LiteFold/GO huggingface dataset:
obsolete induction by virus of host nuclear polyadenylation-dependent mRNA catabolic process (GO:0039598)
Namespace: biological_process
Definition: OBSOLETE. The process in which a virus increases the frequency, rate or extent of the breakdown of host messenger RNA (mRNA) initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target mRNA.
Synonyms: induction by virus of host nuclear poly(A)-dependent mRNA catabolic process; induction by virus of host nuclear polyadenylation-dependent mRNA catabolic process; virus-mediated host mRNA decay by hyperadenylation
Comment: This term was made obsolete because it is unclear what role the viral protein is playing in this process. and there is insufficient evidence to use this term for annotation.
symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter (GO:0039602)
Namespace: biological_process
Definition: Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a host DNA template. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: inhibition of host transcription initiation by virus; suppression by virus of host DNA-dependent transcription, initiation; suppression by virus of host transcription initiation from RNA polymerase II promoter
obsolete TBP-class protein binding involved in viral suppression of host transcription initiation from RNA polymerase II promoter (GO:0039603)
Namespace: molecular_function
Definition: OBSOLETE. Selective and non-covalent interaction of a viral protein with a member of the class of TATA-binding proteins (TBP) in the host, including any of the TBP-related factors (TRFs), which contributes to the viral-suppression of assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a host DNA template.
Comment: The reason for obsoletion is that the term is too specific, and the paper referenced in the term should instead be annotated to GO:0039602 ; suppression by virus of host transcription initiation from RNA polymerase II promoter.
obsolete TFIIB-class transcription factor binding involved in viral suppression of host transcription initiation from RNA polymerase II promoter (GO:0039605)
Namespace: molecular_function
Definition: OBSOLETE. Selective and non-covalent interaction of a viral protein with a member of the TFIIB-class of host transcription factors, which contributes to the viral-suppression of assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a host DNA template.
Comment: The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
symbiont-mediated suppression of host translation initiation (GO:0039606)
Namespace: biological_process
Definition: A process in which a symbiont inhibits or disrupts translation initiation in its host. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: suppression by virus of host translation initiation
obsolete suppression by virus of host translation initiation factor activity by induction of host protein dephosphorylation (GO:0039608)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a virus prevents or reduces the frequency, rate or extent of activity of a host translation initiation factor by promoting dephosphorylation of a host protein.
Comment: The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
obsolete suppression by virus of host translation initiation factor activity (GO:0039611)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a virus prevents or reduces the frequency, rate or extent of activity of a host translation initiation factor.
Synonyms: inactivation of eIF2 activity; inhibition of activity of host translation initiation factor; Inhibition of host translation factors by virus; suppression by virus of host EIF-4E activity
Comment: This term has been obsoleted because it represents a molecular function as a biological process.
obsolete suppression by virus of host protein phosphorylation (GO:0039613)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of phosphorylation of viral or host proteins in a host.
Synonyms: viral inhibition of host protein phosphorylation
Comment: This term was obsoleted because it is a molecular function represented as a biological process.
obsolete induction by virus of host protein phosphorylation (GO:0039614)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a virus activates or increases the frequency, rate or extent of phosphorylation of viral or host proteins in a host.
Comment: This term was obsoleted because it is a molecular function represented as a biological process.
T=2 icosahedral viral capsid (GO:0039616)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=2 symmetry. The T=2 capsid is composed of 12 pentameric dimers.
Comment: The T=2 symmetry is an non-official appellation; strictly speaking the capsid has a T=1 symmetry with each unit composed of a homodimer.
T=3 icosahedral viral capsid (GO:0039617)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
T=pseudo3 icosahedral viral capsid (GO:0039618)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with pseudo T=3 symmetry. The T=pseudo3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
Comment: T=pseudo3 capsids are not T=3 symmetry as described by Caspar and Klug (PMID:14019094) because the basic unit is composed of three different proteins. Since the three subunits are morphologically very similar, the structure is therefore a pseudo T=3.
T=4 icosahedral viral capsid (GO:0039619)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=4 symmetry. The T=4 capsid is composed of 12 pentameric and 30 hexameric capsomeres.
T=7 icosahedral viral capsid (GO:0039620)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=7 symmetry. The T=7 capsid is composed of 12 pentameric and 60 hexameric capsomeres.
Comment: Spherical viruses with T numbers greater than or equal to 7 are skewed. They are therefore described as either right-handed (dextro) or left-handed (laevo).
T=16 icosahedral viral capsid (GO:0039622)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=16 symmetry. The T=16 capsid is composed of 12 pentameric and 150 hexameric capsomeres.
T=25 icosahedral viral capsid (GO:0039623)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=25 symmetry. The T=25 capsid is composed of 12 pentameric and 240 hexameric capsomeres.
viral outer capsid (GO:0039624)
Namespace: cellular_component
Definition: The outer layer of a double or triple concentric icosahedral capsid. Outer capsids are part of reoviridae and cystoviridae virions.
Synonyms: outer capsid
viral inner capsid (GO:0039625)
Namespace: cellular_component
Definition: The inner layer of a double or triple concentric icosahedral capsid. Inner capsids are part of reoviridae and cystoviridae virions.
Synonyms: inner capsid
viral intermediate capsid (GO:0039626)
Namespace: cellular_component
Definition: The intermediate layer of a triple concentric icosahedral capsid. Intermediate capsids are part of reoviridae virions.
Synonyms: intermediate capsid
T=147 icosahedral capsid (GO:0039627)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=147 symmetry. T=147 icosahedral capsid is composed of 12 pentameric and 1460 hexameric capsomeres for a total of 8820 capsid proteins.
T=169 icosahedral viral capsid (GO:0039628)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=169 symmetry. T=169 icosahedral capsid is composed of 12 pentameric and 1680 hexameric capsomeres for a total of 10140 capsid proteins.
Synonyms: T=169 icosahedral capsid
T=219 icosahedral capsid (GO:0039629)
Namespace: cellular_component
Definition: The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=219 symmetry. T=219 icosahedral capsid is composed of 12 pentameric and 2180 hexameric capsomeres for a total of 13140 capsid proteins.
RNA translocase activity (GO:0039630)
Namespace: molecular_function
Definition: Generating a movement along a single- or double-stranded RNA molecule, driven by ATP hydrolysis.
Comment: Note that some gene products that possess DNA translocase activity, such as members of the FtsK/SpoIIIE family, can be fixed in place by interactions with other components of the cell; the relative movement between the protein and DNA bound to it results in movement of the DNA within the cell, often across a membrane.
obsolete RNA translocase activity involved in viral RNA genome packaging (GO:0039632)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded RNA molecule, which contributes to the packaging of viral RNA into a nucleocapsid.
Synonyms: RNA packaging ATPase activity; viral RNA packaging activity
Comment: This term was obsoleted because it represents both a molecular function and a biological process.
obsolete killing by virus of host cell (GO:0039633)
Namespace: biological_process
Definition: OBSOLETE. Any process mediated by a virus that results in the death of a cell in the host organism.
Synonyms: killing by phage of host cells; killing by virus of host cells
Comment: This term was obsoleted because it was redundant with other terms.
symbiont-mediated suppression of host peptidoglycan biosynthetic process (GO:0039635)
Namespace: biological_process
Definition: Any process in which a symbiont stops, prevents, or reduces the frequency, rate or extent of peptidoglycan biosynthesis in the host organism. Peptidoglycans are any of a class of glycoconjugates found in bacterial cell walls, and phages have mechanisms to disrupt their host's cell walls.
Synonyms: suppression by virus of host peptidoglycan biosynthetic process; viral inhibition of host peptidoglycan biosynthesis
symbiont-mediated suppression of host cell wall biogenesis (GO:0039636)
Namespace: biological_process
Definition: Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of cell wall biogenesis in the host organism. Cell wall biogenesis includes the biosynthesis of constituent macromolecules, and the assembly and arrangement of these constituent parts.
Synonyms: suppression by virus of host cell wall biogenesis
obsolete catabolism by virus of host DNA (GO:0039637)
Namespace: biological_process
Definition: OBSOLETE. The breakdown of host DNA, deoxyribonucleic acid, by a virus.
Comment: This term was obsoleted because it was an unnecessary grouping class.
lipopolysaccharide-mediated virion attachment to host cell (GO:0039638)
Namespace: biological_process
Definition: The process by which a virion attaches to a host cell by binding to a lipopolysaccharide (LPS) on the host cell surface.
Synonyms: lipopolysaccharide binding involved in viral attachment to host cell; LPS binding involved in viral attachment to host cell; virion attachment, binding to host lipopolysaccharide
suppression by virus of host cell lysis in response to superinfection (GO:0039639)
Namespace: biological_process
Definition: The prevention or delay of host cell lysis by a pre-existing virus in response to a subsequent infection of the host cell by second virus.
Synonyms: lysis inhibition; suppression by virus of host cell lysis in response to superinfecting virus
viral release via suppression of host peptidoglycan biosynthetic process (GO:0039640)
Namespace: biological_process
Definition: The dissemination of mature viral particles from a host cell, caused by a virus stopping, preventing, or reducing peptidoglycan biosynthesis in the host organism. Peptidoglycans are any of a class of glycoconjugates found in bacterial cell walls.
Synonyms: cytolysis by virus via suppression of host peptidoglycan biosynthetic process; viral exit by cytolysis via suppression of host peptidoglycan biosynthetic process; viral release by cytolysis via suppression of host peptidoglycan biosynthetic process
viral inner membrane (GO:0039641)
Namespace: cellular_component
Definition: The lipid bilayer of a virion contained inside the protein capsid.
Synonyms: virion inner membrane
virion nucleoid (GO:0039642)
Namespace: cellular_component
Definition: The region of a virion in which the nucleic acid is confined.
obsolete suppression by virus of host NF-kappaB cascade (GO:0039644)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a virus stops, prevents, or reduces a host NF-kappaB cascade.
Synonyms: inhibition of host NF-kappa-B by virus; suppression by virus of host NF-kappaB transcription factor activity
Comment: This term was obsoleted because it represents the same process as symbiont-mediated suppression of host canonical NF-kappaB cascade ; GO:0085034.
symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint (GO:0039645)
Namespace: biological_process
Definition: A process in which a symbiont interferes with the normal execution of the host cell G1/S transition checkpoint. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: G1/S host cell cycle checkpoint dysregulation by virus; modulation by virus of host G1/S transition checkpoint; perturbation by virus of host G1/S transition checkpoint
obsolete suppression by virus of host poly(A)-binding protein activity (GO:0039647)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host poly(A)-binding protein (PABP) activity. PABP binds to the poly(A) tail of mRNA to facilitate translation.
Synonyms: inhibition of host poly(A)-binding protein by virus; suppression by virus of host PABP activity
Comment: This term was obsoleted because it represents a molecular function.
symbiont-mediated perturbation of host ubiquitin-like protein modification (GO:0039648)
Namespace: biological_process
Definition: A process by which a symbiont alters ubiquitin-like protein modification of target proteins of either host or symbiont proteins. This includes ubiquitination, SUMOylation, NEDDylation, and ISG15ylation. The ubiquitination status of a protein  affects whether it is targeted to the proteasome for degradation. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: modulation by symbiont of host protein ubiquitination; modulation of host ubiquitin pathway by virus; symbiont-mediated perturbation of host protein SUMOlyation; symbiont-mediated perturbation of host protein ubiquitination
obsolete modulation by virus of host ubiquitin-protein ligase activity (GO:0039649)
Namespace: biological_process
Definition: OBSOLETE. The process in which a virus effects a change in host ubiquitin-protein ligase activity. Ubiquitin-protein ligase activity catalyzes the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
Synonyms: modulation of host E3 ubiquitin ligases by virus
Comment: This term was obsoleted because it represents a molecular function.
obsolete induction by virus of host NF-kappaB cascade (GO:0039652)
Namespace: biological_process
Definition: OBSOLETE. A process in which a virus initiates, promotes, or enhances an NF-kappaB signaling cascade in its host organism.
Synonyms: activation by virus of host NF-kappaB transcription factor activity
Comment: This term was obsoleted because it represents the same process as symbiont-mediated activation of host NF-kappaB signal transduction ; GO:0085033.
symbiont-mediated suppression of host transcription (GO:0039653)
Namespace: biological_process
Definition: A process in which a symbiont inhibits or disrupts transcription of genes into mRNA in its host. For example, symbiont proteins can interfere with host RNA polymerase or with transcription factors. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: host transcription shut-off; host transcription shutoff by virus; suppression by virus of host DNA-dependent transcription; suppression by virus of host transcription
fusion of virus membrane with host endosome membrane (GO:0039654)
Namespace: biological_process
Definition: Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
Synonyms: fusion of virus membrane with host endosomal membrane; viral entry into host cell via caveolae-mediated endocytosis followed by membrane fusion with the endosome membrane; viral entry into host cell via caveolin-mediated endocytosis followed by membrane fusion with the endosome membrane; viral entry into host cell via clathrin-mediated endocytosis followed by membrane fusion with the endosome membrane; viral entry into host cell via endocytosis followed by membrane fusion with host endosome; viral entry into host cell via endocytosis followed by membrane fusion with the endosome membrane; viral penetration via endocytosis followed by caveolae-mediated membrane fusion with the endosome membrane; viral penetration via endocytosis followed by clathrin-mediated membrane fusion with the endosome membrane
obsolete transport of virus in host, cell to cell via plasmodesmata (GO:0039655)
Namespace: biological_process
Definition: OBSOLETE. The transport of a virus between adjacent cells in a multicellular organism using plasmodesmata. Plasmodesma is a fine cytoplasmic channel found in all higher plants, which connects the cytoplasm of one cell to that of an adjacent cell.
Synonyms: spread of virus in host, cell to cell via plasmodesmata; viral movement protein
symbiont-mediated perturbation of host gene expression (GO:0039656)
Namespace: biological_process
Definition: A process in which a symbiont alters or subverts the normal execution of host gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. The host is defined as the larger of the organisms involved in a symbiotic interaction.
Synonyms: modulation by virus of host gene expression; regulation by virus of host gene expression
TBK1-IKKE-DDX3 complex (GO:0039658)
Namespace: cellular_component
Definition: A protein complex containing TBK1 (TANK-binding kinase 1), IKBKE (I-Kappa-B kinase epsilon/IKKE/IKK-epsilon) and the DEAD box family RNA helicase DDX3.
Synonyms: TBK1-IKBKE-DDX3 complex
obsolete suppression by virus of host TBK1-IKBKE-DDX3 complex activity (GO:0039659)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a virus stops, prevents, or reduces the activity of the host TBK1-IKBKE-DDX3 complex.
Synonyms: inhibition of host TBK1-IKBKE-DDX3 complex by virus; suppression by virus of host TBK1-IKKE-DDX3 complex activity
Comment: The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately. See also: suppression by virus of host TBK1 activity; GO:0039723, and suppression by virus of host IKBKE activity; GO:0039724.
structural constituent of virion (GO:0039660)
Namespace: molecular_function
Definition: The action of a molecule that contributes to the structural integrity of a virion.
Synonyms: viral matrix protein
host organelle outer membrane (GO:0039661)
Namespace: cellular_component
Definition: The outer, i.e. cytoplasm-facing in a cellular organelle, lipid bilayer of an organelle envelope, occurring in a host cell.
host cell outer membrane (GO:0039662)
Namespace: cellular_component
Definition: A lipid bilayer that forms the outermost layer of the cell envelope, occurring in a host cell.
Synonyms: host cell envelope outer membrane; outer membrane of host cell
membrane fusion involved in viral entry into host cell (GO:0039663)
Namespace: biological_process
Definition: Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
Synonyms: fusion of virus membrane with host membrane; fusion of virus membrane with host membrane during viral entry; viral entry into host cell via membrane fusion
lysis of host organelle involved in viral entry into host cell (GO:0039664)
Namespace: biological_process
Definition: The viral-induced lysis of an organelle (endosome, lysosome, or caveosome) that is involved in the uptake of a virus into a host cell. Occurs once the virus is within the organelle, and results in transfer of the viral contents from the organelle compartment into the cytoplasm.
Synonyms: viral entry into host cell via endosome membrane lysis; viral entry into host cell via lysis of host organelle membrane; viral membrane-lytic protein; viral penetration via lysis of host organellar membrane
permeabilization of host organelle membrane involved in viral entry into host cell (GO:0039665)
Namespace: biological_process
Definition: Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
Synonyms: viral entry into host cell via permeabilization of host organelle membrane; viral membrane-penetration protein; viral penetration via host endosomal membrane disruption by virus; viral penetration via perforation of host organellar membrane by virus; viral penetration via permeabilization of host organellar membrane
virion attachment to host cell pilus (GO:0039666)
Namespace: biological_process
Definition: The process by which a virion attaches to a host cell by binding to a pilus on the host cell surface. Pili are retractile filaments that protrude from gram-negative bacteria. Filamentous viruses can attach to the pilus tip, whereas icosahedral viruses can attach to the pilus side.
Synonyms: pilus-adsorption protein; pilus-mediated viral adsorption onto host cell; pilus-mediated viral attachment to host cell; viral attachment to host cell pilus