Molecular function
category: Molecular function

Photoreceptor protein
type: Concept
alternative label: Light-sensing protein
alternative label: Photosensor protein
comment: Protein involved in the convertion of light directly into a signal. These proteins are classified in a limited number of families based on the chemical structure of the light-absorbing chromophores involved, and also on protein sequence similarities to discriminate the many photoreceptor proteins that bind a flavin derivative. Accordingly, the most important families are the rhodopsins, the phytochromes, the xanthopsins, the cryptochromes, the phototropins and the BLUF proteins.
subclass of: Chromophore
subclass of: Receptor
subclass of: Sensory transduction
narrower: Retinal protein
category: Molecular function

photoreceptor activity
type: Class
database: go

Photorespiration
type: Concept
comment: Protein involved in a light-dependent process to convert 2-phospho-glycolate (2-PG) into 3-phospho-D-glycerate (3-PG), where oxygen is consumed and carbon dioxide released. It takes place in plants and cyanobacteria during the light period, since in the presence of O(2) their type of Rubisco can catalyze the oxidative fragmentation of ribulose 1,5-biphosphate to 3-PG and 2-PG. 2-PG inhibits the Calvin cycle enzyme triose-phosphate isomerase, and so must be eliminated quickly. In plants 2-PG is recycled to 3-PG via reactions in peroxisomes, mitochondria as well as chloroplasts. For every 2 molecules of 2-PG, one molecule of 3-PG is formed and one molecule of CO(2) is lost. In cyanobacteria it seems there are two mechanisms to deal with 2-PG; a path similar to that described for plants and the bacterial-like glycerate pathway.
subclass of: Biological process
category: Biological process

photorespiration
type: Class
database: go

Photosynthesis
type: Concept
comment: 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). The general reaction is: CO(2) + 2H(2)A = (CH(2)O) + 2A + H(2)O, where 2H(2)A is any reduced compound that can serve as an electron donor. In plants, algae and cyanobacteria H(2)O serves as a reductant, generating O(2). Non-oxygenic organisms use other electron donors, for example H(2)S in purple sulfur bacteria, generating sulfur.
subclass of: Biological process
narrower: Chlorosome
narrower: Photosystem I
narrower: Photosystem II
narrower: Reaction center
category: Biological process

photosynthesis
type: Class
database: go

Photosystem I
type: Concept
alternative label: P700
alternative label: PSI
comment: 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. In linear electron flow, PSII is coupled to PSI and produces a pH gradient, ATP and NADPH. In cyclic electron flow, PSI generates a pH gradient and ATP. PSI is excited best by light at about 700 nm, and is thus sometimes called P700. PSI is an iron-sulfur type reaction center (RC), sharing a common ancestor with the RCs of Heliobacteriaceae, green sulfur and green non-sulfur bacteria.
subclass of: Photosynthesis
subclass of: Cellular component
category: Cellular component

photosystem I
type: Class
database: go

Photosystem II
type: Concept
alternative label: P680
alternative label: PSII
comment: Protein involved in photosystem II (PSII), a complex that uses light energy to mediate electron flow in the chloroplast thylakoid membrane of plants and in cyanobacteria. PSII splits water, releasing hydrogen ions and molecular oxygen. PSII cannot use photons of a wavelength greater than 680 nm, and is thus sometimes called P680. PSII is a quinone type rection center (RC), sharing a common ancestor with the RCs of purple bacteria.
subclass of: Photosynthesis
subclass of: Cellular component
category: Cellular component

photosystem II
type: Class
database: go

Phycobilisome
type: Concept
comment: Protein found in phycobilisome, an accessory light energy harvesting structure on the outer face of the thylakoid membranes in cyanobacteria and red algae. Phycobilisomes are mainly composed of phycobiliproteins (such as allophycocyanin, phycocyanin and phycoerythrin) together with linker polypeptides.
subclass of: Antenna complex
category: Cellular component

phycobilisome
type: Class
database: go

Phytochrome signaling pathway
type: Concept
comment: Protein involved in the relay of information from the activated phytochrome molecule to target genes. Different phytochromes use both separate and common early signaling pathways. These pathways converge downstream in a process of signal integration that regulates photomorphogenesis and the circadian clock. This provides the means by which information from specific wavelengths of light may be amplified and coordinated.
subclass of: Biological process
category: Biological process

red, far-red light phototransduction
type: Class
database: go

red or far-red light signaling pathway
type: Class
database: go

Pigment
type: Concept
comment: Protein which binds or transport pigments, any coloring matter in animals, plants or microorganisms.
subclass of: Ligand
category: Ligand

pigment binding
type: Class
database: go

Plant defense
type: Concept
comment: Protein involved in plant defense, either as part of preexisting, developmentally regulated defense barriers (such as thionins, defensins or hydroxyproline-rich glycoproteins fortifying the cell wall) or as components of the defense responses induced upon pathogen infection during hypersensitive cell death (HR), local acquired resistance (LAR) or systemic acquired resistance (SAR). This includes proteins involved in various pathways, such as the gene-for-gene resistance, the salicylic acid (SA)-dependant resistance, the jasmonate (JA) and/or ethylene (ET)-dependant resistance and the induced systemic resistance (ISR), as well as the final products of those pathways such as the pathogenesis-related proteins.
subclass of: Biological process
narrower: Hypersensitive response
narrower: Pathogenesis-related protein
category: Biological process

Plasmid
type: Concept
comment: Protein encoded on a plasmid, a self-replicating circular DNA that is found in a variety of bacterial, archaeal, fungal, algal and plant species, and can be transferred from one organism to another. Plasmids often carry antibiotic-resistant genes and are widely used in molecular biology as vectors of genes and in cloning.
subclass of: Technical term
category: Technical term

Plasmid copy control
type: Concept
comment: Protein involved in the plasmid copy control, the ability of a plasmid to control its own copy number in a cell. Copy number is a function of the rate at which DNA synthesis is initiated.
subclass of: Biological process
category: Biological process

plasmid maintenance
type: Class
database: go

Plasmid partition
type: Concept
comment: Protein involved in plasmid partition, the process whereby newly replicated plasmids are distributed properly to daughter cells during cell division.
subclass of: Biological process
category: Biological process

plasmid partitioning
type: Class
database: go

Plasminogen activation
type: Concept
comment: Protein involved in the plasminogen activation which occurs when an heterogeneous group of proteolytic enzymes convert plasminogen to plasmin.
subclass of: Biological process
category: Biological process

Plastid
type: Concept
comment: Protein encoded by or localized in a plastid, a semi-autonomous, self-reproducing organelle. Plastids are remnants of a photosynthetic organism that was engulfed by the host, although not all are now photosynthetic. Plastid genomes encode genes for rRNAs, tRNAs and between about 28 and 150 proteins. Plastids can be categorized in 4 main groups: chloroplasts, cyanelles, apicoplasts and non-photosynthetic. The latter are found is some land plants (Epifagus virginiana), chlorophyte algae (Prototheca wickerhamii) and euglenoids (Astasis longa), which do not encode the genes necessary for photosynthesis and so are not photosynthetic but still contain a plastid. Non-photosynthetic plastids probably do not contain thylakoids.
subclass of: Cellular component
narrower: Amyloplast
narrower: Chloroplast
narrower: Cyanelle
narrower: Apicoplast
narrower: Chromoplast
narrower: Organellar chromatophore
narrower: Plastid inner membrane
narrower: Plastid outer membrane
category: Cellular component

plastid
type: Class
database: go

Plastid inner membrane
type: Concept
alternative label: Inner plastidic membrane
alternative label: Inner plastid membrane
alternative label: Plastidic inner membrane
comment: Protein found in or associated with the inner membrane of a plastid, which separates the plastid stroma from the intermembrane space.
subclass of: Membrane
subclass of: Plastid
category: Cellular component

plastid inner membrane
type: Class
database: go

Plastid outer membrane
type: Concept
alternative label: Outer plastidic membrane
alternative label: Outer plastid membrane
alternative label: Plastidic outer membrane
comment: Protein found in or associated with the outer membrane of a plastid, which is the membrane facing the cytoplasm.
subclass of: Membrane
subclass of: Plastid
category: Cellular component

plastid outer membrane
type: Class
database: go

Plastoquinone
type: Concept
comment: Protein which interacts with plastoquinone, a substituted quinone called plastoquinone because it appeared concentrated in the chloroplasts of higher plants. Plastoquinone transfers electrons from the photosystem II reaction center to the cytochrome bf complex and carries protons across the photosynthetic membrane.
subclass of: Ligand
category: Ligand

Platelet aggregation activating toxin
type: Concept
comment: Toxin which induces agonist-induced platelet aggregation, the self-adhesion of platelets via adhesion molecules. Numerous snake venom families have the capacity to induce platelet aggregation.
subclass of: Hemostasis impairing toxin
category: Molecular function

Platelet aggregation inhibiting toxin
type: Concept
comment: Toxin which inhibits agonist-induced platelet aggregation, the self-adhesion of platelets via adhesion molecules. Numerous snake venom families have the capacity to inhibit platelet aggregation.
subclass of: Hemostasis impairing toxin
category: Molecular function

Polyamine biosynthesis
type: Concept
comment: Protein involved in polyamine biosynthesis. The polyamines, e.g. putrescine, cadaverine, agmatine, spermidine and spermine, are wide-spread in all organisms, and have been shown to play a role in the regulation of growth and differentiation of virtually all types of cells.
subclass of: Biological process
category: Biological process

polyamine biosynthetic process
type: Class
database: go

Polysaccharide degradation
type: Concept
comment: Protein involved in polysaccharide degradation, the breakdown of polysaccharides.
subclass of: Carbohydrate metabolism
narrower: Cellulose degradation
narrower: Chitin degradation
narrower: Xylan degradation
category: Biological process

polysaccharide catabolic process
type: Class
database: go

Polysaccharide transport
type: Concept
comment: Protein involved in the transport of polysaccharides.
subclass of: Sugar transport
category: Biological process

polysaccharide transport
type: Class
database: go

Pontocerebellar hypoplasia
type: Concept
alternative label: PCH
alternative label: Pontocerebellar atrophy
comment: Protein which, if defective, causes pontocerebellar hypoplasia, a heterogeneous group of congenital disorders characterized by hypoplasia and atrophy of the cerebellar cortex, dentate nuclei, pontine nuclei and inferior olives. Additional defects of other brain and spinal cord structures can be present, resulting in clinical manifestations that vary among cases.
subclass of: Disease
category: Disease

Pore-mediated penetration of viral genome into host cell
type: Concept
alternative label: Membrane puncture-mediated penetration of viral genome into host cell
comment: Virion-associated pore-forming protein that induces the formation of a transmembrane pore or channel in the host membrane(s) to allow the viral genome to enter the host cytoplasm. This mechanism is used by non-enveloped viruses such as human rhinovirus 2 or poliovirus. Many tailed bacteriophages carry specialized proteins which open a pore or a channel in the host membrane(s) to allow penetration of the virion tail into host envelope and genome delivery into host cytoplasm.
subclass of: Viral penetration into host cytoplasm
category: Biological process

pore-mediated entry of viral genome into host cell
type: Class
database: go

Porin
type: Concept
comment: Membrane protein which in a multimeric form constitutes a water-filled transmembrane channel (a pore). This pore allows the passage of ions and numerous other, non-specific molecules through the membrane. Found in the mitochondrial and plastid outer membrane of eukaryotes, in many Gram-negative bacteria, at least some Corynebacterineae, archaea and in sea anemones.
subclass of: Ion transport
subclass of: Transmembrane
subclass of: Molecular function
category: Molecular function

porin activity
type: Class
database: go

pore complex
type: Class
database: go

Porphyrin biosynthesis
type: Concept
comment: Protein involved in the synthesis of porphyrins which are compounds that contain the porphin structure, e.g. four pyrrole rings connected by methine bridges in a cyclic configuration to which a variety of side chains are attached. Porphyrins often chelate metal ions (Fe, Mg, Co, Zn, Cu, Ni). Examples are, heme proteins (which contain iron porphyrins) like myoglobin, hemoglobin, cytochromes, or related macrocycles including chlorophylls (which have a central magnesium ion) and pheophytins (which are metal free) and vitamin B-12 (which has cobalt).
subclass of: Biological process
category: Biological process

porphyrin-containing compound biosynthetic process
type: Class
database: go

Postsynaptic cell membrane
type: Concept
alternative label: Postsynaptic membrane
comment: Protein characteristic of the postsynaptic membrane. In a chemical synapse, the postsynaptic membrane is the membrane that receives a signal (binds neurotransmitter) from the presynaptic cell and responds via depolarisation or hyperpolarisation. The postsynaptic membrane is separated from the presynaptic membrane by the synaptic cleft.
subclass of: Membrane
subclass of: Synapse
category: Cellular component

postsynaptic membrane
type: Class
database: go

Postsynaptic neurotoxin
type: Concept
comment: Protein which acts as a neurotoxin at the postsynaptic membrane. They bind to acetylcholine receptors and so inhibit their activity.
subclass of: Neurotoxin
narrower: Acetylcholine receptor inhibiting toxin
narrower: Ionotropic glutamate receptor inhibitor
category: Molecular function

host cell postsynaptic membrane
type: Class
database: go

Potassium
type: Concept
comment: Protein which binds at least one potassium, or protein whose function is potassium-dependent. Potassium is an alkali metal, chemical symbol K.
subclass of: Ligand
narrower: Potassium channel
narrower: Potassium transport
narrower: Sodium/potassium transport
category: Ligand

Potassium channel
type: Concept
comment: Protein which is part of a transmembrane protein complex that forms a hydrophilic channel across the lipid bilayer through which potassium ions can diffuse down their electrochemical gradient. The channels are gated and only open in response to a specific stimulus, such as a change in membrane potential (voltage-gated). They are important for the regulation of the resting membrane potential and for the control of the shape and frequency of action potentials.
subclass of: Ion channel
subclass of: Potassium
subclass of: Potassium transport
category: Molecular function

potassium channel activity
type: Class
database: go

potassium ion transmembrane transport
type: Class
database: go

Potassium channel impairing toxin
type: Concept
comment: Protein which interferes with the function of potassium channels which are membrane proteins forming a channel in a biological membrane selectively permeable to potassium ions. They are found in various venoms from snakes, scorpions and spiders.
subclass of: Ion channel impairing toxin
narrower: Voltage-gated potassium channel impairing toxin
narrower: Calcium-activated potassium channel impairing toxin
category: Molecular function

potassium channel regulator activity
type: Class
database: go

Potassium transport
type: Concept
comment: Protein involved in the transport of potassium ions.
subclass of: Ion transport
subclass of: Potassium
narrower: Potassium channel
narrower: Sodium/potassium transport
category: Biological process

potassium ion transport
type: Class
database: go

PQQ
type: Concept
alternative label: Methoxatin
alternative label: Pyrroloquinoline quinone
comment: Protein which non-covalently binds at least one pyrroloquinoline quinone (PQQ) cofactor.
subclass of: Ligand
category: Ligand

PQQ biosynthesis
type: Concept
alternative label: Pyrroloquinoline quinone biosynthesis
comment: Protein involved in the biosynthesis of the cofactor pyrroloquinoline quinone (PQQ).
subclass of: Biological process
category: Biological process

pyrroloquinoline quinone biosynthetic process
type: Class
database: go

Pregnancy
type: Concept
comment: Protein which plays a role in pregnancy, the condition of having a developing embryo or fetus in the body, after union of an ovum and spermatozoon.
subclass of: Biological process
category: Biological process

female pregnancy
type: Class
database: go

Premature ovarian failure
type: Concept
alternative label: Primary ovarian insufficiency
comment: Protein which, if defective, causes premature ovarian failure, a condition characterized by the arrest of normal ovarian function before the age of 40 years, due to a primary ovarian defect. It is characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles (secondary amenorrhea).
subclass of: Disease
category: Disease

Prenylation
type: Concept
comment: Protein which is posttranslationally modified by the attachment of at least one prenyl group (e.g. farnesyl, geranylgeranyl) usually on cysteine residues which are at or near the C-terminal extremity.
subclass of: Lipoprotein
category: PTM

Prenyltransferase
type: Concept
comment: Enzyme that catalyzes the transfer of an isoprenoid (farnesyl or geranylgeranyl) usually on cysteine residues, which are three residues away from the C-terminal extremity.
subclass of: Transferase
category: Molecular function

prenyltransferase activity
type: Class
database: go

Presynaptic neurotoxin
type: Concept
comment: Protein which acts as a neurotoxin at the presynaptic membrane and usually blocks neuromuscular transmission.
subclass of: Neurotoxin
category: Molecular function

host cell presynaptic membrane
type: Class
database: go

Primary ciliary dyskinesia
type: Concept
alternative label: CILD
alternative label: ICS
alternative label: Immotile cilia syndrome
alternative label: PCD
comment: Protein which, if defective, causes primary ciliary dyskinesia, a rare and genetically heterogeneous disorder characterized by sino-pulmonary disease, laterality defects and male infertility. Primary ciliary dyskinesia is due to dysfunction of motile cilia and flagella in various organ systems.
subclass of: Ciliopathy
narrower: Kartagener syndrome
category: Disease

Primary hypomagnesemia
type: Concept
comment: Protein which, if defective, causes primary hypomagnesemia. Primary hypomagnesemia defines a heterogeneous group of disorders characterized by low magnesium serum content due to primary renal or intestinal magnesium wasting. Primary hypomagnesemia disorders generally share symptoms of magnesium depletion, such as tetany and generalized convulsions. They often include associated disturbances in calcium excretion.
subclass of: Disease
category: Disease

Primary microcephaly
type: Concept
comment: Protein which, if defective, causes primary microcephaly. This is a neurodevelopmental condition characterized by a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean, and absence of other syndromic features or significant neurological deficits. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. Primary microcephaly is also known as true microcephaly or microcephaly vera.
subclass of: Disease
category: Disease

Primary mitochondrial disease
type: Concept
alternative label: Mitochondrial disorder
alternative label: Mitochondrial encephalomyopathy
alternative label: Mitochondrial myopathy
alternative label: Oxidative phosphorylation disorder
alternative label: PMD
alternative label: Respiratory chain disorder
comment: Protein which, if defective, causes any one of a clinically heterogeneous group of disorders arising from dysfunction of the mitochondrial respiratory chain. The phenotypic spectrum ranges from isolated diseases affecting single organs to severe multisystem disorders. Common clinical features include ptosis, external ophthalmoplegia, proximal myopathy and exercise intolerance, cardiomyopathy, sensorineural deafness, optic atrophy, pigmentary retinopathy, encephalopathy, seizures, stroke-like episodes, ataxia, and spasticity. Mitochondrial disorders can be caused by mutations of mitochondrial DNA or nuclear DNA that either affect oxidative phosphorylation proteins directly, or affect respiratory chain function by impacting the production of the complex machinery needed to run this process.
subclass of: Disease
narrower: Leber hereditary optic neuropathy
narrower: Leigh syndrome
narrower: MELAS syndrome
narrower: Progressive external ophthalmoplegia
category: Disease

Primosome
type: Concept
comment: Component of the complex involved in the synthesis of RNA primer sequences used in DNA replication. Main components are primases and replicative DNA helicases that move as a unit along the replication fork.
subclass of: Cellular component
category: Cellular component

DNA replication, synthesis of RNA primer
type: Class
database: go

primosome complex
type: Class
database: go

Prion
type: Concept
comment: Protein which is able to form a prion, a self-propagating protein conformation (infectious protein). Formation of prions involves conversion of the native proteins into an infectious, amyloid form. This class of proteins includes the members of the prion family which can form proteinaceous infectious particles responsible for transmissible spongiform encephalopathies (TSE) in many animals, such as Kuru and Creutzfeldt-Jakob syndrome in humans, scrapies in sheep and BSE in cattle. These prion diseases represent special cases of neurodegenerative amyloidoses, because they result from the transmissibility and infectivity of the amyloid.
subclass of: Amyloid
subclass of: Molecular function
category: Molecular function

Progressive external ophthalmoplegia
type: Concept
comment: Protein which, if defective, causes progressive external ophthalmoplegia with mitochondrial DNA deletions. Progressive external ophthalmoplegia (PEO) is characterized by ptosis and weakness of the extraocular muscles. Typical symptoms are ophthalmoparesis and exercise intolerance. Some people also may develop cardiomyopathy, cataracts, ataxia, peripheral neuropathy, hypogonadism or major depression. The diagnosis depends on the demonstration, by Southern blotting, of multiple deletions of mtDNA in muscle biopsy specimens. Both autosomal dominant and autosomal recessive inheritance can occur. The autosomal recessive form, which is often associated with multisystemic disorders, is clinically more heterogenous than the autosomal dominant form and can be more severe.
subclass of: Primary mitochondrial disease
category: Disease

Proline biosynthesis
type: Concept
comment: 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.
subclass of: Amino-acid biosynthesis
category: Biological process

proline biosynthetic process
type: Class
database: go

Proline metabolism
type: Concept
comment: Protein involved in a biochemical reaction with 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.
subclass of: Biological process
category: Biological process

proline metabolic process
type: Class
database: go

Prostaglandin biosynthesis
type: Concept
comment: Protein involved in the biosynthesis of prostaglandins. Prostaglandins are fatty acids composed of 20 carbons with a substituted cyclopentane ring. There are four major classes of prostaglandin, which differ in the position of the double bonds and/or the oxygen substituents on the ring: PGA, PGB, PGE, and PGF. They are found in many mammalian tissues.
subclass of: Fatty acid biosynthesis
subclass of: Prostaglandin metabolism
category: Biological process

prostaglandin biosynthetic process
type: Class
database: go

Prostaglandin metabolism
type: Concept
comment: Protein involved in a biochemical reaction with prostaglandins. Prostaglandins are fatty acids composed of 20 carbons with a substituted cyclopentane ring. There are four major classes of prostaglandin, which differ in the position of the double bonds and/or the oxygen substituents on the ring: PGA, PGB, PGE, and PGF. They are found in many mammalian tissues.
subclass of: Fatty acid metabolism
narrower: Prostaglandin biosynthesis
category: Biological process

prostaglandin metabolic process
type: Class
database: go

Protease
type: Concept
alternative label: Peptidase
alternative label: Peptide hydrolase
alternative label: Proteinase
comment: Enzyme which hydrolyzes peptide bonds.
subclass of: Hydrolase
narrower: Aminopeptidase
narrower: Aspartyl protease
narrower: Carboxypeptidase
narrower: Dipeptidase
narrower: Metalloprotease
narrower: Serine protease
narrower: Thiol protease
narrower: Threonine protease
category: Molecular function

proteolysis
type: Class
database: go

peptidase activity
type: Class
database: go

Protease inhibitor
type: Concept
comment: Protein which inhibits or antagonizes the biosynthesis of proteases or their activity.
subclass of: Molecular function
narrower: Aspartic protease inhibitor
narrower: Metalloprotease inhibitor
narrower: Serine protease inhibitor
narrower: Thiol protease inhibitor
category: Molecular function

Proteasome
type: Concept
alternative label: Macropain
alternative label: Prosome
comment: Protein which is part of the proteasome, a large protein complex in the cytosol that is responsible for degrading proteins which have been marked for destruction by ubiquitination or by some other means.
subclass of: Cellular component
category: Cellular component

proteasome complex
type: Class
database: go

Protein biosynthesis
type: Concept
comment: Protein involved in the biosynthesis of proteins from mRNA molecules. This process, called translation, is carried out by ribosomes, where activated amino acids are added to the nascent polypeptide chain.
subclass of: Biological process
narrower: Elongation factor
narrower: Initiation factor
category: Biological process

translation
type: Class
database: go

Protein kinase inhibitor
type: Concept
comment: Protein which inhibits the activity of a protein kinase.
subclass of: Molecular function
category: Molecular function

protein kinase inhibitor activity
type: Class
database: go

Protein phosphatase
type: Concept
alternative label: Phosphoprotein phosphatase
comment: Enzyme that catalyzes the hydrolysis of phosphate monoesters bonds of phosphoserines, phosphothreonines, phosphotyrosines or phosphoaspartic acids. While many protein phosphatases inhibit the activities of phosphorylation cascades, some activate them.
subclass of: Hydrolase
category: Molecular function

phosphoprotein phosphatase activity
type: Class
database: go

Protein phosphatase inhibitor
type: Concept
comment: Protein which inhibits the activity of a protein phosphatase.
subclass of: Molecular function
category: Molecular function

protein phosphatase inhibitor activity
type: Class
database: go

Protein splicing
type: Concept
comment: Protein which undergoes protein self-splicing, a posttranslational modification involving the excision of an intervening protein sequence (intein) from a protein precursor and the concomitant ligation of the flanking protein fragments (exteins) to form a mature extein protein and the free intein.
subclass of: Autocatalytic cleavage
category: PTM

Protein synthesis inhibitor
type: Concept
comment: Protein which blocks the synthesis of proteins (translation) through various mechanisms, including hydrolysis of cellular tRNA, and inactivation of the 60S subunits of eukaryotic ribosome.
subclass of: Molecular function
category: Molecular function

negative regulation of translation
type: Class
database: go

Protein transport
type: Concept
comment: Protein involved in the intracellular transport of proteins from one location to another. All proteins (except the ones synthesized in mitochondria and plastids) are synthesized on ribosomes in the cytosol. Most proteins remain in the cytosol. Proteins with a signal sequence either become plasma membrane components or are exported from the cell of origin.
subclass of: Transport
narrower: Bacteriocin transport
narrower: Peptide transport
narrower: Translocation
narrower: Bacterial flagellum protein export
category: Biological process

protein transport
type: Class
database: go

Proteoglycan
type: Concept
comment: Protein containing one or more covalently linked and usually sulfated glycosaminoglycans, (e.g., chondroitin sulfate, dermatan sulfate, heparan sulfate, heparin, keratan sulfate). Glycosaminoglycans are polysaccharides made of repeating disaccharides (usually 40-100 times), which consist of uronic acid (or galactose) and hexosamines. Aggrecan, for example, is the major component in articular cartilage.
subclass of: Glycoprotein
narrower: Heparan sulfate
category: PTM

Proteomics identification
type: Concept
comment: Protein whose amino acid sequence has been partially or completely confirmed using publicly available mass spectrometry based data. The mapping from the mass spectrometry data to UniProtKB sequences may be subject to quality metrics from both UniProt and the data providers.
subclass of: Technical term
category: Technical term

Prothrombin activator
type: Concept
comment: Protein which activates prothrombin, the inactive precursor of thrombin. For example, staphylocoagulase, an extracellular protein produced by Staphylococcus aureus, forms a complex with prothrombin which can clot fibrinogen without any proteolytic cleavage of prothrombin.
subclass of: Molecular function
category: Molecular function

positive regulation of peptidase activity
type: Class
database: go

peptidase activator activity
type: Class
database: go

Proto-oncogene
type: Concept
comment: Protein whose normal cellular gene can be converted into a cancer-promoting oncogene by activating mutations, chromosomal translocation or DNA amplification. Once activated a proto-oncogene can promote cell transformation in culture or tumorigenesis in animals. Examples include the regulatory GTPase HRAS, which is commonly activated by dominant gain of function point mutations, and the transcription factor MYC, which can be activated by both chromosomal amplification and chromosomal translocation.
subclass of: Disease
category: Disease

Proton-gated sodium channel impairing toxin
type: Concept
comment: Protein which interferes with the function of proton-gated sodium channels (ASICs) which are membrane proteins forming a channel in a biological membrane selectively permeable to sodium ions, and open in response to an increase of extracellular protons. These toxins are found in various venoms from snakes, spiders, sea anemones, and cone snails.
subclass of: Ion channel impairing toxin
category: Molecular function

Pseudohermaphroditism
type: Concept
comment: Protein which, if defective, causes pseudohermaphroditism, a condition in humans in which the individual has gonads of one sex but shows ambiguous morphologic criteria of sex.
subclass of: Disease
category: Disease

PTM
type: Concept
comment: Keywords assigned to proteins because their sequences can differ from the mere translation of their corresponding genes, due to some post-translational modification.
narrower: Acetylation
narrower: ADP-ribosylation
narrower: Amidation
narrower: Autocatalytic cleavage
narrower: Bromination
narrower: Citrullination
narrower: Cleavage on pair of basic residues
narrower: Covalent protein-DNA linkage
narrower: Covalent protein-RNA linkage
narrower: D-amino acid
narrower: Formylation
narrower: Gamma-carboxyglutamic acid
narrower: Glutathionylation
narrower: Glycoprotein
narrower: Hydroxylation
narrower: Hypusine
narrower: Iodination
narrower: Lipoprotein
narrower: Methylation
narrower: Organic radical
narrower: Oxidation
narrower: Peptidoglycan-anchor
narrower: Phosphopantetheine
narrower: Phosphoprotein
narrower: S-nitrosylation
narrower: Sulfation
narrower: TPQ
narrower: TTQ
narrower: Ubl conjugation
narrower: Zymogen
narrower: Pyrrolidone carboxylic acid
narrower: Quinone
narrower: Thioester bond
narrower: Thioether bond
narrower: CTQ
narrower: LTQ
narrower: Nitration
narrower: Disulfide bond
narrower: Isopeptide bond
subclass of: Concept

Purine biosynthesis
type: Concept
comment: Protein involved in the biosynthesis of purine, a nitrogenous heterocyclic base, e.g. adenine, guanine, hypoxanthine and xanthine. De novo synthesis involves a complex, energy-expensive pathway that yields inosine 5'-monophosphate (IMP), a purine ribonucleotide. AMP and GMP are then formed from IMP in separate pathways. Adenine and guanine are found in both DNA and RNA. Hypoxanthine and xanthine are important intermediates in the synthesis and degradation of the purine nucleotides.
subclass of: Biological process
narrower: GMP biosynthesis
category: Biological process

purine nucleotide biosynthetic process
type: Class
database: go

Purine metabolism
type: Concept
comment: Protein involved in a biochemical reaction with purines. Purines are nitrogenous heterocyclic bases, e.g. adenine, guanine, hypoxanthine and xanthine. The degradation of purines leads to uric acid, which is excreted in primates, birds and some other animals. In many other vertebrates uric acid is degraded further to the excretory product allantoin.
subclass of: Biological process
category: Biological process

purine nucleobase metabolic process
type: Class
database: go

Purine salvage
type: Concept
comment: 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.
subclass of: Biological process
category: Biological process

purine ribonucleoside salvage
type: Class
database: go

Putrescine biosynthesis
type: Concept
alternative label: 1,4-butanediamine biosynthesis
alternative label: 1,4-diaminobutane biosynthesis
comment: Protein involved in the biosynthesis of putrescine, a foul-smelling polyamine. This metabolic precursor of the polyamines spermine and spermidine is often produced during breakdown of some of the amino acids by bacteria.
subclass of: Biological process
category: Biological process

putrescine biosynthetic process
type: Class
database: go

Pyridine nucleotide biosynthesis
type: Concept
comment: Protein involved in the biosynthesis of the pyridine nucleotides NAD and NADP. NAD may be synthesized de novo from aspartate and dihydroxyacetone phosphate or from tryptophan. NAD may also be synthesized from nicotinamide or nicotinic acid. NADP is formed via the phosphorylation of NAD by NAD+ kinase.
subclass of: Biological process
category: Biological process

pyridine nucleotide biosynthetic process
type: Class
database: go

Pyridoxal phosphate
type: Concept
comment: Protein which uses at least one pyridoxal phosphate as cofactor or protein required for its synthesis. This coenzyme, derived from vitamin B6, is important in amino acid metabolism, e.g., in reactions involving transamination, decarboxylation, racemization, elimination or replacement.
subclass of: Ligand
category: Ligand

Pyridoxine biosynthesis
type: Concept
alternative label: Pyridoxol biosynthesis
alternative label: Vitamin B6 biosynthesis
comment: Protein involved in the biosynthesis of pyridoxine, a precursor to the coenzyme pyridoxal phosphate.
subclass of: Biological process
category: Biological process

pyridoxine biosynthetic process
type: Class
database: go

Pyrimidine biosynthesis
type: Concept
comment: Protein involved in the biosynthesis of pyrimidine, a nitrogenous heterocyclic base, e.g. uracil, thymine, cytosine and orotic acid. Pyrimidines are synthesized from carbamoyl phosphate and aspartate. Ribose-5-phosphate is then attached to yield pyrimidine ribonucleotides. Cytosine is found in both DNA and RNA. Uracil is found only in RNA. Thymine is normally found in DNA. Sometimes tRNA contains some thymine as well as uracil.
subclass of: Biological process
category: Biological process

pyrimidine nucleotide biosynthetic process
type: Class
database: go

Pyrogen
type: Concept
comment: Protein producing fever. The major endogenous pyrogen in mammals is probably interleukin-1, which is produced by activated macrophages and acts on the hypothalamic thermoregulatory centre.
subclass of: Inflammatory response
subclass of: Molecular function
category: Molecular function

fever generation
type: Class
database: go

Pyropoikilocytosis
type: Concept
alternative label: HPP
comment: Protein which, if defective, causes hereditary pyropoikilocytosis (HPP), a recessively inherited hemolytic anemia characterized by microspherocytosis, poikilocytosis (deformation of the erythrocytes), and an unusual thermal sensitivity of red cells. Frequently associated with abnormalities in alpha-spectrin, one of the principal structural proteins of the erythrocyte membrane skeleton.
subclass of: Hereditary hemolytic anemia
category: Disease

Pyrrolidone carboxylic acid
type: Concept
alternative label: Pyro-Glu
alternative label: Pyroglutamic acid
comment: Protein which is posttranslationally modified by the cyclization of a N-terminal glutamine.
subclass of: PTM
category: PTM

Pyrrolysine
type: Concept
comment: Protein which contains a pyrrolysine, a naturally occurring amino acid so far only found in some archaeal proteins. Pyrrolysine is a lysine in an amide linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate.
subclass of: Coding sequence diversity
category: Coding sequence diversity

Pyruvate
type: Concept
comment: Protein which uses at least one pyruvate as cofactor (pyruvoyl) or substrate, or protein required for pyruvate synthesis or degradation. Pyruvate is an intermediate compound in the metabolism of carbohydrates, proteins and fats.
subclass of: Ligand
category: Ligand

Queuosine biosynthesis
type: Concept
alternative label: Nucleoside Q biosynthesis
comment: Protein involved in the synthesis of queuosine (nucleoside Q), a modified guanosine derivative found only in tRNAs for aspartic acid, asparagine, histidine and tyrosine. It can pair with either C or U.
subclass of: Biological process
category: Biological process

queuosine biosynthetic process
type: Class
database: go

Quinate metabolism
type: Concept
comment: Protein involved in the biochemical reactions of quinate. Quinate is the ionized form of quinic acid which is found in plants, e.g. in cinchona bark.
subclass of: Biological process
category: Biological process

quinate metabolic process
type: Class
database: go

Quinone
type: Concept
comment: Protein which interacts with quinones. Quinones are aromatic dicarbonyl compounds, where the two carbonyl groups are usually in the para position. Most naturally occuring quinones contain a long isoprenoid side chain, and are divided in two major structural groups, the naphtoquinones and benzoquinones; the number of isoprene units depends on the organism. These highly hydrophobic molecules are mainly involved in electron transport, as electron carriers in redox reactions. For example, ubiquinone (coenzyme Q) and menaquinone (vitamin K2) are essential components of the respiratory electron transport chain. Plastoquinone, found in chloroplasts and in cyanobacteria, functions as one of the carrier molecules of the electron transport chain in photosynthesis. Phylloquinone (vitamin K1) is the major form of vitamin K found in plants. Chlorobiumquinone, demethylmenaquinone, alpha-tocopherolquinone, rhodoquinone, epoxyubiquinone and caldariellaquinone are other quinones found in several species.
subclass of: PTM
category: PTM

quinone binding
type: Class
database: go

Quorum sensing
type: Concept
comment: Protein involved in quorum sensing (QS). QS is a phenomenon whereby the accumulation of signaling molecules enables a single cell to sense the number of bacteria (cell density). The bacterial reponse to QS includes adaptation to availability of nutrients, defence against other microorganisms which may compete for the same nutrients and the avoidance of toxic compounds potentially dangerous for the bacteria.
subclass of: Biological process
category: Biological process

quorum sensing
type: Class
database: go

Reaction center
type: Concept
comment: Protein which is a component of the reaction center, a system consisting of proteins and cofactors which facilitate light energy and electron transfer in plants. The system also acts as a light-driven electron pump across the photosynthetic membrane of photosynthetic bacteria.
subclass of: Photosynthesis
subclass of: Cellular component
category: Cellular component

Receptor
type: Concept
comment: Protein which binds to, or responds to, a ligand with high specificity.
subclass of: Molecular function
narrower: G-protein coupled receptor
narrower: Photoreceptor protein
narrower: Host cell receptor for virus entry
category: Molecular function

Redox-active center
type: Concept
comment: Protein which possesses at least one active center which mediates its participation in redox reactions, usually via reversible oxidation of a cysteine residue leading to a cysteine-sulfenic acid that can either be stabilized, or react with an unmodified cysteine residue and form a stable but reversible disulfide bond.
subclass of: Domain
category: Domain

Reference proteome
type: Concept
comment: Protein which is part of a reference proteome. Reference proteomes are a subset of proteomes that have been selected either manually or algorithmically according to a number of criteria to provide a broad coverage of the tree of life and a representative cross-section of the taxonomic diversity found within UniProtKB, as well as the proteomes of well-studied model organisms and other species of interest for biomedical research.
subclass of: Technical term
category: Technical term

Repeat
type: Concept
comment: Protein which contains a stretch of amino acids present in multiple copies.
subclass of: Domain
category: Domain

Repressor
type: Concept
comment: Protein which interferes with transcription, usually by binding to specific sites on DNA. Also used for proteins which repress translation.
subclass of: Molecular function
category: Molecular function

Respiratory chain
type: Concept
alternative label: Electron transport chain
alternative label: Respiration chain
comment: Protein involved in respiratory chain. In aerobic respiration electrons are transferred from metabolites to molecular oxygen through a series of redox reactions mediated by an electron transport chain. The resulting free energy is used for the formation of ATP and NAD. In anaerobic respiration analogous reactions take place with an inorganic compound other than oxygen as ultimate electron acceptor.
subclass of: Electron transport
category: Biological process

respirasome
type: Class
database: go

Restriction system
type: Concept
alternative label: Restriction-modification system
comment: Protein involved in the restriction system present in many bacteria and archaea. This defense mechanism is composed principally of a restriction endonuclease and a methylase. The restriction endonuclease cuts the invading DNA of viruses (or phages) at a specific recognition site. The bacterial DNA is protected by the methylase which adds a methyl group to a specific nucleotide, immediately following replication, in the same target site as the restriction enzyme.
subclass of: Biological process
category: Biological process

DNA restriction-modification system
type: Class
database: go

Restriction-modification system evasion by virus
type: Concept
comment: Viral anti-restriction protein that counteracts the host restriction-modification (R-M) system. R-M system is a prokaryotic host defense system that recognizes incoming unmodified viral DNA and rapidly degrades it. Methylation and phosphorothioation (S-modification) are two known modifications used by the host to to label its genomic DNA as 'self'. Many prokaryotic viruses have evolved antirestriction strategies such as expressing their own methylase, stimulating the host methylase so that it confers protection to the virus genome or shutting down host restriction endonuclease.
subclass of: Host-virus interaction
category: Biological process

evasion by virus of host restriction-modification system
type: Class
database: go

Retinal protein
type: Concept
comment: Protein found in the retina or, in the case of bacteriorhodopsin, in the purple membrane of halobacteria, and which acts as a photoreceptor and which binds a retinal chromophore.
subclass of: Chromophore
subclass of: Photoreceptor protein
category: Molecular function

phototransduction
type: Class
database: go

Retinitis pigmentosa
type: Concept
comment: Protein which, if defective, causes retinitis pigmentosa, a hereditary progressive degeneration of the neuroepithelium of the retina,.
subclass of: Disease
category: Disease

Retinol-binding
type: Concept
alternative label: Vitamin A-binding
comment: Protein which binds retinol, one of the active form of Vitamin A, a fat-soluble vitamin derived from carotenes. It is a precursor of retinal, the light-absorbing group of visual pigments. Vitamin A is also required for growth.
subclass of: Ligand
category: Ligand

retinol binding
type: Class
database: go

Rhamnose metabolism
type: Concept
alternative label: 6-deoxy-L-mannose metabolism
comment: Protein involved in the biochemical reactions of rhamnose. Rhamnose is a methylpentose sugar structurally derived from mannose. The L-isomer occurs naturally as a component of many plant glycosides and in lipopolysaccharides of some bacteria with 2 membranes (Gram-negative bacteria).
subclass of: Biological process
category: Biological process

rhamnose metabolic process
type: Class
database: go

Rhizomelic chondrodysplasia punctata
type: Concept
alternative label: RCDP
comment: Protein which, if defective, causes rhizomelic chondrodysplasia punctata (RCDP). This lethal autosomal recessive disease is characterized by proximal limb shortening, severely disturbed endochondrial bone formation, and intellectual disability. RCDP type 1 (RCDP1) is the classical and most common form. It is a peroxisome biogenesis disorder caused by mutations in the PEX7 gene, which encodes the PTS2-receptor peroxin-7. RCDP type 2 (RCDP2) and RCDP type 3 (RCDP3) result from single peroxisomal enzyme deficiencies: dihydroxyacetone phosphate synthase is deficient in RCDP2 and dihydroxyacetone phosphate acyltransferase in RCDP3. Both enzymes are involved in the biosynthesis of plasmalogens.
subclass of: Disease
category: Disease

Riboflavin biosynthesis
type: Concept
alternative label: Vitamin B2 biosynthesis
comment: Protein involved in the synthesis of riboflavin (Vitamin B2), which consists of ribose attached to a flavin moiety. It is synthesized by all green plants and most microorganisms and occurs free in milk, the retina, whey and urine. It is found in most cells as a component of the coenzymes flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN).
subclass of: Biological process
category: Biological process

riboflavin biosynthetic process
type: Class
database: go

Ribonucleoprotein
type: Concept
comment: Proteins conjugated with ribonucleic acid (RNA). Ribonucleoprotein are involved in a wide range of cellular processes. Besides ribosomes, in eukaryotic cells both initial RNA transcripts in the nucleus (hnRNA) and cytoplasmic mRNAs exist as complexes with specific sets of proteins. Processing (splicing) of the former is carried out by small nuclear RNPs (snRNPs). Other examples are the signal recognition particle responsible for targetting proteins to endoplasmic reticulum and a complex involved in termination of transcription.
subclass of: Molecular function
narrower: Ribosomal protein
narrower: Signal recognition particle
category: Molecular function

ribonucleoprotein complex
type: Class
database: go

Ribosomal frameshifting
type: Concept
comment: Protein produced by programmed ribosomal frameshifting, a translational recoding mechanism which causes the ribosome to alter its reading of the genetic code to produce either an alternative product not directly encoded by the mRNA or two or more different isoforms.
subclass of: Coding sequence diversity
category: Coding sequence diversity

Ribosomal protein
type: Concept
comment: Protein of the ribosome, large ribonucleoprotein particles where the translation of messenger RNA (mRNA) into protein occurs. They are both free in the cytoplasm and attached to membranes of eukaryotic and prokaryotic cells. Ribosomes are also present in all plastids and mitochondria, where they translate organelle-encoded mRNA.
subclass of: Ribonucleoprotein
category: Molecular function

ribosome
type: Class
database: go

Ribosomal skipping
type: Concept
comment: Protein produced by ribosomal 'skipping', in which a specific sequence in the nascent peptide chain prevents the ribosome from creating the peptide bond with the next proline. Nevertheless, translation continues and gives rise to a second chain. This mechanism results in apparent co-translational cleavage of the polyprotein. This process is induced by a '2A-like', or CHYSEL (cis-acting hydrolase element) sequence.
subclass of: Coding sequence diversity
category: Coding sequence diversity

Ribosome biogenesis
type: Concept
comment: Protein involved in the synthesis of ribosomes.
subclass of: Biological process
category: Biological process

ribosome biogenesis
type: Class
database: go

RNA editing
type: Concept
comment: Protein which is derived from an RNA which has been modified by RNA editing, a process that changes the nucleotide sequence of an RNA from that of the DNA template encoding it. RNA editing can be due to nucleotide conversion, insertion and/or deletion.
subclass of: Coding sequence diversity
category: Coding sequence diversity

RNA repair
type: Concept
comment: Protein involved in the repair of RNA, the various biochemical processes by which damaged RNA can be restored.
subclass of: Biological process
category: Biological process

RNA repair
type: Class
database: go

RNA suppression of termination
type: Concept
comment: Protein which is derived from an mRNA by suppression of termination, a process in which a tRNA misreads a termination codon thereby producing a longer protein. RNA secondary structure after the stop codon plays a role in this process. The efficiency of suppression of termination is about 10% for most viruses. Termination suppression is involved in polyprotein synthesis of gamma and epsilon retroviruses, as well as all togaviridae.
subclass of: Coding sequence diversity
category: Coding sequence diversity

RNA termination-reinitiation
type: Concept
comment: Protein which is derived from an mRNA by termination-reinitiation, a process in which ribosomes translate the upstream ORF but following termination, a proportion of 40S subunits remain tethered to the mRNA and reinitiates at the start codon of the downstream ORF to another open reading frame. Termination-reinitiation operates in animals and yeast translational systems.
subclass of: Coding sequence diversity
category: Coding sequence diversity

RNA translational shunting
type: Concept
comment: Protein which is derived from an mRNA by translational shunting, a process in which ribosomes are loaded onto mRNA at the 5'-cap structure, start scanning for a short distance before bypassing the large internal leader region and initiating at a downstream start site. Shunting operates in plants, animals, and yeast translational systems, both in vivo and in vitro.
subclass of: Coding sequence diversity
category: Coding sequence diversity

RNA-binding
type: Concept
comment: Protein which binds to RNA.
subclass of: Molecular function
narrower: rRNA-binding
narrower: tRNA-binding
category: Molecular function

RNA binding
type: Class
database: go

RNA-directed DNA polymerase
type: Concept
alternative label: Reverse transcriptase
comment: Enzyme (EC 2.7.7.49) which synthesizes (-)DNA on a (+)RNA template. They are encoded by the pol gene of retroviruses and by certain retrovirus-like elements.
subclass of: Nucleotidyltransferase
category: Molecular function

RNA-directed DNA polymerase activity
type: Class
database: go

RNA-directed RNA polymerase
type: Concept
comment: Enzyme (EC 2.7.7.48) which synthesizes (+)RNA on a (-)RNA template. They are encoded by many viruses.
subclass of: Nucleotidyltransferase
category: Molecular function

RNA-dependent RNA polymerase activity
type: Class
database: go

RNA-mediated gene silencing
type: Concept
alternative label: Cosuppression
alternative label: Post-transcriptional gene silencing
alternative label: PTGS
alternative label: Quelling
alternative label: RNAi
alternative label: RNA interference
alternative label: TGS
alternative label: Transcriptional gene silencing
comment: Protein involved in RNA-mediated gene silencing. This term describes a number of related processes which use 21- to 25-nucleotide RNAs to repress the expression of specific target genes. These processes include the post-transcriptional regulation of mRNA by either RNA interference (RNAi) or endogenously encoded microRNAs (miRNAs) and the transcriptional regulation of mRNA by RNAi-mediated chromatin silencing. RNAi is generally triggered by the presence of dsRNA produced by bidirectional transcription or by the transcription of an inverted repeat or hairpin sequence. dsRNA is processed into small interfering RNAs (siRNAs) of around 21 nucleotide which are then incorporated into the RNA-induced silencing complex (RISC), which cleaves mRNAs with sequences fully complementary to the siRNA. miRNAs differ from siRNAs principally in their biogenesis. miRNA genes encode precursors with complex hairpin structures which are processed by endonucleolytic cleavage to form mature miRNAs. Like siRNAs, miRNAs function in RISC-like complexes. Animal miRNAs generally inhibit translation of target mRNAs following imperfect base pairing to the 3'-untranslated region (3'-UTR), while most plant miRNAs show nearly precise complementarity to coding regions of target mRNAs and trigger mRNA degradation similar to siRNAs. Finally, in RNAi-mediated chromatin silencing, siRNAs derived from repeat element transcripts are incorporated into the nuclear RNAi-induced initiator of transcriptional silencing complex (RITS), where they guide chromatin modifications such as histone methylation which lead to transcriptional silencing.
subclass of: Biological process
category: Biological process

RNA-mediated gene silencing
type: Class
database: go

Rotamase
type: Concept
comment: Enzyme (EC 5.2.1.8) which accelerates the folding of proteins by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
subclass of: Isomerase
category: Molecular function

peptidyl-prolyl cis-trans isomerase activity
type: Class
database: go

rRNA processing
type: Concept
alternative label: Ribosomal RNA processing
comment: Protein involved in the processing of the primary rRNA transcript to yield a functional rRNA. This includes the cleavage and other modifications.
subclass of: Biological process
category: Biological process

rRNA processing
type: Class
database: go

rRNA-binding
type: Concept
comment: Protein which binds to ribosomal RNA.
subclass of: RNA-binding
category: Molecular function

rRNA binding
type: Class
database: go

Ryanodine-sensitive calcium-release channel impairing toxin
type: Concept
alternative label: Ryanodine receptor inhibitor
alternative label: Ryr inhibitor
comment: Protein which interferes with the function of ryanodine receptors (Ryr) which are a class of intracellular calcium channels in various forms of excitable animal tissue like muscles and neurons. These toxins are mostly found in scorpion and snake venom.
subclass of: Calcium channel impairing toxin
category: Molecular function

S-adenosyl-L-methionine
type: Concept
alternative label: AdoMet
alternative label: AdoMet radical
alternative label: radical S- adenosylmethionine
alternative label: S-adenosylmethionine
alternative label: S-adenosyl methionine
alternative label: S-adenosyl-methionine
alternative label: SAM
alternative label: SAM radical
comment: Protein which binds at least one S-adenosyl-L-methionine (SAM), or protein whose function is SAM-dependent. S-adenosyl-L-methionine, a conjugate of the nucleotide adenosine and the amino acid methionine, is a substrate/cofactor in numerous enzyme-catalyzed reactions. Enzymatic reactions that involve interactions of proteins with S-adenosyl-L-methionine include transfer of methyl, thiomethyl, aminoalkyl and adenosyl groups. It not only provides methyl groups to be transferred in numerous biological reactions, but also acts as a precursor in the biosynthesis of polyamines and metal ion chelating compounds. It is also a source of catalytic 5'-deoxyadenosyl radicals produced as reaction intermediates by a superfamily of radical enzymes. It is also involved in decarboxylation reactions.
subclass of: Ligand
category: Ligand

S-layer
type: Concept
comment: Protein of the paracrystalline mono-layered assembly which coats the surface of bacteria and archaea.
subclass of: Cell wall
category: Cellular component

S-layer
type: Class
database: go

S-nitrosylation
type: Concept
comment: Protein which is posttranslationally modified by the attachment of a nitric oxide group on the sulfur atom of one or more cysteine residues.
subclass of: PTM
category: PTM

Sarcoplasmic reticulum
type: Concept
comment: Protein found in a special form of agranular reticulum located in the sarcoplasm of striated muscle. The agranular reticulum comprises and comprising a system of smooth-surfaced tubules which form a plexus around each myofibril.
subclass of: Cellular component
category: Cellular component

sarcoplasmic reticulum
type: Class
database: go

Schiff base
type: Concept
comment: Enzyme which forms a covalent enzyme-substrate complex, a Schiff's base or ketimine between the amino group of a lysine residue of the enzyme and the carbonyl group of the substrate.
subclass of: Ligand
category: Ligand

Schizophrenia
type: Concept
alternative label: SCZD
comment: Protein which, if defective, is associated with schizophrenia, a multifactorial psychotic disorder characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior).
subclass of: Disease
category: Disease

SCID
type: Concept
alternative label: Severe combined immunodeficiency disease
alternative label: Severe congenital immunodeficiency disease
comment: Protein which, if defective, causes severe combined (or congenital) immunodeficiency disease. An heterogeneous group of inherited disorders characterized by gross functional impairment of the immune system.
subclass of: Disease
category: Disease

Secreted
type: Concept
comment: Protein secreted into the cell surroundings.
subclass of: Cellular component
narrower: Cell wall
narrower: Extracellular matrix
narrower: Surface film
narrower: Capsule
category: Cellular component

extracellular region
type: Class
database: go

Seed storage protein
type: Concept
comment: Protein required for the development or growth of seeds.
subclass of: Storage protein
category: Molecular function

nutrient reservoir activity
type: Class
database: go

Segmentation polarity protein
type: Concept
alternative label: Segment polarity protein
comment: Protein involved in the division of the embryo into segments and which is responsible for determining the internal polarity of the segments. Segment polarity gene mutations are lethal and change the pattern and, often the polarity, of every segment.
subclass of: Developmental protein
category: Molecular function

segment polarity determination
type: Class
database: go

Selenium
type: Concept
comment: Protein which binds at least one selenium, or protein whose function is selenium-dependent. Selenium is a nonmetallic trace element, chemical symbol Se.
subclass of: Ligand
category: Ligand

Selenocysteine
type: Concept
alternative label: 3-selenyl-L-alanine
comment: Protein which contains a selenocysteine, a naturally occurring amino acid in both eukaryotic and prokaryotic organisms.
subclass of: Coding sequence diversity
category: Coding sequence diversity

Self-incompatibility
type: Concept
comment: Protein involved in the self-incompatibility system, which is to say the inability of pollen grains to fertilize flowers of the same plant or a close relative. This mechanism ensures out-breeding in certain plant species.
subclass of: Biological process
category: Biological process

rejection of self pollen
type: Class
database: go

Senior-Loken syndrome
type: Concept
alternative label: Juvenile nephronophthisis with Leber amaurosis
alternative label: Loken-Senior syndrome
alternative label: Renal dysplasia and retinal aplasia
alternative label: Renal-retinal syndrome
alternative label: Senior-Loeken syndrome
comment: Protein which, if defective, causes Senior-Loken syndrome, a genetically and clinically heterogeneous disease characterized by nephronophthisis and retinal abnormalities manifesting as congenital retinal blindness or retinitis pigmentosa. Senior-Loken syndrome can be associated with manifestations such as cerebellar ataxia and skeletal abnormalities including cone epiphyses.
subclass of: Ciliopathy
category: Disease

Sensory transduction
type: Concept
comment: Protein involved in sensory transduction, the process by which a cell converts an extracellular signal, such as light, taste, sound, touch or smell, into electric signals.
subclass of: Biological process
narrower: Olfaction
narrower: Photoreceptor protein
narrower: Vision
narrower: Taste
category: Biological process

response to stimulus
type: Class
database: go

Septation
type: Concept
comment: Protein involved in septation, the formation of a separating wall (septum) between daughter cells during cell division.
subclass of: Cell division
category: Biological process

division septum assembly
type: Class
database: go

Serine biosynthesis
type: Concept
comment: 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.
subclass of: Amino-acid biosynthesis
category: Biological process

L-serine biosynthetic process
type: Class
database: go

Serine esterase
type: Concept
comment: Enzyme which catalyzes the hydrolysis of esters and is characterized by a catalytically active serine residue in its active site.
subclass of: Hydrolase
category: Molecular function

carboxylic ester hydrolase activity
type: Class
database: go

Serine protease
type: Concept
alternative label: Serine endopeptidase
alternative label: Serine peptidase
alternative label: Serine proteinase
comment: Proteolytic enzyme with a serine residue (Ser) in its active site. The reactivity of the serine residue is ensured by the vicinity of a histidine and an aspartate residue (catalytic triad), all three residues are required for the charge relay system to take place.
subclass of: Protease
category: Molecular function

serine-type peptidase activity
type: Class
database: go

Serine protease homolog
type: Concept
comment: Protein which is related to serine proteases but seems to have no proteolytic activity.
subclass of: Molecular function
category: Molecular function

Serine protease inhibitor
type: Concept
alternative label: Serine endopeptidase inhibitor
alternative label: Serine peptidase inhibitor
alternative label: Serine proteinase inhibitor
comment: Protein which inhibits serine proteases, a group of proteolytic enzymes which are characterized by a catalytically active serine residue in their active site.
subclass of: Protease inhibitor
category: Molecular function

serine-type endopeptidase inhibitor activity
type: Class
database: go

Serine/threonine-protein kinase
type: Concept
comment: Protein which catalyzes the phosphorylation of serine or threonine residues on target proteins by using ATP as phosphate donor. Such phosphorylation may cause changes in the function of the target protein. Protein kinases share a conserved catalytic core common to both serine/ threonine and tyrosine protein kinases.
subclass of: Kinase
category: Molecular function

protein serine/threonine kinase activity
type: Class
database: go

Serotonin biosynthesis
type: Concept
alternative label: 5-HT
alternative label: 5-hydroxytryptamine
comment: Protein involved in the synthesis of the biochemical messenger and regulator serotonin which is formed by the hydroxylation and subsequent decarboxylation of L-tryptophan. In humans, serotonin mediates several important physiological functions, including neurotransmission, gastrointestinal motility, hemostasis and cardiovascular integrity.
subclass of: Biological process
category: Biological process

serotonin biosynthetic process
type: Class
database: go

Sexual differentiation
type: Concept
comment: 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.
subclass of: Differentiation
category: Biological process

sex differentiation
type: Class
database: go

SH2 domain
type: Concept
comment: Protein with at least one Src homology 2 (SH2) domain. The SH2 domain, which was first identified in the oncoproteins Src and Fps, is about 100 amino-acid residues long. It functions as a regulatory module of intracellular signaling cascades by interacting with high affinity to phosphotyrosine-containing target peptides in a sequence-specific and strictly phosphorylation-dependent manner.
subclass of: Domain
category: Domain

SH3 domain
type: Concept
comment: Protein with at least one Src homology 3 (SH3) domain It is a small protein domain of about 50 amino-acid residues first identified as a conserved sequence in the non-catalytic part of several cytoplasmic protein tyrosine kinases (e.g. Src). Since then, it has been found in a great variety of other intracellular or membrane-associated proteins. The SH3 module might mediate the assembly of specific protein complexes by binding to proline-rich peptides.
subclass of: Domain
category: Domain

SH3-binding
type: Concept
comment: Protein with at least one SH3-binding site and which mediates the binding to the Src homology 3 (SH3) region, a module present in a large group of proteins, including cytoskeletal elements and signaling proteins.
subclass of: Domain
category: Domain

SH3 domain binding
type: Class
database: go

Short QT syndrome
type: Concept
alternative label: SQTS
comment: Protein which, if defective, causes short QT syndrome, a heart disorder characterized by the presence of a short QT interval on ECG, associated with syncope, palpitations, cardiac arrest and sudden death.
subclass of: Disease
category: Disease

Sialic acid
type: Concept
comment: Protein with at least one sialic acid. The term "sialic acid" refers to the group of sugars including neuraminic acid and its derivatives, not to a specific sugar. They are widely distributed in bacteria and animal tissue as components of polysaccharides, glycoproteins and glycolipids. They are typically the terminal residues on cell surface oligosaccharides.
subclass of: Glycoprotein
subclass of: Ligand
category: Ligand

Sigma factor
type: Concept
comment: Initiation factors that bind to bacterial DNA-dependent RNA polymerases and promote attachment to specific initiation sites on DNA. Following attachment, the sigma factor is released.
subclass of: Transcription regulation
subclass of: Molecular function
category: Molecular function

regulation of DNA-templated transcription
type: Class
database: go

sigma factor activity
type: Class
database: go

Signal
type: Concept
alternative label: Signal peptide
alternative label: Signal sequence
comment: Protein which has a signal sequence, a peptide usually present at the N-terminus of proteins and which is destined to be either secreted or part of membrane components. The signal sequence (usually 20-30 amino acids long) interacts with the signal recognition particle and directs the ribosome to the endoplasmic reticulum where co-translational insertion takes place. Signal peptides are highly hydrophobic but have some positively charged amino acids. Normally, the signal sequence is removed from the growing peptide chain by specific peptidases (signal peptidases) located on the cisternal face of the endoplasmic reticulum.
subclass of: Domain
category: Domain

Signal recognition particle
type: Concept
comment: Protein of the signal recognition particle (SRP) which is a cytosolic ribonucleoprotein complex that induces elongation arrest of nascent presecretory and membrane proteins until the ribosome becomes associated with the rough endoplasmic reticulum or the prokaryotic cytoplasmic membrane.
subclass of: Ribonucleoprotein
subclass of: Cellular component
category: Cellular component

signal recognition particle, endoplasmic reticulum targeting
type: Class
database: go

Signal transduction inhibitor
type: Concept
comment: Protein which inhibits signal transduction, the process by which extracellular signals induce intracellular responses. Usually a hormone or neurotransmitter binds to a cell surface receptor which is coupled to a second messenger system, such as that involving cAMP, or to an ion channel. The final downstream consequence of signal transduction is a change in the cell's function, such as a modification in glucose uptake or in cell division. Such a change may be the result of an activation or an inhibition event.
subclass of: Molecular function
category: Molecular function

negative regulation of signal transduction
type: Class
database: go

Signal-anchor
type: Concept
comment: Single-pass transmembrane protein (type II, III, and IV) possessing a membrane-spanning domain which targets the protein to the ER membrane. Typical features of signal-anchors are the presence of positively charged residues on the amino terminal side followed by an apolar segment of approx. 20 residues. The amino-acid composition is not very different from typical signal sequences.
subclass of: Transmembrane
category: Domain

Signalosome
type: Concept
alternative label: COP9 complex
alternative label: COP9 signalosome
alternative label: COP9 signalosome complex
alternative label: CSN
comment: Protein of the signalosome complex, a multifunctional protein complex essential for development and possibly involved in the regulation of protein degradation.
subclass of: Cellular component
category: Cellular component

COP9 signalosome
type: Class
database: go

Silk protein
type: Concept
comment: Protein found in silk, a strong, soft, lustrous fiber made of fibroin, a structural protein consisting almost entirely of stacked antiparallel beta pleated sheets. It is produced by certain spiders and by the larvae of certain bombycine moths.
subclass of: Molecular function
category: Molecular function

Sodium
type: Concept
comment: Protein which binds at least one sodium, or protein whose function is sodium-dependent. Sodium is an alkali metal, chemical symbol Na.
subclass of: Ligand
narrower: Sodium transport
narrower: Sodium/potassium transport
narrower: Sodium channel
category: Ligand

Sodium channel
type: Concept
comment: Protein which is part of a cation channel permeable for sodium found in the plasma membrane and in intracellular membranes. Sodium channels have been classified according to their gating mechanisms, which may depend on changes in the transmembrane electric field (voltage-gated sodium channels) or not (non-voltage-gated sodium channels, e.g. degenerins which are permeable also to lithium and potassium). Voltage-gated sodium channels, by opening in response to membrane depolarization, allow sodium entry and thus the propagation of depolarization along the plasma membrane of nerve, muscle and other electrically excitable cells. They play a role in different processes such as sensation, emotions, thought and movement. Another class of sodium channel is the degenerin/epithelial sodium channel (ENaC) superfamily, which is a group of proteins involved in diverse biological processes, including sodium homeostasis, salt taste, nociception, pain transduction, touch sensation and mechanotransduction.
subclass of: Ion channel
subclass of: Sodium transport
subclass of: Sodium
category: Molecular function

sodium channel activity
type: Class
database: go

Sodium transport
type: Concept
comment: Protein involved in the movement of sodium ions across energy-transducing cell membranes. Primary active sodium transport is coupled to an energy-yielding chemical reaction such as ATP hydrolysis. Secondary active transport utilizes the voltage and ion gradients produced by the primary transport to drive the cotransport of other ions or molecules. These may be transported in the same (symport) or opposite (antiport) direction.
subclass of: Ion transport
subclass of: Sodium
narrower: Sodium/potassium transport
narrower: Sodium channel
category: Biological process

sodium ion transport
type: Class
database: go

Sodium/potassium transport
type: Concept
comment: Protein involved in the active transport system which simultaneously moves two potassium ions into the cell and three sodium ions out of the cell.
subclass of: Potassium
subclass of: Potassium transport
subclass of: Sodium transport
subclass of: Sodium
category: Biological process

SOS mutagenesis
type: Concept
comment: Protein involved in the DNA repair system also known as error-prone repair in which apurinic DNA molecules are repaired by the incorporation of a base that may be the wrong base but that permits replication.
subclass of: SOS response
category: Biological process

SOS response
type: Concept
alternative label: SOS repair system
alternative label: SOS response system
alternative label: SOS system
comment: Protein involved in an SOS response, which implies the coordinated activation of diverse unlinked genes (ca. 20 in E.coli) involved in DNA repair, error-prone DNA replication, etc., in response to severe DNA damage. The SOS system is tightly regulated and its expression only occurs when absolutely required.
subclass of: DNA damage
narrower: SOS mutagenesis
category: Biological process

SOS response
type: Class
database: go

Spermatogenesis
type: Concept
comment: Protein involved in sperm cell development. A process whereby primordial germ cells form mature spermatozoa, which includes spermatocytogenesis (successive mitotic and meiotic divisions) and spermiogenesis (a metamorphic change).
subclass of: Differentiation
category: Biological process

spermatogenesis
type: Class
database: go

Spermidine biosynthesis
type: Concept
alternative label: N-(3-aminopropyl)-1,4-butanediamine
comment: Protein involved in the synthesis of spermidine, a widely distributed polyamine which acts as a growth factor for some microorganisms and stabilizes the membrane structure of bacteria, as well as the structure of ribosomes, some viruses and the DNA of many organisms.
subclass of: Biological process
category: Biological process

spermidine biosynthetic process
type: Class
database: go

Sphingolipid metabolism
type: Concept
comment: Protein involved in the biochemical reactions of sphingolipids. These are structurally complex saponifiable lipids which contain a fatty acid covalently linked to the amino alcohol sphingosine (or a related base), as backbone structure, to which is attached a polar head group. They are synthesized in the Golgi complex and are important membrane components in both plant and animal cells. They are present in especially large amounts in brain and nerve tissue.
subclass of: Lipid metabolism
category: Biological process

sphingolipid metabolic process
type: Class
database: go

Spinocerebellar ataxia
type: Concept
alternative label: ADCA
alternative label: Autosomal dominant cerebellar ataxia
alternative label: Autosomal dominant spinocerebellar ataxia
alternative label: Olivopontocerebellar atrophy
alternative label: OPCA
alternative label: SCA
alternative label: Spinocerebellar atrophy
comment: Protein which, if defective, causes autosomal dominant spinocerebellar ataxia, a clinically and genetically heterogeneous group of autosomal dominant cerebellar ataxias (ADCA). Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements. Spinocerebellar ataxia is caused by degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. Three clinical types are distinguished, according to the extent of extra-cerebellar signs: cerebellar ataxia with additional features like optic atrophy, ophthalmoplegia, bulbar and extrapyramidal signs, peripheral neuropathy and dementia, is known as ADCA type I; cerebellar ataxia with retinal degeneration and pigmentary macular dystrophy is defined as ADCA type II; pure cerebellar ataxia without additional signs is classified as ADCA type III.
subclass of: Neurodegeneration
category: Disease

Spliceosome
type: Concept
comment: Protein of the spliceosome, a very large complex of small nuclear RNA/protein particles (snRNPs) which assemble with pre-mRNA to achieve RNA splicing.
subclass of: mRNA splicing
subclass of: Cellular component
category: Cellular component

spliceosomal complex
type: Class
database: go

Sporozoite
type: Concept
comment: Protein expressed in the sporozoite stage which is the infectious stage of the malaria parasite. Malaria is transmitted by mosquitos to the vertebrate host. This term also refers to the motile infectious stage of other sporozoans (parasitic protozoans).
subclass of: Developmental stage
category: Developmental stage

Sporulation
type: Concept
comment: Protein involved in the production of spores, i.e. sporulation.
subclass of: Biological process
narrower: Conidiation
category: Biological process

sporulation resulting in formation of a cellular spore
type: Class
database: go

Starch biosynthesis
type: Concept
comment: Protein involved in the synthesis of starch, the carbohydrate storage of plants. Starch consists of amylose (a linear alpha(1-4)-glucan) and amylopectin (an alpha(1-4)-glucan with alpha(1-6)-branch points). Starch (glucans and amylopectins) is synthesised via the ADP-glucose pathway by three key enzymes: ADP-glucose pyrophosphorylase, starch synthases and starch branching enzymes. The randomly branched glucan molecules are then specifically debranched via a debranching enzyme in order to produce amylopectins. Amylopectins are branched in highly ordered clusters and are crystalline in nature, but also contain covalently bound phosphate.
subclass of: Biological process
category: Biological process

starch biosynthetic process
type: Class
database: go

Stargardt disease
type: Concept
alternative label: SD
comment: Protein which, if defective, causes Stargardt disease (SD). SD is a hereditary degeneration of the macula lutea occurring between the ages of six and twenty, marked by rapid loss of visual accuity and by abnormal appearance and pigmentation of the macular aerea.
subclass of: Disease
category: Disease

Steroid biosynthesis
type: Concept
comment: In vivo synthesis of steroids (steroidogenesis), a large group of complex polycyclic lipids that consist of a 17-carbon ring system. Examples are bile acids, sterols, various hormones and saponins.
subclass of: Lipid biosynthesis
narrower: Sterol biosynthesis
narrower: Brassinosteroid biosynthesis
category: Biological process

steroid biosynthetic process
type: Class
database: go

Steroid metabolism
type: Concept
comment: Protein involved in the biochemical reactions of steroids. Steroids are a large group of complex tetracyclic lipids that consist of a 17-carbon-ring system. Examples are bile acids, sterols, various hormones and saponins.
subclass of: Lipid metabolism
narrower: Bile acid catabolism
narrower: Sterol metabolism
category: Biological process

steroid metabolic process
type: Class
database: go

Steroid-binding
type: Concept
comment: Protein which binds steroids.
subclass of: Lipid-binding
category: Ligand

steroid binding
type: Class
database: go

Steroidogenesis
type: Concept
comment: Biosynthesis of steroid hormones which takes place in the mitochondria of the adrenal cortex. Oxidation of two adjacent carbon atoms in the side chain of cholesterol, followed by the cleavage between them, produces pregnenolone, a precursor of all other steroid hormones. The hydroxylation and oxygenation reactions are catalyzed by cytochrome P450 and mixed-functions oxidases that use NADPH and O2.
subclass of: Biological process
category: Biological process

Sterol biosynthesis
type: Concept
comment: Protein involved in the synthesis of sterols, any steroid alcohol which are components of cell membranes in plants, animals and fungi.
subclass of: Steroid biosynthesis
subclass of: Sterol metabolism
narrower: Cholesterol biosynthesis
category: Biological process

sterol biosynthetic process
type: Class
database: go

Sterol metabolism
type: Concept
comment: Protein involved in the metabolism of sterols, any steroid alcohol. Sterols are components of cell membranes in plants, animals and fungi.
subclass of: Steroid metabolism
narrower: Cholesterol metabolism
narrower: Sterol biosynthesis
category: Biological process

Stickler syndrome
type: Concept
alternative label: STL
comment: Protein which, if defective, causes Stickler syndrome (STL), also known as hereditary progressive arthro-ophthalmopathy. It is a genetically and phenotypically heterogeneous disorder with ocular, oro-facial, auditory and skeletal manifestations. Clinical features include high myopia, vitreo-retinal degeneration, retinal detachment, cleft palate, midfacial hypoplasia, osteoarthritis, and sensorineural hearing loss. Inheritance is autosomal dominant.
subclass of: Disease
category: Disease

Storage protein
type: Concept
comment: Protein which is a source of nutrients for the development or growth of an organism.
subclass of: Molecular function
narrower: Seed storage protein
category: Molecular function

Streptomycin biosynthesis
type: Concept
comment: Protein involved in the synthesis of streptomycin, an antibiotic substance produced by the soil actinomycete Streptomyces griseus. The three parts of the molecule (streptidine-6-P, dTDP-dihydrostreptose and N-methyl-glucosamine) are synthesized by separate biochemical pathways and the subunits brought together at the end. The final intermediate in the pathway, streptomycin P, becomes biologically active upon removal of the phosphate. The synthesis of the key streptomycin biosynthesis enzymes is mainly regulated by differing levels of factor A. Streptomycin binds to the small subunit of ribosomes of prokaryotic cells and causes inhibition and misreading.
subclass of: Antibiotic biosynthesis
category: Biological process

streptomycin biosynthetic process
type: Class
database: go

Stress response
type: Concept
comment: Protein involved in the response to stress, a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of some stressful conditions. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation, hypertonicity, amino acid deprivation).
subclass of: Biological process
category: Biological process

Sugar transport
type: Concept
comment: Protein involved in the transfer of sugars across a biological membrane by a carrier protein.
subclass of: Transport
narrower: Polysaccharide transport
category: Biological process

carbohydrate transport
type: Class
database: go

Sulfate respiration
type: Concept
alternative label: Dissimilatory sulfate reduction
comment: Protein involved in sulfate respiration, which is the use of sulfate (or other oxidized compounds of sulfur) as the terminal electron acceptor in the anaerobic respiratory metabolism of sulfate- or sulfur-reducing bacteria.
subclass of: Biological process
category: Biological process

anaerobic respiration
type: Class
database: go

Sulfate transport
type: Concept
comment: Protein involved in the translocation of sulfate, or sulfate-containing compounds, such as thiosulfate, across a biological membrane.
subclass of: Transport
category: Biological process

sulfate transport
type: Class
database: go

Sulfation
type: Concept
alternative label: Sulfatation
comment: Protein which is posttranslationally modified by the attachment of at least one sulfate group to a tyrosine residue. Serine and threonine may also serve as sulfate group acceptors.
subclass of: PTM
category: PTM

Superantigen
type: Concept
alternative label: SAG
comment: Bacterial or virus secreted protein that induces a strong T-lymphocyte activity. When a normal antigen stimulates 0,001% of the body's T-cells, superantigens can stimulate up to 20% of body's T-cells. They simultaneously interact with the Vb domain of the T-cell receptor (TCR) and with the class II major histocompatibility complex (MHC) molecules on the surface of an antigen-presenting cell. This compels the MHC to interact with the TCR, thereby inducing T-cells activation. Most superantigens are bacterial toxins, but some are produced by viruses. Staphylococcal enterotoxins are the best known superantigens.
subclass of: Molecular function
category: Molecular function

Superinfection exclusion
type: Concept
comment: Viral protein that is expressed by a prokaryotic virus, integrated or not, to help protect the host cell from superinfection, a process by which a cell that has previously been infected by one virus subsequently gets coinfected with a different strain of the virus, or another virus. Superinfection exclusion can be achieved for example by expressing viral enzymes that alter a portion of a surface receptor thereby blocking entry of incoming viruses with this receptor specificity. Exclusion protein can also target and block the ejection and/or DNA delivery by new incoming phages.
subclass of: Host-virus interaction
category: Biological process

superinfection exclusion
type: Class
database: go

Suppressor of RNA silencing
type: Concept
alternative label: Suppressor of RNAi
alternative label: Suppressor of RNA interference
comment: Protein which suppresses host RNA-mediated gene silencing. The most common form of RNA-mediated gene silencing is RNA interference (RNAi), a sequence-specific RNA-degradation mechanism that operates as a natural antiviral system in plants and invertebrates cells. RNAi is mediated by small interfering RNAs (siRNA) of about 21- to 25-nt that target homologous RNAs for destruction. RNA silencing by endogenous micro-RNAs (miRNAs) may also play a role in the antiviral defences of mammals. miRNAs differ from siRNAs in that they generally base pair imperfectly with target RNAs and inhibit their translation by an unknown mechanism.
subclass of: Molecular function
category: Molecular function

Surface film
type: Concept
comment: 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.
subclass of: Gaseous exchange
subclass of: Secreted
category: Cellular component

Sushi
type: Concept
comment: 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. This type of structure, also designated SCR (Short Consensus Repeat), is predominantly present in proteins associated with the complement system.
subclass of: Domain
category: Domain

Symport
type: Concept
comment: Protein involved in the transport of solutes across a biological membrane in one direction, which depends on the transport of another solute in the same direction. One molecule can move up an electrochemical gradient because the movement of the other molecule is more favorable. Example: the sodium/glucose co-transport.
subclass of: Transport
category: Biological process

symporter activity
type: Class
database: go

Synapse
type: Concept
comment: Protein found in the synapses. Synapses are the communicating cell-cell junctions that allow signals to pass from a nerve cell to a target cell. In a chemical synapse, the signal is carried by a neurotransmitter which diffuses across a narrow synaptic cleft and activates a receptor on the postsynaptic membrane of the target cell. The target may be a dendrite, cell body, neuronal axon, a specialized region of a muscle or a secretory cell. In an electrical synapse, a direct connection is made between the cytoplasms of two cells via gap junctions.
subclass of: Cellular component
narrower: Postsynaptic cell membrane
narrower: Synaptosome
category: Cellular component

synapse
type: Class
database: go

Synaptosome
type: Concept
comment: Protein found in synaptosomes, the pinched-off nerve endings and their contents of vesicles and cytoplasm together with the attached subsynaptic area of the membrane of the postsynaptic cell. They are largely artificial structures produced by fractionation after selective centrifugation of nervous tissue homogenates.
subclass of: Synapse
category: Cellular component

neuron projection
type: Class
database: go

Syncytium formation induced by viral infection
type: Concept
alternative label: Induction by virus of host cell-cell fusion
alternative label: Polykaryons formation in virally infected cells
comment: Viral protein that mediates fusion of an infected cell with neighboring cells leading to the formation of multi-nucleate enlarged cells called syncytia. Usually these syncytia are the result of expression of a viral fusion protein at the host cell membrane during viral replication. Viruses such as herpesviruses are known to induce the formation of syncytia.
subclass of: Biological process
category: Biological process

positive regulation of syncytium formation by virus
type: Class
database: go

Systemic lupus erythematosus
type: Concept
alternative label: SLE
comment: Protein involved in the systemic lupus erythematosus (SLE), a chronic autoimmune disease where the immune system is over-active and produces too many abnormal antibodies that react with the patient's own tissues. The exact cause of lupus is not known, but heredity, environment and hormonal changes may be involved. The immune complex deposition in many tissues leads to the manifestations of the disease. Immune complexes can be deposited in glomeruli, skin, lungs, synovium, mesothelium, and other places. Many SLE patients develop renal complications.
subclass of: Disease
category: Disease

T cell receptor
type: Concept
comment: The T cell receptor (TCR) is the antigen receptor expressed on CD4-positive and CD8-positive T lymphocytes that recognizes complexes of peptides bound to self-MHC molecules on the surface of antigen presenting cells. Structurally, TCR is composed of a heterodimer of two disulfide-linked transmembrane polypeptide chains designated alpha and beta, each containing one terminal immunoglobulin (Ig)-like variable domain, one Ig-like constant domain, a hydrophobic transmembrane region and a short cytoplasmic region. A less common type of TCR, composed of gamma and delta chains, is found on a small subset of T cells and recognizes different forms of antigens. Each T cell expresses a unique TCR that is generated by randomly assorting genes. This ensures that T cells can respond (at the population level) to almost any infection.
subclass of: Adaptive immunity
subclass of: Cellular component
category: Cellular component

T cell receptor complex
type: Class
database: go

T=1 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=1 symmetry to protect the viral genome. The T=1 capsid is composed of 60 subunits, each subunit occupying a quasi-equivalent position. The capsid diameter ranges from 18 to 35 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=1 icosahedral viral capsid
type: Class
database: go

T=13 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=13 symmetry to protect the viral genome. The T=13 capsid is composed of 780 subunits, each subunit occupying a quasi-equivalent position. Its diameter ranges from 70 to 80 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=13 icosahedral viral capsid
type: Class
database: go

T=147 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=147 symmetry to protect the viral genome. The T=147 capsid is composed of 8820 subunits. Its diameter is about 185 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=147 icosahedral capsid
type: Class
database: go

T=16 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=16 symmetry to protect the viral genome. The T=16 capsid is composed of 960 subunits, each subunit occupying a quasi-equivalent position. Its diameter is about 100 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=16 icosahedral viral capsid
type: Class
database: go

T=169 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=169 symmetry to protect the viral genome. The T=169 capsid is composed of 10140 subunits. Its diameter is about 165-190 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=169 icosahedral viral capsid
type: Class
database: go

T=2 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=2* symmetry to protect the viral genome. The T=2* capsid is composed of 120 subunits. The T=2* symmetry does not exist under the rules described by Caspar and Klug, strictly speaking the capsid has a T=1 symmetry composed of 60 dimeric subunits. The capsid diameter is about 40 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=2 icosahedral viral capsid
type: Class
database: go

T=219 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=219 symmetry to protect the viral genome. The T=219 capsid is composed of 13140 subunits. Its diameter is about 130-160 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=219 icosahedral capsid
type: Class
database: go

T=25 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=25 symmetry to protect the viral genome. The T=25 capsid is composed of 1500 subunits, each subunit occupying a quasi-equivalent position. Its diameter is about 90 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=25 icosahedral viral capsid
type: Class
database: go

T=3 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=3 symmetry to protect the viral genome. The T=3 capsid is composed of 180 subunits, each subunit occupying a quasi-equivalent position. The capsid diameter ranges from 26 to 40 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=3 icosahedral viral capsid
type: Class
database: go

T=4 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=4 symmetry to protect the viral genome. The T=4 capsid is composed of 240 subunits, each subunit occupying a quasi-equivalent position. The capsid diameter ranges from 30 to 40 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=4 icosahedral viral capsid
type: Class
database: go

T=7 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a T=7 symmetry to protect the viral genome. The T=7 capsid is composed of 420 subunits, each subunit occupying a quasi-equivalent position. Papillomavirus and Polyomavirus T=7 capsids are composed of pentameric capsomeres for a total of 360 capsid proteins. Its diameter ranges from 45 to 60 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=7 icosahedral viral capsid
type: Class
database: go

T=pseudo3 icosahedral capsid protein
type: Concept
comment: Viral protein that forms an icosahedral capsid with a pseudo T=3 symmetry to protect the viral genome. The pseudo T=pseudo3 capsid is composed of 180 subunits. Each subunit does not occupy a quasi-equivalent position, therefore the structure is called pseudo. The capsid diameter ranges from 26 to 40 nm.
subclass of: Capsid protein
subclass of: Virion
category: Cellular component

T=pseudo3 icosahedral viral capsid
type: Class
database: go

Tachyzoite
type: Concept
alternative label: Endodyozoite
alternative label: Endozoite
comment: Protein expressed in the infectious tachyzoite stage, a rapidly growing, lytic and disease-causing stage in the life stage of coccidians (e.g. Toxoplasmy). Tachyzoites, which can infect most nucleated cells, replicate inside a parasitophorous vacuole, egress, and then infect neighboring cells. Aggregates of numerous tachyzoites are called clones, terminal colonies, or groups.
subclass of: Developmental stage
category: Developmental stage

Target cell cytoplasm
type: Concept
alternative label: Target cytoplasm
comment: Protein found in a target cell cytoplasm, the contents of a target cell within the plasma membrane and which, in eukaryotic cells, surrounds the host nucleus. This term is used to describe a toxin located in the cytoplasm of a target cell.
subclass of: Cellular component
category: Cellular component

Target cell membrane
type: Concept
alternative label: Target cytoplasmic membrane
alternative label: Target plasmalemma
alternative label: Target plasma membrane
comment: Protein found in or associated with a target cell membrane, the selectively permeable membrane which separates the target cell cytoplasm from its surroundings. This term is used to describe a toxin located to the cell membrane of a target cell.
subclass of: Target membrane
category: Cellular component

Target membrane
type: Concept
comment: Protein which is membrane-bound or membrane-associated with the target membrane, a lipid bilayer which surrounds target cell enclosed spaces and compartments. This selectively permeable structure is essential for effective separation of a target cell or targeet cell organelle from its surroundings. This term is used to describe a toxin located to a membrane of a target cell.
subclass of: Membrane
narrower: Target cell membrane
category: Cellular component

other organism cell membrane
type: Class
database: go

Taste
type: Concept
alternative label: Gustation
comment: Protein involved in taste signal transduction. Human perceives five basic taste qualities: bitter, salty, sour, sweet, and umami, the taste of glutamate. Taste perception begins when a taste-eliciting molecule, or tastant, interacts with specialized receptors in the membrane of taste receptor cells. Taste responses to bitter, sweet, and umami compounds are initiated by G-protein-coupled receptors and transduced via G-protein signaling cascades. Salty and sour tastes are transduced by ion channels.
subclass of: Sensory transduction
category: Biological process

sensory perception of taste
type: Class
database: go

Taste-modifying protein
type: Concept
alternative label: Sweet-taste protein
alternative label: TMP
comment: Protein that function as a natural sweetener or flavor enhancer. TMPs are found in the fruit or seed of several plants and show no primary sequence similarity. TMPs interact with taste receptors in a potent and specific manner. TMPs are natural and have been used by some cultures for centuries. West Africans have long used TMPs to improve flavor and suppress bitterness of food and drink.
subclass of: Molecular function
category: Molecular function

Taxol biosynthesis
type: Concept
alternative label: Paclitaxel biosynthesis
comment: Protein involved in the synthesis of taxol, a complex diterpenoid isolated from the bark of yew (Taxus) species. Taxol is a potent antimitotic agent with activity against a number of leukamias and solid tumors. It has become a chemotherapeutic drug under the generic name of paclitaxel.
subclass of: Biological process
category: Biological process

paclitaxel biosynthetic process
type: Class
database: go

Technical term
type: Concept
comment: Keywords assigned to proteins according to 'technical' reasons.
narrower: 3D-structure
narrower: Genetically modified food
narrower: Hybridoma
narrower: Pharmaceutical
narrower: Plasmid
narrower: Transposable element
narrower: ERV
narrower: Direct protein sequencing
narrower: Extinct organism protein
narrower: Reference proteome
narrower: Proteomics identification
subclass of: Concept

Teichoic acid biosynthesis
type: Concept
alternative label: C polysaccharide biosynthesis
comment: Protein involved in the synthesis of teichoic acid, a polymer of mainly glycerol phosphate or ribitol phosphate substituted extensively with amino acids and/or sugars. Teichoic acid occurs in the cell wall of Gram-positive bacteria.
subclass of: Biological process
category: Biological process

teichoic acid biosynthetic process
type: Class
database: go

Tellurium resistance
type: Concept
comment: Protein that confers resistance to tellurium.
subclass of: Biological process
category: Biological process

response to tellurium ion
type: Class
database: go

Telomere
type: Concept
comment: Protein involved in telomere replication, length regulation, structure, etc. The telomere is a nucleoprotein structure comprising the terminal section of a eukaryotic chromosome. It has a specialized structure which is replicated by a special process, thereby counteracting the tendency of a chromosome to be shortened during each round of replication.
subclass of: Chromosome
category: Cellular component

chromosome, telomeric region
type: Class
database: go

Terminal addition
type: Concept
comment: Protein involved in the random addition of deoxynucleoside 5'-triphosphate to the 3'end of a DNA initiator.
subclass of: Nucleotidyltransferase
subclass of: Biological process
category: Biological process

DNA nucleotidylexotransferase activity
type: Class
database: go

DNA modification
type: Class
database: go

Tetrahydrobiopterin biosynthesis
type: Concept
comment: Protein involved in the synthesis of tetrahydrobiopterin, the reduced form of dihydrobiopterin, a reduced pteridine derivative related to folic acid. It is a coenzyme for the enzyme phenylalanine-4-hydroxylase which is involved in phenylalanine degradation.
subclass of: Biological process
category: Biological process

tetrahydrobiopterin biosynthetic process
type: Class
database: go

Thiamine biosynthesis
type: Concept
alternative label: Aneurin biosynthesis
alternative label: Thiamin biosynthesis
alternative label: Vitamin B1 biosynthesis
comment: Protein involved in the synthesis of thiamine, a water-soluble vitamin member of the vitamin B complex. It occurs in cells largely as its active coenzyme form thiamine pyrophosphate, formerly called cocarboxylase. Thiamine is necessary in the diet of most vertebrates and some microorganisms. Its deficiency causes beriberi in man and polyneuritis in birds. Thiamine pyrophosphate serves as coenzyme in aldehyde-group transfers.
subclass of: Biological process
category: Biological process

thiamine biosynthetic process
type: Class
database: go

Thiamine catabolism
type: Concept
alternative label: Aneurin catabolism
alternative label: Thiamin catabolism
alternative label: Vitamin B1 catabolism
comment: Protein involved in the degradation of thiamine, a water-soluble vitamin which is a member of the vitamin B complex. It occurs in cells largely as its active coenzyme form thiamine pyrophosphate, formerly called cocarboxylase. Thiamine is necessary in the diet of most vertebrates and some microorganisms. Its deficiency causes beriberi in man and polyneuritis in birds. Thiamine pyrophosphate serves as a coenzyme in aldehyde-group transfers.
subclass of: Biological process
category: Biological process

thiamine catabolic process
type: Class
database: go

Thiamine pyrophosphate
type: Concept
alternative label: TDP
alternative label: Thiamin diphosphate
alternative label: Thiamin pyrophosphate
alternative label: TPP
comment: Protein which contains at least one thiamine pyrophosphate, the active form of vitamin B1 (thiamine). It is a required coenzyme for the pyruvate decarboxylase, pyruvate dehydrogenase and ketoglutarate dehydrogenase reactions.
subclass of: Ligand
category: Ligand

Thick filament
type: Concept
comment: Protein found in, or associated with, the thick filaments which are formed by bipolar myosin-II filaments (12-14 nm in diameter, 1.6 mm long) found striated muscle. Myosin filaments elsewhere are often referred to as 'thick filaments', although their length may be considerably less. The myosin heads project from the thick filament in a regular fashion.
subclass of: Muscle protein
subclass of: Cellular component
category: Cellular component

myosin filament
type: Class
database: go

Thioester bond
type: Concept
alternative label: Thiolester bond
comment: Protein which is posttranslationally modified by the formation of a thioester crosslink between two amino acids in the polypeptidic chain(s), usually formed between a cysteine side chain and the carboxamide group of an asparagine or glutamine side chain.
subclass of: PTM
category: PTM

Thioether bond
type: Concept
comment: Protein which is posttranslationally modified by the formation of a thioether crosslink between two amino acids in the polypeptidic chain(s), usually formed between a cysteine side chain and the side chain of a serine or a threonine.
subclass of: PTM
category: PTM

Thiol protease
type: Concept
alternative label: Sulfhydryl protease
alternative label: Thiol peptidase
alternative label: Thiol proteinase
comment: Proteolytic enzyme with a cysteine residue (Cys) in its active site. There are many families of thiol proteases. The most well known one is the papain family (C1 in MEROPS classification) which is known to exist in most eukaryotes.
subclass of: Protease
category: Molecular function

cysteine-type peptidase activity
type: Class
database: go

Thiol protease inhibitor
type: Concept
alternative label: Thiol peptidase inhibitor
alternative label: Thiol proteinase inhibitor
comment: Protein which inhibits the activity of a thiol protease, a class of proteases that contains an active site cysteine residue (Cys), e.g. papain, cathepsins, etc.
subclass of: Protease inhibitor
category: Molecular function

cysteine-type endopeptidase inhibitor activity
type: Class
database: go

Threonine biosynthesis
type: Concept
comment: Protein involved in the synthesis of the essential amino acid threonine.
subclass of: Amino-acid biosynthesis
category: Biological process

threonine biosynthetic process
type: Class
database: go

Threonine protease
type: Concept
comment: Proteolytic enzyme with a threonine residue (Thr) in its active site. The prototype members of this class of enzymes are the proteasome catalytic subunits.
subclass of: Protease
category: Molecular function

threonine-type endopeptidase activity
type: Class
database: go

Thrombophilia
type: Concept
alternative label: Recurrent venous thrombosis
comment: Protein which, if defective, causes thrombophilia, a disorder of hemostasis in which the individuals are prone to serious spontaneous thrombosis.
subclass of: Blood coagulation
subclass of: Disease
category: Disease

Thylakoid
type: Concept
comment: Protein located in or on the thylakoid, a membranous cisterna of the chloroplast. Thylakoids stack up to form the grana or stay as single cisternae and interconnect the grana. The thylakoid contains the photosynthetic pigments, reaction centers and electron-transport chain. Thylakoid, where photosynthesis occurs, are also found in cyanelles and in photosynthetic bacteria where they are the extensive invaginations of the plasma membrane.
subclass of: Cellular component
category: Cellular component

thylakoid
type: Class
database: go

Thyroid hormone
type: Concept
comment: Protein precursor of thyroid hormones which are secreted by the thymus gland and participate in the development of the lymphoid system as well as the maturation of the cellular immune response. Also used for proteins which bind thyroid hormones or thyroid hormone receptor antagonists.
subclass of: Hormone
category: Molecular function

Thyroid hormones biosynthesis
type: Concept
comment: Protein involved in the synthesis of thyroid hormones.
subclass of: Biological process
category: Biological process

hormone biosynthetic process
type: Class
database: go

Tight junction
type: Concept
comment: Protein which is a component of the tight junction or are associated with it. These specialized regions of the plasma membrane prevent the diffusion of dissolved molecules between adjacent epithelial cells, seal off body cavities such as intestine or stomach lumen and prevent the diffusion of membrane proteins and glycolipids between the apical and basolateral regions of the plasma membrane.
subclass of: Cell junction
category: Cellular component

bicellular tight junction
type: Class
database: go

Tissue remodeling
type: Concept
comment: Protein involved in tissue remodeling. As an example the matrix-degrading plasminogen activators (PAs) and matrix metalloproteinases (MMPs) are general proteolytic enzyme systems which mediate tissue remodeling and tissue destruction in a variety of physiological and pathological conditions, including ovulation, angiogenesis, implantation, tumor invasion and inflammatory diseases such as rheumatoid arthritis (RA).
subclass of: Biological process
category: Biological process

tissue remodeling
type: Class
database: go

TonB box
type: Concept
comment: Protein with a TonB box. In Escherichia coli the TonB protein interacts with outer membrane receptor proteins that carry out high-affinity binding and energy-dependent uptake of specific substrates into the periplasmic space. These substrates are either poorly permeable through the porin channels or are encountered at very low concentrations. In the absence of TonB these receptors bind their substrates but do not carry out active transport. TonB also interacts with some colicins and is involved in the energy dependent, irreversible steps of bacteriophages phi-80 and T1 infection.
subclass of: Domain
category: Domain

Topoisomerase
type: Concept
comment: Enzymes capable of altering the degree of supercoiling of double-stranded DNA molecules. Various topoisomerases can increase or relax supercoiling, convert single-stranded rings to intertwined double-stranded rings, tie and untie knots in single stranded and duplex rings or catenate and decatenate duplex rings. Any enzyme that cleaves only one strand of a DNA duplex and then reseals it is classified as a type I topoisomerase (Topo I). Type II topoisomerases (Topo II) change DNA topology by breaking and rejoining double-stranded DNA.
subclass of: Isomerase
category: Molecular function

DNA topoisomerase activity
type: Class
database: go

Toxin
type: Concept
comment: Naturally-produced poisonous protein that damages or kills other cells, or the producing cells themselves in some cases in bacteria. Toxins are produced by venomous and poisonous animals, some plants, some fungi and some pathogenic bacteria. Animal toxins (mostly from snakes, scorpions, spiders, sea anemones and cone snails) are generally secreted in the venom of the animal.
subclass of: Molecular function
narrower: Cardiotoxin
narrower: Enterotoxin
narrower: Neurotoxin
narrower: Ion channel impairing toxin
narrower: Myotoxin
narrower: Dermonecrotic toxin
narrower: Hemostasis impairing toxin
narrower: G-protein coupled receptor impairing toxin
narrower: Complement system impairing toxin
narrower: Cell adhesion impairing toxin
narrower: Viral exotoxin
category: Molecular function

toxin activity
type: Class
database: go

Toxin-antitoxin system
type: Concept
alternative label: Toxin-antitoxin module
comment: Bacterial, archaeal or viral protein belonging to a toxin-antitoxin (TA) system. Toxin protein expression is poisonous to the cell and is counteracted by its co-expressed, short-lived "antidote" antitoxin. Antitoxins can be protein (type II, IV, V, VI) or RNA (type I, III) and act directly or indirectly on the toxin protein or transcript. Genes for the 2 components are closely linked; in many type II TA systems the toxin-antitoxin complex regulates transcription of its operon. Toxins belong to recognizable protein families, antitoxins usually do not. Orphan toxin genes are occasionally found in complete genomes.
subclass of: Biological process
category: Biological process

TPQ
type: Concept
alternative label: Topaquinone
comment: Protein which is posttranslationally modified on a tyrosine residue to form TPQ. This modification of a strictly conserved active-site tyrosine residue proceeds via the hydroxylation of tyrosine to Topa (Trihydroxyphenylalanine) and then to TPQ (Topaquinone). It is a self-processing pathway requiring only the protein, copper and molecular oxygen. TPQ is the redox cofactor of most copper-containing amine oxidases.
subclass of: PTM
category: PTM

TPR repeat
type: Concept
alternative label: Tetratricopeptide repeat
comment: Protein with at least one TPR repeat. The TPR repeat of typically 34 amino acids was first described in the yeast cell division control protein 23 (CDC23) and later found to occur in a large number of proteins. A function for this repeat seems to be protein-protein interaction.
subclass of: Domain
category: Domain

Transcription
type: Concept
comment: Protein involved in the transfer of genetic information from DNA to messenger RNA (mRNA) by DNA-directed RNA polymerase. In the case of some RNA viruses, protein involved in the transfer of genetic information from RNA to messenger RNA (mRNA) by RNA-directed RNA polymerase.
subclass of: Biological process
narrower: DNA-directed RNA polymerase
narrower: Transcription regulation
category: Biological process

Transcription antitermination
type: Concept
comment: Protein involved in transcription antitermination, the process whereby RNA polymerase is allowed to read through specific RNA secondary structures that normally terminate transcription.
subclass of: Transcription regulation
category: Biological process

transcription antitermination
type: Class
database: go

Transcription regulation
type: Concept
comment: Protein involved in the regulation of the transcription process.
subclass of: Transcription
narrower: Sigma factor
narrower: Transcription termination
narrower: Transcription antitermination
category: Biological process

Transcription termination
type: Concept
comment: Protein involved in transcription termination.
subclass of: Transcription regulation
category: Biological process

DNA-templated transcription termination
type: Class
database: go

Transducer
type: Concept
comment: Protein which converts an input signal into an output signal of a different form.
subclass of: Molecular function
narrower: G-protein coupled receptor
category: Molecular function

signal transduction
type: Class
database: go

Transferase
type: Concept
comment: Enzyme that transfers a chemical group, e.g. a methyl group or a glycosyl group from one compound (donor) to another compound (acceptor).
subclass of: Molecular function
narrower: Acyltransferase
narrower: Aminotransferase
narrower: Glycosyltransferase
narrower: Kinase
narrower: Methyltransferase
narrower: Nucleotidyltransferase
narrower: Prenyltransferase
category: Molecular function

transferase activity
type: Class
database: go

Transit peptide
type: Concept
comment: Proteins which have an N-terminal presequence which directs them to an organelle (chloroplast, mitochondria, microbody, cyanelle). The transit peptide is required for their transport across the relevant membranes from their site of synthesis in the cytoplasm.
subclass of: Domain
category: Domain

Translation regulation
type: Concept
comment: Protein involved in the regulation of peptide formation on ribosomes, directed by messenger RNA (mRNA).
subclass of: Biological process
category: Biological process

regulation of translation
type: Class
database: go

Translational shunt
type: Concept
alternative label: Ribosomal shunt
alternative label: Ribosome shunt
alternative label: Shunting
comment: Protein which is involved in the translational shunt, an unusual translation process in which ribosomes are loaded onto mRNA at the 5'-cap structure, start scanning for a short distance before bypassing the large internal leader region and initiating at a downstream start site. Shunting operates in plants, animals, and yeast translational systems, both in vivo and in vitro.
subclass of: Molecular function
category: Molecular function

Translocase
type: Concept
comment: Protein that uses enzyme activity to effect transmembrane transport, as exemplified by transmembrane transport coupled to ATP hydrolysis and oxidoreductases involved in transmembrane proton or electron transport. Not to be confused with ligand-gated ion channels or other transmembrane transporters without enzyme activity.
subclass of: Molecular function
category: Molecular function

Translocation
type: Concept
comment: Protein involved in the transport of proteins across a membrane. As an example translocation into the nucleus occurs via nuclear pores which allow rapid diffusion of small molecules. Larger molecules (maximum 9 nm) take longer. Translocation into the mitochondria or chloroplast occurs at sites of adhesion between the outer and inner membranes and is driven by ATP hydrolysis as well as the electrochemical gradient of the inner membrane.
subclass of: Protein transport
narrower: Nuclear pore complex
category: Biological process

Transmembrane
type: Concept
comment: Protein with at least one transmembrane domain, a membrane-spanning helical or beta-stranded domain embedded in a membrane.
subclass of: Membrane
subclass of: Domain
narrower: Porin
narrower: Signal-anchor
narrower: Transmembrane helix
narrower: Transmembrane beta strand
category: Domain

Transmembrane beta strand
type: Concept
comment: Protein with at least one transmembrane beta stranded domain, a membrane-spanning stretch, typically 5-10 amino acids long, whose peptide backbones are almost fully extended with the sidechains of two neighboring residues projected in the opposite direction from the backbone. Two or more hydrogen bonded (parallel or anti-parallel) beta strands form a beta sheet. A beta barrel is formed by a closed beta sheet around a central pore. Beta barrels consist usually of an even number of beta strands (between 8 and 24), they are found only in bacterial outer membranes, mitochondria and plastids.
subclass of: Membrane
subclass of: Transmembrane
category: Domain

Transmembrane helix
type: Concept
alternative label: Alpha-helical transmembrane
alternative label: Pauling-Corey-Branson alpha helix
comment: Protein with at least one transmembrane helical domain, a membrane-spanning domain with an hydrogen-bonded helical configuration, including alpha-, 3-10-, and pi-helices. The transmembrane alpha-helix is very common, while the 3-10-helix is found at the ends of alpha-helices and the pi-helix, is more rare.
subclass of: Membrane
subclass of: Transmembrane
category: Domain

Transport
type: Concept
comment: Protein involved in the transport of a molecule (metabolite, protein, etc), a ion or an electron across cell membranes, inside the cell or in a tissue fluid.
subclass of: Biological process
narrower: Amino-acid transport
narrower: Antiport
narrower: Electron transport
narrower: Ion transport
narrower: Lipid transport
narrower: mRNA transport
narrower: Neurotransmitter transport
narrower: Oxygen transport
narrower: Phosphate transport
narrower: Protein transport
narrower: Sugar transport
narrower: Sulfate transport
narrower: Symport
narrower: Viral movement protein
narrower: Phosphonate transport
narrower: Ammonia transport
narrower: ER-Golgi transport
category: Biological process

Transposable element
type: Concept
alternative label: Transposon
comment: Protein encoded by a transposable element, or transposon, a mobile DNA segment that can replicate and insert a copy at another site within the genome. Simple transposons only contains genes needed for insertion. More complex types also carry genes with functions unrelated to insertion, e.g. genes for resistance to antibiotics or heavy metals.
subclass of: Technical term
category: Technical term

Transposition
type: Concept
comment: Protein involved in the movement of a specific DNA sequence - generally known as a transposable element or transposon - to another location within the genome by replication of the sequence and insertion of the copy at its target site, at random or at some specific site. Proteins necessary for the transposition, such as the enzyme transposase, are usually encoded by the transposable element itself.
subclass of: Biological process
category: Biological process

transposition
type: Class
database: go

Tricarboxylic acid cycle
type: Concept
alternative label: Citric acid cycle
alternative label: Krebs cycle
alternative label: TCA cycle
comment: Protein involved in the tricarboxylic acid cycle, a series of metabolic reactions in aerobic cellular respiration, which occurs in the mitochondria of animals and plants and in which acetyl-CoA, formed from pyruvate produced during glycolysis, is completely oxidized to CO2 via the interconversion of various carboxylic acids. It results in the reduction of NAD and FAD to NADH and FADH2, whose reducing power is then used indirectly in the synthesis of ATP by oxidative phosphorylation. The TCA cycle also provides intermediates for many other biosynthetic processes.
subclass of: Biological process
category: Biological process

tricarboxylic acid cycle
type: Class
database: go

Trimethoprim resistance
type: Concept
comment: Protein that confers, on bacteria or other microorganisms, the ability to withstand the antibacterial agent trimethroprim that inhibits dihydrofolate reductase (DHFR), an enzyme required for de novo glycine and purine synthesis.
subclass of: Antibiotic resistance
category: Biological process

Triplet repeat expansion
type: Concept
comment: Protein encoded by a gene which has a triplet repeat expansion, i.e. the increase of triplet (trinucleotide) repeats within the gene sequence. The length of such repeats is frequently polymorphic, and there is often a correlation between repeat length and disease severity.
subclass of: Coding sequence diversity
category: Coding sequence diversity

tRNA processing
type: Concept
alternative label: Transfer RNA processing
alternative label: tRNA biosynthesis
comment: Protein involved in the processing of the primary tRNA transcript to yield a functional tRNA. Transcription of tRNA genes results in a large precursor molecule which may even contain sequences for several tRNA molecules. This primary transcript is subsequently processed by cleavage and by modification of the appropriate bases.
subclass of: Biological process
category: Biological process

tRNA processing
type: Class
database: go

tRNA-binding
type: Concept
alternative label: Transfer RNA binding
comment: Protein which binds transfer RNA, for example some ribosomal proteins or some aminoacyl-tRNA synthetases.
subclass of: RNA-binding
category: Molecular function

tRNA binding
type: Class
database: go

Trophozoite
type: Concept
comment: Protein expressed in the trophozoite stage, a motile replicating and disease-causing stage of in the life cycle of some sporozoan parasites.
subclass of: Developmental stage
category: Developmental stage

Trypanosomiasis
type: Concept
comment: Protein involved in trypanosomiasis, a human or animal disease caused by Trypanosoma, a genus of parasitic flagellate protozoa. Such diseases include African sleeping sickness, Nagana and American Chagas' disease.
subclass of: Disease
category: Disease

Tryptophan biosynthesis
type: Concept
comment: Protein involved in the synthesis of the aromatic amino acid tryptophan (Trp) in bacteria, fungi and plants from chorismate. Trp is needed to synthesize proteins and as a precursor to niacin, serotonin and melatonin.
subclass of: Aromatic amino acid biosynthesis
category: Biological process

tryptophan biosynthetic process
type: Class
database: go

Tryptophan catabolism
type: Concept
comment: Protein involved in the degradation of the aromatic amino acid tryptophan (Trp).
subclass of: Biological process
category: Biological process

tryptophan catabolic process
type: Class
database: go

TTQ
type: Concept
alternative label: Tryptophan tryptophylquinone
comment: Protein which contains at least one tryptophan tryptophylquinone (TTQ) cross-link modification. TTQ, the cofactor of methylamine dehydrogenase (MADH), is formed by oxidation of the indole ring of a tryptophan to form tryptophylquinone followed by covalent cross-linking with another tryptophan residue. MADH converts primary amines to their corresponding aldehydes plus ammonia. During the catalytic cycle, TTQ mediates electron transfer from the substrate to a copper protein, amicyanin. These electrons are transferred to the respiratory chain via a C-type cytochrome.
subclass of: PTM
category: PTM

Tumor antigen
type: Concept
alternative label: Cancer antigen
comment: Protein on the surfaces of tumor cells detected by cell-mediated immunity. Different categories of tumor antigens which induce cytotoxic T lymphocyte (CTL) responses in vitro and in vivo, have been identified. These are, namely, "cancer testis" (CT) antigens expressed in different tumours and normal testis, melanocyte differentiation antigens, point mutations of normal genes, self antigens that are overexpressed in malignant tissues and viral antigens.
subclass of: Molecular function
category: Molecular function

Tumor suppressor
type: Concept
alternative label: Anti-oncogene
alternative label: Antitumor
comment: Protein that suppresses tumorigenesis. Tumor suppressors generally function as negative regulators of cell cycle progression or cell proliferation. They may act to enforce cell cycle arrest in response to specific signals, such as DNA damage, thereby allowing DNA repair to occur prior to DNA replication. Tumor suppressors that act in this way include TP53 and its downstream effector CDKN1A/p21. They may also act to induce programmed cell death (apoptosis) in response to specific developmental signals or under circumstances where DNA repair cannot be completed. Tumor suppressors that act in this way include PTEN and BAX.
subclass of: Disease
category: Disease

Tungsten
type: Concept
comment: Protein which binds at least one tungsten atom, or protein whose function is tungsten-dependent. Tungsten is a metallic element, chemical symbol W.
subclass of: Ligand
category: Ligand

Two-component regulatory system
type: Concept
alternative label: Phosphorelay system
alternative label: Phospho-relay system
alternative label: Two-component sensory transduction system
alternative label: Two-component signal transduction system
alternative label: Two-component system
comment: Protein involved in a system responding to environmental changes characterized usually by a sensor kinase in the cell membrane that phosphorylates itself in response to a signal and a response regulator to which the phosphoryl group is transferred. The responder is typically a DNA-binding protein that regulates transcription. Several of these systems are quite complex, involving many proteins in a signaling cascade or contributing to several responses simultaneously. They are involved in a variety processes such as chemotaxis, osmoregulation, magnesium transport, pH tolerance, sporulation, or response of virulent species to host cell's environments.
subclass of: Biological process
category: Biological process

phosphorelay signal transduction system
type: Class
database: go

Tyrosine biosynthesis
type: Concept
comment: Protein involved in the synthesis of the aromatic amino acid tyrosine. In microorganisms and plants, tyrosine is synthesized from chorismate via a simple pathway using prephenate as an intermediate. In rat, this nonessential amino acid is produced by hydroxylating the essential amino acid phenylalanine.
subclass of: Aromatic amino acid biosynthesis
category: Biological process

tyrosine biosynthetic process
type: Class
database: go

Tyrosine catabolism
type: Concept
comment: Protein involved in the degradation of the aromatic amino acid tyrosine. In mammals, tyrosine degradation is catalyzed by a series of 5 enzymatic reactions which yield acetoacetate (ketogenic) and the Krebs cycle intermediate fumarate (glucogenic).
subclass of: Biological process
category: Biological process

tyrosine catabolic process
type: Class
database: go

Tyrosine-protein kinase
type: Concept
comment: Enzyme which catalyzes the transfer of the terminal phosphate of ATP to a specific tyrosine residue on its target protein. Many of these kinases play significant roles in development and cell division. Tyrosine-protein kinases can be divided into two subfamilies: receptor tyrosine kinases, which have an intracellular tyrosine kinase domain, a transmembrane domain and an extracellular ligand-binding domain; and non-receptor (cytoplasmic) tyrosine kinases, which are soluble, cytoplasmic kinases.
subclass of: Kinase
category: Molecular function

protein tyrosine kinase activity
type: Class
database: go

Ubiquinone
type: Concept
alternative label: Coenzyme Q
alternative label: CoQ
comment: Protein which interacts with ubiquinone. This fat soluble benzoquinone has a long isoprenoid side chain, which varies in length depending on the species. For example, S.cerevisiae has CoQ-6, E.coli has CoQ-8, rat and R.capsulatus have CoQ-9 and S.pombe, G.suboxydans and humans have CoQ-10. Ubiquinone is a carrier of hydrogen atoms (protons plus electrons) and functions as an ubiquitous coenzyme in redox reactions, where it is first reduced to the enzyme-bound intermediate radical semiquinone and in a second reduction to ubiquinol (Dihydroquinone; CoQH2). Ubiquinone is not tightly bound or covalently linked to a protein complex but is very mobile.
subclass of: Ligand
category: Ligand

Ubiquinone biosynthesis
type: Concept
alternative label: Coenzyme Q biosynthesis
alternative label: CoQ biosynthesis
comment: Protein involved in the synthesis of ubiquinone which involves the conversion of chorismate into 4-hydroxy-benzoate, to which is added six to ten isoprene units to form polyprenyl phenol. The addition of a further oxygen atom at C3, followed by the transfer of three methyl groups from S-adenosine methionine gives rise to ubiquinol, which is further reduced to ubiquinone (6-polyprenyl-2,3-dimethoxy-5-methyl-1,4-benzoquinone).
subclass of: Biological process
category: Biological process

ubiquinone biosynthetic process
type: Class
database: go

Ubl conjugation
type: Concept
alternative label: Sumoylation
alternative label: Ubiquitination
alternative label: Ubiquitin conjugation
alternative label: Ubiquitin-like modifier conjugation
alternative label: Ubiquitinylation
comment: Protein which is posttranslationally modified by the attachment of at least one ubiquitin-like modifier protein, such as ubiquitin, SUMO, APG12, URM1 or RUB1. Ubiquitin, for example, is linked through a isopeptide bond between its C-terminus and the epsilon group of a lysine residue present on either another ubiquitin-like modifier protein or a target protein.
subclass of: PTM
category: PTM

Ubl conjugation pathway
type: Concept
alternative label: Ubiquitin conjugation pathway
alternative label: Ubiquitin-like modifier conjugation pathway
comment: Protein involved in ubiquitin-like modifier processing, activation, conjugation or deconjugation such as Ubl-activating enzymes (E1s), Ubl-conjugating enzymes (E2s), Ubl-protein ligases (E3s), some thiol proteases (Ubiquitin carboxyl-terminal hydrolases (UCH), Ubiquitin-specific processing proteases (UBP) and ubiquitin-like proteases) and the ubiquitin-like modifier proteins. Besides signaling proteolysis, ubiquitination for example can be a signal for trafficking, kinase activation and other nonproteolytic fates.
subclass of: Biological process
category: Biological process

Unfolded protein response
type: Concept
alternative label: ER stress pathway
alternative label: ER stress response
alternative label: UPR
comment: Protein involved in the unfolded protein response. An accumulation of unfolded proteins in the ER lumen triggers a stress response, resulting in the transcriptional induction in the nucleus of a set of genes, whose products are involved in protein folding, assembly and modification as well as in phospholipid biosynthesis. The unfolded protein response (UPR) is the intracellular pathway that mediates signaling from the endoplasmic reticulum (ER) to the nucleus. UPR is also tightly linked to ER-associated protein degradation (ERAD). UPR is a ubiquitous mechanism observed in all eukaryotes from humans to yeast.
subclass of: Biological process
category: Biological process

response to unfolded protein
type: Class
database: go

Urea cycle
type: Concept
alternative label: Krebs-Henseleit cycle
comment: Protein involved in the urea cycle. This is a metabolic pathway in which ammonia, produced during amino acid degradation, is converted to urea in the liver, through a series of reactions that are distributed between the mitochondrial matrix and the cytosol.
subclass of: Biological process
category: Biological process

urea cycle
type: Class
database: go

Usher syndrome
type: Concept
alternative label: Sensorineural deafness with retinitis pigmentosa
alternative label: Usher's syndrome
comment: Protein which, if defective, causes Usher syndrome, an autosomal recessive disorder characterized by sensorineural hearing loss and retinitis pigmentosa leading to visual impairment. There are three clinical subtypes: Usher syndrome type 1 (USH1), characterized by congenital profound deafness, constant vestibular dysfunction, and prepubertal onset of retinitis pigmentosa; Usher syndrome type 2 (USH2), associated with moderate to severe hearing loss, normal vestibular function, and onset of retinitis pigmentosa during the second decade of life; and Usher syndrome type 3 (USH3), characterized by progressive hearing loss, variable vestibular function, and adult onset retinitis pigmentosa.
subclass of: Deafness
category: Disease

Vacuole
type: Concept
comment: Protein related to the vacuole of a cell. The precise form and function of vacuoles may vary between phyla. Plant vacuoles are among the best characterized. They are generally large fluid-filled compartments in the cytoplasm, bounded by a membrane called the tonoplast; individual vacuoles can fuse to form larger species. Examples include the lytic vacuole, the storage vacuole and the lutoid. One important function of plant vacuoles is the maintenance of hydrostatic pressure. Other eukaryotes employ vacuoles for a variety of purposes, including storage (as in the yeast lysosome/vacuole), secretion and phagocytosis. In Protozoa, contractile vacuoles can be used to discharge water from the cytoplasm to the external environment.
subclass of: Cellular component
category: Cellular component

vacuole
type: Class
database: go

Vanadium
type: Concept
comment: Protein whose function is vanadium-dependent. Vanadium is a transition metal, chemical symbol V.
subclass of: Ligand
category: Ligand

Vasoactive
type: Concept
comment: Protein which is vasoactive, i.e. has a constricting or dilating effect on the caliber of blood vessels.
subclass of: Molecular function
narrower: Vasoconstrictor
narrower: Vasodilator
category: Molecular function

blood vessel diameter maintenance
type: Class
database: go

Vasoconstrictor
type: Concept
comment: Protein which constricts the caliber of blood vessels.
subclass of: Vasoactive
category: Molecular function

vasoconstriction
type: Class
database: go

Vasodilator
type: Concept
comment: Protein which dilates the caliber of blood vessels.
subclass of: Vasoactive
category: Molecular function

vasodilation
type: Class
database: go

Viral attachment to host adhesion receptor
type: Concept
comment: Virion surface protein implicated in the initial binding to a specific host adhesion molecule. Adhesion receptors can be for example proteoglycans, sialic acids or a protein receptor. This initial attachment is not sufficient for triggering virus entry into host cell. In prokaryotic viruses, the primary attachment is called reversible adsorption.
subclass of: Virion
subclass of: Viral attachment to host cell
category: Biological process

adhesion receptor-mediated virion attachment to host cell
type: Class
database: go

Viral attachment to host cell
type: Concept
alternative label: Virion attachment to host cell surface
comment: Viral surface protein implicated in the binding to specific host surface molecule(s). This binding can lead to virion entry into the host cell, it can trigger signaling pathways, or it can allow the virion to be carried by the host cell to a specific organ.
subclass of: Host-virus interaction
subclass of: Virion
subclass of: Virus entry into host cell
narrower: Viral attachment to host cell pilus
narrower: Viral attachment to host adhesion receptor
narrower: Viral attachment to host entry receptor
narrower: Viral attachment to host cell flagellum
category: Biological process

virion attachment to host cell
type: Class
database: go

Viral attachment to host cell flagellum
type: Concept
comment: Virion protein involved in the primary attachment to host flagellar receptor. This attachment allows the prokaryotic virus to move along the host flagellum to find its entry receptor for viral genome penetration. Some prokaryotic viruses such as bacteriophages Chi or PV22 specifically interact with their host's flagellum, move toward the base of the flagellum to come in contact with the host cytoplasmic membrane and deliver the viral genome into the host cytoplasm.
subclass of: Virion
subclass of: Viral attachment to host cell
category: Biological process

virion attachment to host cell flagellum
type: Class
database: go

Viral attachment to host cell pilus
type: Concept
comment: Virion protein involved in the interaction with bacterial pili, which are retractile filaments that protrude from bacteria with 2 membranes (Gram-negative bacteria). Binding to the pilus is followed by retraction of the pilus, which translocates the bound virion to the bacterial surface and allows subsequent viral genome penetration into host cytoplasm. Bacteriophages M13, f1, fd, R17, Qbeta, Pf1, Pf3, phiKMV or phi6 for example utilize the host cell pilus as an attachment structure.
subclass of: Virion
subclass of: Viral attachment to host cell
category: Biological process

virion attachment to host cell pilus
type: Class
database: go

Viral attachment to host entry receptor
type: Concept
comment: Virion surface protein implicated in the binding to a secondary specific host surface molecule(s), which triggers the internalization of viral genome and possibly other viral components into the host cell. In prokaryotic viruses, the attachment to a host entry receptor is called irreversible adsorption.
subclass of: Virion
subclass of: Viral attachment to host cell
category: Biological process

entry receptor-mediated virion attachment to host cell
type: Class
database: go

Viral baseplate protein
type: Concept
comment: Viral protein part of the virion base plate of tailed prokaryotic viruses such as Caudovirales. The baseplate is a multiprotein component at the end of the tail and to which fibers of tailed phages may be attached. Sometimes referred to as the tail tip or tip structure in Siphoviridae.
subclass of: Viral tail protein
category: Cellular component

virus tail, baseplate
type: Class
database: go

Viral budding
type: Concept
comment: Viral protein involved in the budding of a viral particle through a cellular membrane into the extracellular space or into a cellular compartment.
subclass of: Viral release from host cell
narrower: Viral budding via the host ESCRT complexes
category: Biological process

viral budding
type: Class
database: go

Viral budding via the host ESCRT complexes
type: Concept
comment: Viral protein which recruits the cellular ESCRT (Endosomal Sorting Complex Required for Transport) to mediate host-assisted viral budding. Specific motifs in enveloped viruses' proteins called late assembly domains (L-domains) are responsible for recruiting the ESCRT machinery directly or via ESCRT-associated proteins like PDCD6IP.
subclass of: Host-virus interaction
subclass of: Viral budding
category: Biological process

viral budding via host ESCRT complex
type: Class
database: go

Viral capsid assembly
type: Concept
alternative label: Viral procapsid assembly
comment: Viral protein involved in the assembly of the capsid. In most cases virion assembly is spontaneous, but viruses like adenoviruses, herpesviruses, microviruses and tailed bacteriophages need the help of scaffolding proteins to assemble their capsid. Maturation steps that remove the scaffolding proteins and induce structural changes in the assembled capsid are also often part of the assembly process.
subclass of: Viral release from host cell
narrower: Viral capsid maturation
category: Biological process

viral capsid assembly
type: Class
database: go

Viral capsid maturation
type: Concept
alternative label: Viral procapsid maturation
comment: Viral protein involved in the refolding and structural rearrangements of the procapsid shell that give rise to the more stable mature capsid structure. These maturation events occur during the intracellular capsid assembly process. In many cases, procapsid maturation is initiated by the activation of a viral protease. Most bacterial viruses as well as Herpesviruses assemble as a procapsid that mature through a massive conformational change of the surface shell.
subclass of: Viral capsid assembly
category: Biological process

viral procapsid maturation
type: Class
database: go

Viral contractile tail ejection system
type: Concept
alternative label: Viral genome injection via long contractile tail
comment: Viral protein that constitutes the contractile ejection system carried by some tailed prokaryotic viruses such as the Myoviridae. This structure is able to penetrate the host cell envelope, to deliver the viral genome, and possibly some specific proteins, into the cell cytoplasm. A contractile ejection system is composed at least of the contractile sheath, the internal noncontractile tube, the baseplate and the terminator complex. Sheath contraction drives the rigid internal tube through the host cell envelope. Proteins of the ejection apparatus can play an active or a structural role in ejection.
subclass of: Virion
subclass of: Viral genome ejection through host cell envelope
subclass of: Molecular function
narrower: Viral tail sheath protein
category: Molecular function

viral genome ejection through host cell envelope, contractile tail mechanism
type: Class
database: go

Viral DNA replication
type: Concept
comment: Viral protein involved in the synthesis of multiple copies of the viral DNA genome. The replicated genomes provide support for further viral transcription or are assembled into progeny virions.
subclass of: DNA replication
subclass of: Biological process
category: Biological process

viral DNA genome replication
type: Class
database: go

Viral envelope protein
type: Concept
comment: Protein of the viral envelope, a lipoprotein membrane which forms the outermost layer of the virion in certain viruses.
subclass of: Virion
category: Cellular component

viral envelope
type: Class
database: go

Viral exotoxin
type: Concept
comment: Virally encoded toxin that acts as a host virulence factor against another organism. Viral exotoxins are mostly expressed from integrated viral genomes. Bacterium host, bacterial populations, and the encoding virus/provirus probably benefit from the expression of such exotoxins. Although prokaryotic viruses can kill their host if they switch to the lytic cycle, provirus encoding exotoxins (e.g. shiga toxin, diphtheria toxin) are often retained for the sake of bacterial utility.
subclass of: Toxin
subclass of: Modulation of host virulence by virus
category: Molecular function

Viral extrusion
type: Concept
comment: Viral protein involved in the extrusion of viral particles from the host prokaryotic cell. Extrusion is a concerted mechanism of assembly and secretion used by filamentous phages to release mature viral particles without inducing host cell lysis.
subclass of: Viral release from host cell
category: Biological process

viral extrusion
type: Class
database: go

Viral genome circularization
type: Concept
comment: Viral protein that is involved in or facilitates the conversion of a linear double stranded DNA viral genome into a circular form, either by homologous recombination between redundant ends or by association of complementary single stranded ends (sticky ends). Circular genomes can support rolling circle replication and, for many viruses, genome circularization is also necessary for latency.
subclass of: Virus entry into host cell
category: Biological process

viral genome circularization
type: Class
database: go

Viral genome ejection through host cell envelope
type: Concept
alternative label: Viral genome ejection through host membranes
comment: Viral protein that constitutes the ejection system carried by some prokaryotic viruses. These structures are able to penetrate the host cell envelope in order to deliver the viral genome, and possibly also some specific proteins, into the cell cytoplasm.
subclass of: Viral penetration into host cytoplasm
narrower: Viral tail tube protein
narrower: Viral contractile tail ejection system
narrower: Viral long flexible tail ejection system
narrower: Viral short tail ejection system
category: Biological process

viral genome ejection through host cell envelope
type: Class
database: go

Viral genome excision
type: Concept
comment: Viral protein involved in latent provirus DNA excision from the host genome following induction. Bacteriophage lambda for example expresses an excisionase that manages excision of the viral genome from the host genome.
subclass of: Biological process
category: Biological process

provirus excision
type: Class
database: go

Viral genome integration
type: Concept
comment: Viral protein involved in the integration of a virus genome into the host DNA. Integrated viral DNA is referred to as a provirus in the case of retroviruses or prophage in the case of prokaryotic viruses. The integrated viral genome does not necessarily make new DNA copies of itself while integrated into a host genome. Instead, it can remain latent and be passively replicated along with the host genome and passed on to the original cell's offspring; all descendants of the infected cell will also bear it in their genomes. The host's environmental conditions changes can however reactivate the virus leading to viral transcription and production of new infectious viruses (productive infection). Integration is a crucial step in replication of retroviruses, as well as some phages. Integration is not part of the viral replication cycle of phycodnaviruses, adeno-associated virus type 2, and human herpesvirus 6A genome, but can occasionally occur.
subclass of: DNA integration
subclass of: Virus entry into host cell
category: Biological process

viral genome integration into host DNA
type: Class
database: go

establishment of integrated proviral latency
type: Class
database: go

Viral genome packaging
type: Concept
comment: Protein involved in actively packaging the replicated viral genome into a protective shell or envelope. Such packaging proteins are present for example in adenoviruses, herpesviruses and tailed bacteriophages. In bacteriophages, the packaging proteins complex is involved in recognizing and selecting a neo-synthesized viral genome in order to translocate it into a pre-assembled empty procapsid. DNA cleavage is sometimes coupled to genome packaging as well as maturation steps that induce structural changes in the assembled capsid.
subclass of: Viral release from host cell
category: Biological process

viral genome packaging
type: Class
database: go

Viral immunoevasion
type: Concept
alternative label: Immunoevasin
alternative label: Viral host defense evasion
alternative label: Viral immune evasion
comment: Viral protein involved in host immune evasion thereby optimizing viral growth and dissemination. Viral immune evasion strategies are typical of viruses which persist in their host throughout life. For example: Herpesviridae, Adenoviridae, Poxviridae and Retroviridae have developed subversions of the MHC class I antigen-presentation pathway. In order to reduce the effectiveness of cytotoxic T-lymphocytes immunity, they express proteins that either down-modulate MHC class I expression (degradation or mislocalization) or interfere with the antigen binding/presentation process (down-regulation of the expression of the transporter associated with antigen processing TAP). Some proteins of these virus families also down-regulate other molecules involved in immune recognition.
subclass of: Host-virus interaction
narrower: Inhibition of host adaptive immune response by virus
narrower: Inhibition of host chemokines by virus
narrower: Inhibition of host complement factors by virus
narrower: Inhibition of host innate immune response by virus
narrower: Modulation of host dendritic cell activity by virus
narrower: Modulation of host immunity by viral IgG Fc receptor-like protein
narrower: Evasion of host immunity by viral interleukin-like protein
narrower: Modulation of host NK-cell activity by virus
category: Biological process

Viral ion channel
type: Concept
alternative label: Viroporin
comment: Small transmembrane protein that homo-oligomerizes to form a viral ion channel usually expressed in the viral envelope and host cell membranes. These channels affect membrane permeability to ions and play an important role in facilitating virus entry, assembly and release, as well as modulating the ion homeostasis of host cells. Viral ion channels are not necessarily required for the production of infectious virions, although their expression usually significantly increases growth. During influenza A virus entry for example, the M2 proton channel allows protons from the acidic endosome to enter the enveloped virion, initiating pH-dependent uncoating of the genome. In certain influenza A subtypes, M2 also equilibrates the intraluminal pH of the trans-Golgi network with the cytoplasm, preventing premature conformational changes in the viral fusion protein during budding.
subclass of: Ion transport
subclass of: Ion channel
category: Molecular function

pore formation by virus in membrane of host cell
type: Class
database: go

obsolete integral to membrane of host cell
type: Class
database: go

protein complex oligomerization
type: Class
database: go

Viral latency
type: Concept
alternative label: Viral lysogeny
comment: Viral protein expressed primarily to establish, maintain or terminate latency, the part of the viral life cycle during which a virus lies dormant (latent) within a cell. This part of the virus life cycle is called the lysogenic part in prokaryotic viruses. During latency, the viral genome can either exist as a provirus integrated in the host genome (proviral latency) or as a linear or circular plasmid in the host cell (episomal latency). The virus does not replicate, but is passively duplicated when the host divides. In eukaryotes for example, HHV-1 and HHV-3 establish episomal latency in neurons. HIV is integrated as a provirus in the genome of resting CD4-positive T cells, allowing the virus to persist for years. Following changes in the environmental conditions of the host, reactivation of the virus can occur leading to viral transcription and production of new infectious viruses.
subclass of: Biological process
narrower: Viral reactivation from latency
narrower: Viral latency initiation and maintenance
category: Biological process

viral latency
type: Class
database: go

Viral latency initiation and maintenance
type: Concept
comment: Viral protein expressed primarily to establish and maintain latency, the part of the viral life cycle during which a virus lies dormant (latent) within a cell. This part of the virus life cycle is called the lysogenic part in prokaryotic viruses. During latency, the viral genome can either exist as a provirus integrated in the host genome (proviral latency) or as a linear or circular plasmid in the host cell (episomal latency). The virus does not replicate, but is passively duplicated when the host divides.
subclass of: Viral latency
category: Biological process

Viral long flexible tail ejection system
type: Concept
alternative label: Viral genome injection via long noncontractile tail
comment: Viral protein that constitutes the noncontractile ejection system carried by some long-tailed prokaryotic viruses such as the Siphoviridae. This ejection system is composed at least of a noncontractile tube and a tail tip which is able to penetrate the host cell envelope to deliver the viral genome, and possibly some specific proteins, into the cell cytoplasm. Proteins of the ejection apparatus can play an active or a structural role in ejection.
subclass of: Virion
subclass of: Viral genome ejection through host cell envelope
subclass of: Molecular function
category: Molecular function

viral genome ejection through host cell envelope, long flexible tail mechanism
type: Class
database: go

Viral matrix protein
type: Concept
comment: Protein that organises and maintains virion structure. It usually interacts directly with cellular membranes and is involved in the budding process. In some enveloped RNA viruses, it acts as a bridge between virion membrane and nucleocapsid.
subclass of: Virion
category: Cellular component

structural constituent of virion
type: Class
database: go

Viral movement protein
type: Concept
comment: Plant viral protein that enables the viral nucleic acid to move between adjacent plant cells via the plasmodesmata.
subclass of: Transport
subclass of: Molecular function
category: Molecular function

transport of virus in host, cell to cell
type: Class
database: go

Viral nucleoprotein
type: Concept
alternative label: Viral nucleocapsid protein
comment: Viral protein conjugated with nucleic acid (DNA or RNA).
subclass of: Virion
subclass of: Molecular function
category: Molecular function

viral nucleocapsid
type: Class
database: go

Viral occlusion body
type: Concept
comment: Protein component of the viral occlusion body, a crystalline protein matrix which surrounds the nucleocapsids of some insect viruses (baculoviridae, entomopoxvirinae, cypovirus). Viral occlusion bodies are produced either in the nucleus (baculoviridae) or in the cytoplasm (poxvirinae and cypovirus) of the infected cells and confer resistance to adverse environmental conditions on viruses. They are made from polyhedrin (nucleopolyhedrovirus, cypovirus), granulin (granulovirus), spheroidin and spherulin (entomopox-virinae) and are dissolved by the alkaline pH of the insect gut, thus resulting in the release of infectious virus particles.
subclass of: Cellular component
category: Cellular component

viral occlusion body
type: Class
database: go

Viral penetration into host cytoplasm
type: Concept
alternative label: Translocation of virus into host cell
alternative label: Virion penetration into host cell
comment: Viral protein involved in the entry of the entire virion, some of its contents or at least its genetic material into the host cell cytoplasm. Entry is achieved through pore formation, membrane fusion, pilus retraction, ejection, permeabilization and/or endocytosis mechanisms. Penetration reactions occur mainly in five locations: the cell membrane, early and late endosomes, caveosomes, and the ER. In prokaryotes, membrane fusion, pore formation through a puncturing device, ejection, pilus retraction or permeabilization occur at the plasma membrane, as well as at the outer membrane in prokaryotes with 2 membranes.
subclass of: Virus entry into host cell
narrower: Virus endocytosis by host
narrower: Fusion of virus membrane with host membrane
narrower: Viral genome ejection through host cell envelope
narrower: Pore-mediated penetration of viral genome into host cell
narrower: Viral penetration via permeabilization of host membrane
narrower: Viral penetration via lysis of host organellar membrane
narrower: Viral penetration into host cytoplasm via pilus retraction
category: Biological process

viral entry into host cell
type: Class
database: go

Viral penetration into host cytoplasm via pilus retraction
type: Concept
comment: Viral protein involved in the entry of the virion into the host cytoplasm via the host pili, which are retractile filaments that protrude from bacteria with 2 membranes (Gram-negative bacteria). Entry of bound prokaryotic viruses such as filamentous viruses is achieved through the retraction of host pilus and translocation of the virion through the basis of the pilus to reach the host cytoplasm. Examples of bacteriophages which utilize the host cell pilus to penetrate into host cytoplasm are bacteriophages M13, f1, fd, R17.
subclass of: Virion
subclass of: Viral penetration into host cytoplasm
category: Biological process

viral entry into host cell via pilus retraction
type: Class
database: go

Viral penetration into host nucleus
type: Concept
alternative label: Entry of virus into host nucleus
alternative label: Virion entry into host nucleus
alternative label: Virion penetration into host nucleus
comment: Viral protein necessary for the penetration of the viral genome into the host cell nucleus either via active nuclear transport through nuclear pore complexes (NPCs) or DNA injection through the nuclear membrane. Nuclear membrane permeabilization might also be possible. Viruses can also enter the nucleus during mitosis when the nuclear membrane temporarily disintegrates (e.g. most retroviruses). All these strategies to cross the nuclear envelope barrier are associated with various levels of capsid disassembly, since virus can pass intact (e.g. papovaviruses) or, in the case of injection, only the viral genome enters the nucleus (e.g. herpesviruses).
subclass of: Virus entry into host cell
category: Biological process

viral penetration into host nucleus
type: Class
database: go

Viral penetration via lysis of host organellar membrane
type: Concept
comment: Viral membrane-lytic protein, usually associated with the viral capsid or released through partial programmed disassembly of the capsid, that induces major rupture of the bilayer integrity of host endosomal, lysosomal, or caveosomal membrane to allow viral escape and penetration into the cytoplasm. These viral lytic proteins may need to be activated, mostly through endosomal acidic pH or receptor binding to display membrane lytic activity. Viruses such as human adenoviruses group C and D lyse the host endosomal membrane to penetrate into the host cytoplasm.
subclass of: Viral penetration into host cytoplasm
category: Biological process

lysis of host organelle involved in viral entry into host cell
type: Class
database: go

Viral penetration via permeabilization of host membrane
type: Concept
alternative label: Viral penetration via host membrane disruption by virus
alternative label: Viral penetration via perforation of host membrane by virus
comment: Viral membrane-penetration protein, usually associated with the viral capsid or released through partial programmed disassembly of the capsid, that locally permeabilizes the bilayer of a host membrane to allow virion penetration into the cytoplasm. Viral membrane-penetration proteins often need to be activated, mostly through endosomal acidic pH or receptor binding to display their membrane penetrating activity. Non-enveloped viruses such as parvovirus, human reovirus, BDV, BTV, rotavirus, papillomavirus, Flock house virus permeabilize the host endosomal membrane to penetrate the host cytoplasm.
subclass of: Viral penetration into host cytoplasm
category: Biological process

permeabilization of host organelle membrane involved in viral entry into host cell
type: Class
database: go

viral entry via permeabilization of inner membrane
type: Class
database: go

Viral primary envelope fusion with host outer nuclear membrane
type: Concept
comment: Viral protein implicated in fusion of the herpesviruses' primary envelope with the host outer nuclear membrane during egress. During egress, herpesviruses acquire a transitory, primary envelope as they bud at the inner nuclear membrane and gain access to the perinuclear space. This membrane is lost by fusing with the outer nuclear membrane during nuclear exit.
subclass of: Viral release from host cell
category: Biological process

fusion of viral membrane with host outer nuclear membrane
type: Class
database: go

Viral reactivation from latency
type: Concept
alternative label: Release from viral latency
comment: Viral protein involved in virus reactivation from latency to replication, thereby putting an end to the latency phase in the viral life cycle. Changes in the environmental conditions of the host often reactivate the virus leading to viral transcription and production of new infectious viruses (productive infection).
subclass of: Viral latency
subclass of: Biological process
category: Biological process

release from viral latency
type: Class
database: go

Viral receptor tropism switching
type: Concept
comment: A switch in the host range specificity occurs in some bacterial viruses through massive sequence variation of their host-binding receptor. Sequence variation can be induced by site-specific inversion of a DNA segment in their genome or by a diversity-generating retroelement. Inversion is catalyzed by a specific recombinase called invertase and consists of a reciprocal recombination event within two inverted repeats present in the viral genome that leads to the alternate expression of two different sets of genes involved in tail fiber biosynthesis. Mu-like viruses and P1-like viruses, for example, encode a recombinase responsible for the switch in the targeted host. Diversity-generating retroelements (DGR) like in BPP-1 virus also allow tropism switching by creating a mutant copy of an invariant DNA template repeat by transcription and reverse transcription and introducing this mutated sequence in the receptor-binding protein sequence.
subclass of: Virus entry into host cell
category: Biological process

viral tropism switching
type: Class
database: go

Viral release from host cell
type: Concept
comment: Viral protein involved in the release of virions from an infected cell to allow cell-to-cell spread of virus. Once assembled at the replication site, viral particles can be released by budding, exocytosis, extrusion or host cell lysis. Some viruses also mediate direct transport of their viral genome to adjacent cells thanks to movement proteins.
subclass of: Biological process
narrower: Viral capsid assembly
narrower: Viral genome packaging
narrower: Host cell lysis by virus
narrower: Virion maturation
narrower: Viral primary envelope fusion with host outer nuclear membrane
narrower: Microtubular outwards viral transport
narrower: Viral budding
narrower: Viral tail assembly
narrower: Viral extrusion
category: Biological process

viral release from host cell
type: Class
database: go

Viral RNA replication
type: Concept
comment: Viral protein involved in the SYnthesis of multiple copies of the viral RNA genome. The replicated genomes provide support for further viral transcription or are assembled into progeny virions.
subclass of: Biological process
category: Biological process

viral RNA genome replication
type: Class
database: go

Viral short tail ejection system
type: Concept
alternative label: Viral genome injection via short noncontractile tail
comment: Virion protein that constitutes the noncontractile ejection system carried by some short-tailed prokaryotic viruses such as some Podoviridae. This ejection system is composed at least of the tail tube and ejection proteins. Upon receptor binding, proteins located inside the capsid (head) rearrange to extend the tail tube, creating a channel spanning the periplasmic space. This hydrophilic channel directs the viral genome, and possibly some specific proteins, into the cytoplasm and protects it from periplasmic nucleases. Once the viral genome is in the host cytoplasm, the channel collapses and seals. Bacteriophage T7 for example expresses ejection proteins that partition into the host outer and cytoplasmic membranes and allow transport of viral DNA across the host envelope. Proteins of the ejection apparatus can play an active or a structural role in ejection.
subclass of: Virion
subclass of: Viral genome ejection through host cell envelope
subclass of: Molecular function
category: Molecular function

viral genome ejection through host cell envelope, short tail mechanism
type: Class
database: go

Viral tail assembly
type: Concept
comment: Viral protein involved in tail assembly. Some tailed bacteriophages need chaperones that help with the assembly of their tail.
subclass of: Viral release from host cell
narrower: Viral tail fiber assembly
category: Biological process

viral tail assembly
type: Class
database: go

Viral tail fiber assembly
type: Concept
comment: Viral protein involved in tail fibers or spike assembly. Some tailed bacteriophages need chaperones that help with the assembly of their fibers or spikes. T4 for example encodes a general tail fiber chaperone that is needed for the correct assembly of the short and long tail fiber proteins.
subclass of: Viral tail assembly
category: Biological process

virus tail fiber assembly
type: Class
database: go

Viral tail fiber protein
type: Concept
comment: Viral fibrous protein part of the virion fiber, which is a thin long rod like structure, unique or multiple, appended to the tail of prokaryotic viruses and used for attachment to the host cell. Shorter appendages are called tail spikes (e.g. Podoviridae) or whiskers.
subclass of: Viral tail protein
category: Cellular component

virus tail, fiber
type: Class
database: go

Viral tail protein
type: Concept
comment: Viral protein part of the virion tail of prokaryotic viruses such as Caudovirales. The tail is usually composed of a tube, a tail sheath when contractile, a base plate or tip and tail long or short fibers.
subclass of: Virion
narrower: Viral baseplate protein
narrower: Viral tail tube protein
narrower: Viral tail sheath protein
narrower: Viral tail fiber protein
category: Cellular component

virus tail
type: Class
database: go

Viral tail sheath protein
type: Concept
comment: Viral protein part of the virion tail sheath of prokaryotic viruses. The tail sheath is an external contractile envelope wrapping the tail tube in some viruses (e.g. Myoviridae).
subclass of: Viral tail protein
subclass of: Viral contractile tail ejection system
category: Cellular component

virus tail, sheath
type: Class
database: go

Viral tail tube protein
type: Concept
comment: Viral protein part of the virion tail tube of prokaryotic viruses such as Caudovirales. The tail tube is the channel for DNA ejection into the host cytoplasm and can be wrapped in an external contractile envelope in some viruses (e.g. Myoviridae). Also called tail shaft in some Siphoviridae.
subclass of: Viral genome ejection through host cell envelope
subclass of: Viral tail protein
category: Cellular component

virus tail, tube
type: Class
database: go

Viral transcription
type: Concept
comment: Viral Protein involved in the synthesis of messenger RNAs. The process can occur in the host cell nucleus or cytoplasm, and the genomic template can be viral DNA or RNA, single- or double-stranded.
subclass of: Biological process
narrower: IFIT mRNA restriction evasion by virus
category: Biological process

viral transcription
type: Class
database: go

Virion
type: Concept
comment: Viral protein detected in the virion.
subclass of: Cellular component
narrower: Capsid protein
narrower: Viral envelope protein
narrower: Viral matrix protein
narrower: Viral nucleoprotein
narrower: Virion tegument
narrower: Helical capsid protein
narrower: T=1 icosahedral capsid protein
narrower: T=2 icosahedral capsid protein
narrower: T=3 icosahedral capsid protein
narrower: T=pseudo3 icosahedral capsid protein
narrower: T=4 icosahedral capsid protein
narrower: T=7 icosahedral capsid protein
narrower: T=13 icosahedral capsid protein
narrower: T=16 icosahedral capsid protein
narrower: T=25 icosahedral capsid protein
narrower: T=147 icosahedral capsid protein
narrower: T=169 icosahedral capsid protein
narrower: T=219 icosahedral capsid protein
narrower: Viral attachment to host cell
narrower: Viral attachment to host cell pilus
narrower: Viral tail protein
narrower: Capsid inner membrane protein
narrower: Viral attachment to host adhesion receptor
narrower: Viral attachment to host entry receptor
narrower: Degradation of host cell envelope components during virus entry
narrower: Degradation of host peptidoglycans during virus entry
narrower: Degradation of host capsule during virus entry
narrower: Fusion of virus membrane with host outer membrane
narrower: Viral attachment to host cell flagellum
narrower: Viral penetration into host cytoplasm via pilus retraction
narrower: Viral contractile tail ejection system
narrower: Viral long flexible tail ejection system
narrower: Viral short tail ejection system
category: Cellular component

virion component
type: Class
database: go

Virion maturation
type: Concept
alternative label: Viral procapsid maturation
comment: Viral protein involved in the maturation of the immature virion into the mature virion, once the virion has been released from the host cell. Maturation usually involves proteolysis events and changes in the folding of the virion proteins.
subclass of: Viral release from host cell
category: Biological process

virus maturation
type: Class
database: go

Virion tegument
type: Concept
comment: Viral structural protein of the tegument, a protein structure that resides between the capsid and envelope of herpesviruses and which appears amorphous in electron micrographs.
subclass of: Virion
category: Cellular component

viral tegument
type: Class
database: go

Virulence
type: Concept
comment: Protein involved in virulence, the degree of pathogenicity within a group or species of microorganisms or viruses, as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. In some cases, the virulence factor can be borne by another organism in symbiosis with the one whose virulence is increased. Some prokaryotic viruses/proviruses for example bear exotoxins that increase the virulence of their host. A well-known bacterial exotoxin encoded by a provirus is the diphtheria toxin.
subclass of: Biological process
narrower: Modulation of host virulence by virus
category: Biological process

Virus endocytosis by host
type: Concept
comment: Viral protein involved in virus internalization by the host cell via endocytosis. Endocytosis can occur via: clathrin-mediated endocytosis, caveolin-mediated endocytosis or clathrin- and caveolae-independent endocytosis.
subclass of: Viral penetration into host cytoplasm
narrower: Clathrin-mediated endocytosis of virus by host
narrower: Caveolin-mediated endocytosis of virus by host
narrower: Clathrin- and caveolin-independent endocytosis of virus by host
category: Biological process

endocytosis involved in viral entry into host cell
type: Class
database: go

Virus entry into host cell
type: Concept
comment: Viral protein involved in the virion entry into a host cell. Entry is a multistep process that mostly requires binding to the target cell, penetration into the host cell cytoplasm, intracellular transport of viral components and genome release to the replication site of the virus.
subclass of: Biological process
narrower: Viral attachment to host cell
narrower: Viral penetration into host cytoplasm
narrower: Viral penetration into host nucleus
narrower: Cytoplasmic inwards viral transport
narrower: Viral genome integration
narrower: Degradation of host cell envelope components during virus entry
narrower: Viral genome circularization
narrower: Viral receptor tropism switching
category: Biological process

Vision
type: Concept
comment: Protein involved in vision, the special sense by which objects in the external environment are perceived by the light they give off or reflect, which stimulates the photoreceptors in the retina.
subclass of: Sensory transduction
narrower: Autoimmune uveitis
category: Biological process

visual perception
type: Class
database: go

Vitamin A
type: Concept
alternative label: Retinol
comment: Protein which interacts with any form of the fat-soluble vitamin A. There are three active forms of vitamin A: retinol, retinal (retinaldehyde) and retinoic acid, which are all derived from the plant beta-carotene (provitamin A). Vitamin A is essential to night vision and is also required for epithelium differentiation, bone development, reproduction and the immune response. Symptoms associated with a deficiency of vitamin A are night blindness, changes in the eyes, poor bone development, weak tooth enamel and dry skin.
subclass of: Ligand
category: Ligand

retinal binding
type: Class
database: go

Vitamin C
type: Concept
alternative label: Ascorbic acid
comment: Protein which contains at least one vitamin C as cofactor. This water-soluble vitamin is a reducing agent in a number of reactions. As cofactor, it is required for the hydroxylation of proline residues in collagen, and in many other metabolic reactions such as in the catabolism of tyrosine and the synthesis of bile acids. Deficiency in vitamin C leads to the disease scurvy.
subclass of: Ligand
category: Ligand

L-ascorbic acid binding
type: Class
database: go

Vitamin D
type: Concept
comment: Protein which interacts with any form of the fat-soluble vitamin D or protein whose transcription is regulated by the biologically active form of vitamin D, i.e. 1,25-dihydroxy vitamin D3 (1,25 dihydroxycholecalciferol) also termed calcitriol. Active calcitriol is derived from ergosterol (produced in plants) and 7-dehydrocholesterol (produced in the skin). Ergocalciferol (vitamin D2) and cholecalciferol (vitamin D3) are formed by UV irradiation of ergosterol and 7-dehydrocholesterol, respectively, and processed by the same enzymatic pathway in the body to D2-calcitriol and D3-calcitriol. Deficiency in vitamin D leads to the disease rickets, in children, and osteomalacia, in adults.
subclass of: Ligand
category: Ligand

vitamin D binding
type: Class
database: go

VLDL
type: Concept
comment: 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. These lipoproteins are transported by the blood to muscle and adipose tissue, where activation of lipoprotein lipase by apoC-II causes the release of free fatty acids from the triacylglycerols of the VLDL.
subclass of: Cellular component
category: Cellular component

very-low-density lipoprotein particle
type: Class
database: go

Voltage-gated calcium channel impairing toxin
type: Concept
alternative label: Cav channel inhibitor
comment: Protein which interferes with the function of voltage-gated calcium channels (Cav) which are membrane proteins forming a channel in a biological membrane selectively permeable to calcium ions and open in response to a change in membrane potential. They are mostly found spider and cone snail venoms.
subclass of: Calcium channel impairing toxin
category: Molecular function

Voltage-gated channel
type: Concept
alternative label: Voltage-gated cation channel
alternative label: Voltage-gated ion channel
comment: Protein which is a component of a voltage-gated channel. Voltage-gated ion channels are responsible for the electrical activity in a variety of cell types. They probably exist in all life forms.
subclass of: Ion transport
subclass of: Ion channel
category: Molecular function

voltage-gated monoatomic ion channel activity
type: Class
database: go

regulation of monoatomic ion transmembrane transport
type: Class
database: go

Voltage-gated chloride channel impairing toxin
type: Concept
comment: Protein which interferes with the function of voltage-gated chloride channels (ClC) which are membrane proteins forming a channel in a biological membrane selectively permeable to chloride ions, and open in response to a change in membrane potential. They are found in venoms from scorpions.
subclass of: Chloride channel impairing toxin
category: Molecular function

chloride channel regulator activity
type: Class
database: go

Voltage-gated potassium channel impairing toxin
type: Concept
comment: Protein which interferes with the function of voltage-gated potassium channels (Kv) which are membrane proteins forming a channel in a biological membrane selectively permeable to potassium ions and open in response to a change in membrane potential. They are mostly found in scorpion and spider venoms.
subclass of: Potassium channel impairing toxin
category: Molecular function

Voltage-gated sodium channel impairing toxin
type: Concept
comment: Protein which interferes with the function of voltage-gated sodium channels (Nav) which are membrane proteins forming a channel in a biological membrane selectively permeable to sodium ions, and open in response to a change in membrane potential. They are found in various venoms from snakes, scorpions and spiders.
subclass of: Ion channel impairing toxin
category: Molecular function

sodium channel regulator activity
type: Class
database: go

von Willebrand disease
type: Concept
comment: Protein which, if defective, causes von Willebrand disease, a hemorrhagic disorder in which the von Willebrand factor is either quantitatively or qualitatively abnormal. Usually inherited as an autosomal dominant trait though rare kindreds are autosomal recessive. Symptoms vary depending on severity and disease type but may include prolonged bleeding time, deficiency of factor VIII and impaired platelet adhesion.
subclass of: Blood coagulation
subclass of: Disease
category: Disease

Waardenburg syndrome
type: Concept
alternative label: WS
comment: Protein which, if defective, causes Waardenburg syndrome, an autosomal dominant disorder, characterized by sensorineural deafness associated with pigmentary changes of the irides, hair and skin; each of these features may be uni- or bilateral. On the basis of the presence or absence of dystopia canthorum (lateral displacement of the inner corner of the eye), Waardenburg syndrome type 1 (WS1) and type 2 (WS2) are distinguished. Additionally, the association of WS1 with limb anomalies defines Waardenburg syndrome type 3 (WS3), while the association of Waardenburg features with Hirschsprung disease defines Waardenburg syndrome type 4 (WS4).
subclass of: Deafness
category: Disease

WD repeat
type: Concept
alternative label: Trp-Asp repeat
alternative label: WD-40 repeat
comment: Protein which contains at least one WD repeat, a conserved domain of about 40 amino acids in length. Most copies contain a central conserved Trp-Asp motif.
subclass of: Domain
category: Domain

Whooping cough
type: Concept
comment: Protein involved in the induction of whooping cough, a respiratory infection caused by the very small Gram-negative aerobic coccobacillus Bordetella pertussis. It is characterized by paroxysmal coughing often ending in a characteristic inspiratory gasp (whoop). The bacterium is a pathogen for humans and possibly for higher primates.
subclass of: Disease
category: Disease

Williams-Beuren syndrome
type: Concept
alternative label: WBS
comment: Protein which, if defective, causes Williams-Beuren syndrome (WBS), a contiguous gene deletion syndrome involving genes from chromosome band 7q11.23. It is a rare developmental autosomal dominant disorder characterized by cardiovascular abnormalities, elfin face, mental and statural deficiency, characteristic dental malformation, and infantile hypercalcemia.
subclass of: Disease
category: Disease

Wnt signaling pathway
type: Concept
alternative label: Wnt signaling cascade
alternative label: Wnt signalling pathway
alternative label: Wnt signal transduction pathway
comment: Protein involved in the Wnt signaling pathway. Wnts are a large family of cysteine-rich secreted glycoproteins that control development in organisms ranging from nematodes to mammals. Wnt genes are defined by sequence homology to the original members of the family, Wnt1 in the mouse and wingless (wg) in Drosophila. Wnt signaling is a very complex pathway which includes numerous ligands, receptors and transcriptional effectors. There is a well-characterized canonical pathway as well as diverse, less-characterized noncanonical pathways. Several components of Wnt signaling are implicated in the genesis of human cancer.
subclass of: Biological process
category: Biological process

Wnt signaling pathway
type: Class
database: go

Xeroderma pigmentosum
type: Concept
comment: Protein which, if defective, causes xeroderma pigmentosum, an autosomal recessive disease characterized by extreme photosensitivity to ultraviolet light and the development of multiple skin cancers.
subclass of: Disease
category: Disease

Xylan degradation
type: Concept
alternative label: Xylan hydrolysis
comment: Protein involved in the hydrolysis of xylan to xylose and other sugars. Xylan is a major component of hemicellulose, which is the second most common plant material in nature. The structures of xylans are complex, and several enzymes are involved in their breakdown. Xylan degrading enzymes are produced by a variety of microorganisms.
subclass of: Polysaccharide degradation
category: Biological process

xylan catabolic process
type: Class
database: go

Xylose metabolism
type: Concept
comment: Protein involved in the biochemical reactions with the 5-carbon sugars xylose or xylulose. Xylose is the second most abundant sugar found in hardwood and agricultural residues.
subclass of: Carbohydrate metabolism
category: Biological process

D-xylose metabolic process
type: Class
database: go

Zellweger syndrome
type: Concept
alternative label: Cerebrohepatorenal syndrome
alternative label: Cerebro-hepato-renal syndrome
alternative label: CHR syndrome
alternative label: ZWS
comment: Protein which, if defective, causes Zellweger syndrome, a fatal peroxisome biogenesis disorder associated with severe abnormalities in the brain, liver and kidney and death soon after birth. This disease is characterized by the presence of empty peroxisomes in the cells due to impaired transport of peroxisomal proteins into the peroxisomes.
subclass of: Peroxisome biogenesis disorder
category: Disease

Zinc
type: Concept
comment: Protein which binds at least one zinc atom, or protein whose function is zinc-dependent. Zinc is a metallic trace element, chemical symbol Zn.
subclass of: Ligand
narrower: LIM domain
narrower: Zinc-finger
narrower: Zinc transport
category: Ligand

Zinc transport
type: Concept
comment: Protein involved in the transport of zinc.
subclass of: Ion transport
subclass of: Zinc
category: Biological process

zinc ion transport
type: Class
database: go

Zinc-finger
type: Concept
comment: Protein which contains at least one zinc finger. A small, functional, independently folded domain that requires coordination of one or more zinc ions to stabilize its structure. Zinc fingers vary widely in structure, as well as in function, which ranges from DNA or RNA binding to protein-protein interactions and membrane association.
subclass of: Metal-binding
subclass of: Zinc
subclass of: Domain
category: Domain

Zymogen
type: Concept
alternative label: Proenzyme
comment: The enzymatically inactive precursor of mostly proteolytic enzymes.
subclass of: PTM
category: PTM