Brenley's Suggested Terms
Jump to navigation
Jump to search
[Term] id: GO:0098001 name: reversible bacteriophage attachment, binding of host cell surface receptor namespace: biological_process def: "Process by which a bacteriophage, using its tail fibers, spikes or a baseplate component, initially recognizes and binds to its specific receptor on the host cell surface. This process is reversible and allows the release of a bacteriophage without affecting infection." [phi:0000005, GOC:bm] comment: This process was historically defined by the release, by Waring blending or sonication, by dilution and centrifugation, or by filtration and washing, of infective virions from their complexes with cells, thus contrary to what is observed after irreversible adsorption. synonym: "phage reversible adsorption" RELATED [] is_a: GO:0046813 ! virion attachment, binding of host cell surface receptor created_by: brenley creation_date: 2012-07-18T15:16:21Z ! Ask Philippe M whether this process is specific to bacteriophages or whether this reversible process occurs in other viruses.
[Term] id: GO:0098002 name: irreversible bacteriophage attachment, binding of host cell surface receptor namespace: biological_process def: "The processes by which a bacteriophage initially commits to infection by binding the host receptor irreversibly. Disruption of the phage:cell complex at this step results in the loss of infective phage virions since the process is characterized by conformational changes of bacteriophage head and tail proteins and injection of bacteriophage proteins into the infected cell." [phi:0000006] synonym: "phage irreversible adsorption" RELATED [] is_a: GO:0046813 ! virion attachment, binding of host cell surface receptor created_by: brenley creation_date: 2012-07-18T15:26:09Z ! Ask Philippe M whether this process is specific to bacteriophages or whether this irreversible process occurs in other viruses.
[Term] id: GO:0098003 name: virus tail assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form a virus tail." [phi:0000015, GOC:bm] synonym: "bacteriophage tail assembly" RELATED [] relationship: part_of GO:0019068 ! virion assembly is_a: GO:0022415 ! viral reproductive process created_by: brenley creation_date: 2012-07-18T16:01:59Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098004 name: virus tail fiber assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form a virus tail fiber." [phi:0000011, GOC:bm] relationship: part_of GO:0098003 ! virus tail assembly is_a: GO:0022415 ! viral reproductive process created_by: brenley creation_date: 2012-07-18T16:08:15Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098005 name: virus head-tail joining namespace: biological_process def: "Process by which virus heads and tails are attached to each other." [phi:0000012, GOC:bm] synonym: "phage head tail joining" RELATED [] relationship: part_of GO:0019068 ! virion assembly is_a: GO:0022415 ! viral reproductive process created_by: brenley creation_date: 2012-07-18T16:11:59Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098006 name: viral DNA genome packaging, headful namespace: biological_process def: "The encapsulation of the viral genome within the capsid where DNA is packaged into the capsid until the capsid is full." [phi:0000020, GOC:bm] comment: Generalized transducing phages usually use this mode of packaging. synonym: "phage headful packaging" RELATED [GOC:bm] is_a: GO:0019073 ! viral DNA genome packaging created_by: brenley creation_date: 2012-07-18T16:15:09Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098007 name: structural constituent of virion namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of a virus." [] synonym: "structural constituent of phage" RELATED [] is_a: GO:0005198 ! structural molecule activity created_by: brenley creation_date: 2012-07-18T16:28:49Z ! SCRAP- use 'structural molecule activity ; GO:0005198' and column 16.
[Term] id: GO:0098008 name: structural constituent of virion capsid namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of the virus head or capsid." [phi:0000064] synonym: "structural constituent of phage capsid" RELATED [] synonym: "structural constituent of phage head" RELATED [] is_a: GO:0098007 ! structural constituent of virion created_by: brenley creation_date: 2012-07-18T16:31:26Z ! SCRAP- use 'structural molecule activity ; GO:0005198' and column 16.
[Term] id: GO:0098009 name: virus terminase, large subunit namespace: cellular_component def: "The part of the viral terminase complex that contains the translocase activity. The large subunit typically comprises pentameric protein complex" [phi:0000073, GOC:bm] is_a: GO:xxxxx ! protein complex relationship: part_of GO:0043493 ! virus terminase complex comment: This term should only be used when the large subunit consists of more than one polypeptide. created_by: brenley creation_date: 2012-07-25T10:13:00Z ! Becky renamed GO:0043493 from 'phage terminase complex' to 'viral terminase complex'. ! ADDED: 6th Aug 2012.
[Term] id: GO:0098010 name: structural constituent of viral tail namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of the tail of a virus." [phi:0000081] synonym: "structural constituent of bacteriophage tail" EXACT [] is_a: GO:0098007 ! structural constituent of virion created_by: brenley creation_date: 2012-07-18T16:34:02Z ! SCRAP- use 'structural molecule activity ; GO:0005198' and column 16.
[Term] id: GO:0098011 name: structural constituent of virus procapsid namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of the procapsid of a virus." [phi:0000065] synonym: "structural constituent of phage procapsid/prohead." RELATED [] is_a: GO:0098007 ! structural constituent of virion created_by: brenley creation_date: 2012-07-18T16:35:37Z ! SCRAP- use 'structural molecule activity ; GO:0005198' and column 16.
[Term] id: GO:0098012 name: structural constituent of viral tail tube namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of the internal tube of the contractile tails of certain viruses through which the DNA is ejected into the host cytoplasm." [phi:0000083] comment: Specific to Myoviridae phages with contractile tails. synonym: "structural constituent of bacteriophage tail tube" EXACT [] is_a: GO:0098010 ! structural constituent of viral tail created_by: brenley creation_date: 2012-07-18T16:41:50Z ! SCRAP- use 'structural molecule activity ; GO:0005198' and column 16.
[Term] id: GO:0098013 name: structural constituent of viral tail sheath namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of the external tube of certain virus tails that is responsible for the contraction of the tail to ensure ejection of viral DNA into the host cytoplasm." [phi:0000084] comment: Only applies to Myoviridae phages with a contractile tail. synonym: "structural constituent of bacteriophage tail sheath" EXACT [] is_a: GO:0098010 ! structural constituent of viral tail created_by: brenley creation_date: 2012-07-18T16:45:06Z ! SCRAP- use 'structural molecule activity ; GO:0005198' and column 16.
[Term] id: GO:0098014 name: structural constituent of viral tail shaft namespace: molecular_function def: "The action of a molecule that contributes to the structural integrity of the tail tube of certain non-contractile tailed viruses." [phi:0000085] comment: Only applies to Siphoviridae phages with non-contractile tails. synonym: "structural constituent of bacteriophage tail shaft" EXACT [] is_a: GO:0098010 ! structural constituent of viral tail created_by: brenley creation_date: 2012-07-18T16:47:54Z ! SCRAP- use 'structural molecule activity ; GO:0005198' and column 16.
[Term] id: GO:0098015 name: virus tail namespace: cellular_component def: "Part of the virion that may be used to recognize, attach and inject the viral genome and accessory proteins into the host cell." [phi:0000174, GOC:bm] comment: Many bacteriophages with dsDNA genomes, or Caudovirales, which have a double stranded DNA genome. The tail can be short (Podoviridae), long and non-contractile (Siphoviridae) or long and contractile (Myoviridae). The tail is the channel through which the phage genome is injected into the host bacterial cell. synonym: "bacteriophage tail" NARROW [] is_a: GO:0044423 ! virion part created_by: brenley creation_date: 2012-07-18T17:04:46Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098016 name: non-lytic viral extrusion namespace: biological_process def: "Process of releasing mature virus particles by passing through membranes without causing cytolysis and without incorporation of host membranes into mature virion." [phi:0000250] comment: Filamentous bacteriophage are released this way. synonym: "phage excretion" EXACT [] relationship: part_of GO:0046754 ! non-lytic viral exocytosis created_by: brenley creation_date: 2012-07-19T11:06:20Z ! Jane to make this a subtype of viral release.
[Term] id: GO:0098017 name: viral capsid, major subunit namespace: cellular_component def: "The part of the viral capsid that comprises the most common capsomere type. E.g. in a T=3 icosahedral capsid, which is composed of 12 pentameric and 20 hexameric capsomeres, the hexameric capsomeres are major subunits." [phi:0000066, GOC:bm] synonym: "Major head protein" EXACT [phi:0000066] synonym: "Major capsomere" EXACT [GOC:bm, GOC:jl, GOC:bf] relationship: part_of GO:0019028 ! viral capsid is_a: GO:0046727 ! capsomere created_by: brenley creation_date: 2012-07-19T11:21:21Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098018 name: viral capsid, minor subunit namespace: cellular_component def: "The part of the viral capsid that comprises the less common capsomere type. E.g. in a T=3 icosahedral capsid, which is composed of 12 pentameric and 20 hexameric capsomeres, the pentameric capsomeres are minor subunits." [phi:00000185, GOC:bm] synonym: "minor head protein" EXACT [phi:0000185] relationship: part_of GO:0019028 ! viral capsid is_a: GO:0046727 ! capsomere created_by: brenley creation_date: 2012-07-19T11:28:18Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098019 name: virus tail, major subunit namespace: cellular_component def: "The part of the viral tail that comprises the most common subunit type." [phi:0000082, GOC:bm] comment: Particularly applies to the major subunits of the tailed bacteriophage types Myoviridae and Siphoviridae. synonym: "Major tail protein" EXACT [phi:0000082] relationship: part_of GO:0098015 ! virus tail is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T11:32:55Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098020 name: virus tail, minor subunit namespace: cellular_component def: "The part of the viral tail that comprises the least common subunit type." [phi:0000178, GOC:bm] comment: Particularly used to describe the minor subunits of the tailed bacteriophage types Myoviridae and Siphoviridae. synonym: "bacteriophage minor protein subunit" RELATED [] synonym: "minor tail protein" EXACT [] relationship: part_of GO:0098015 ! virus tail is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T11:36:25Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098021 name: viral capsid, decoration namespace: cellular_component def: "Component of the virus capsid (head), located on the outer head surface. Involved in the stabilization of the head structure and usually non-essential." [phi:0000069] synonym: "decoration protein" RELATED [] relationship: part_of GO:0019028 ! viral capsid is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T11:52:53Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098022 name: viral capsid, fiber namespace: cellular_component def: "A type of capsid decoration composed of fiber structures." [phi:0000176] synonym: "head/capsid fiber" RELATED [] xref: phi:0000070 "phage head/capsid fiber" is_a: GO:0098021 ! viral capsid, decoration created_by: brenley creation_date: 2012-07-19T11:56:32Z ! Removed 'phi' IDs for now, till we work out which is correct: have emailed Brenley. ! ADDED: 6th Aug 2012.
[Term] id: GO:0098023 name: virus tail, tip namespace: cellular_component def: "The basal end of the virus tail, which is used by the virus to attach to the host cell." [phi:0000087] synonym: "bacteriophage tail tip" RELATED [] relationship: part_of GO:0098015 ! virus tail is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T14:13:02Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098024 name: virus tail, fiber namespace: cellular_component def: "The fibrous region of the virus tail used to scan, recognize and attach to the host cell." [phi:0000024, phi:0000175] comment: For tailed bacteriophages, fibers typically bind to particular LPS, polysaccharide or protein receptors on the cell surface. synonym: "bacteriophage tail fiber" EXACT [] relationship: part_of GO:0098015 ! virus tail is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T14:14:50Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098025 name: virus tail, baseplate namespace: cellular_component def: "Multiprotein component at the distal (head) end of the tail to which fibers of tailed viruses may be attached." [phi:0000088] comment: Tail fibers are often attached to the baseplate of Caudovirales (tailed bacteriophages with dsDNA genomes). Sometimes referred to as the tail tip or tip structure in Siphoviridae. synonym: "bacteriophage baseplate" EXACT [] synonym: "tail structure" RELATED [] synonym: "tail tip" RELATED [] relationship: part_of GO:0098015 ! virus tail is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T14:16:51Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098026 name: virus tail, tube namespace: cellular_component def: "The internal tube of the contractile tails of some viruses. It is the channel for DNA ejection into the host cytoplasm." [phi:0000026] comment: Applies in particular the Myovirirdae bacteriophages. synonym: "bacteriophage tail tube" RELATED [] relationship: part_of GO:0098015 ! virus tail is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T14:21:28Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098027 name: virus tail, sheath namespace: cellular_component def: "The external contractile envelope of the tails of some viruses. Its contraction ensures ejection of the virus DNA into the host cytoplasm." [phi:0000084] synonym: "bacteriophage tail sheath" RELATED [] relationship: part_of GO:0098015 ! virus tail is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T14:23:27Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098028 name: virus tail, shaft namespace: cellular_component def: "The tube of the non-contractile tails of some viruses." [phi:0000085] comment: Term applies in particular to the Siphoviridae bacteriophages. It is the channel for DNA translocation into the host cytoplasm in these phages. synonym: "bacteriophage tail shaft" EXACT [] relationship: part_of GO:0098015 ! virus tail is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T14:24:28Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098029 name: icosahedral viral capsid, spike namespace: cellular_component def: "A short structure attached to an icosahedral virion capsid, and used for attachment to the host cell." [phi:0000208] relationship: part_of GO:0019030 ! icosahedral viral capsid is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T14:37:11Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098030 name: icosahedral viral capsid, neck namespace: cellular_component def: "A region of constriction located below the head and above the tail sheath of viruses with contractile tails (Myoviridae)." [phi:0000205, phi:0000309] relationship: part_of GO:0019030 ! icosahedral viral capsid is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T14:56:28Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098031 name: icosahedral viral capsid, collar namespace: cellular_component def: "A small disk located at the base of some icosahedral virus capsids." [phi:0000206, phi:0000308] relationship: part_of GO:0019030 ! icosahedral viral capsid is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T15:01:12Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098032 name: icosahedral viral capsid, collar fiber namespace: cellular_component def: "A fiber attached to the collar structure of some icosahedral viral capsids." [phi:0000207, phi:0000307] relationship: part_of GO:0098031 ! icosahedral viral capsid, collar is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T15:05:16Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098033 name: icosahedral viral capsid, neck fiber namespace: cellular_component def: "A fiber attached to the neck at the base of some icosahedral viral capsids." [phi:0000075, phi:0000310] relationship: part_of: GO:0098030 ! icosahedral viral capsid, neck is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-07-19T15:07:39Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098034 name: viral RNA genome packaging, nucleation namespace: biological_process def: "Process by which the capsid proteins nucleate around the viral RNA genome." [] is_a: GO:0019074 ! viral RNA genome packaging created_by: brenley creation_date: 2012-07-20T11:35:16Z ! JANE TO LOOK AT AND ADD… self-assembly.
[Term] id: GO:0098035 name: viral DNA genome packaging via site-specific sequence recognition namespace: biological_process def: "The encapsulation of the viral DNA genome within the capsid which proceeds via cleavage of the viral DNA at specific sites by a viral terminase." [] is_a: GO:0019073 ! viral DNA genome packaging created_by: brenley creation_date: 2012-07-20T11:36:49Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098036 name: viral DNA genome packaging, 3' extended cos packaging namespace: biological_process def: "The encapsulation of the viral DNA genome within the capsid which proceeds via cleavage of the viral DNA at specific sites to produce 3' protruding ends." [phi:0000021] is_a: GO:0098035 ! viral DNA genome packaging via site-specific sequence recognition created_by: brenley creation_date: 2012-07-20T11:38:40Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098037 name: viral DNA genome packaging, 5' extended cos packaging namespace: biological_process def: "The encapsulation of the viral DNA genome within the capsid which proceeds via cleavage of the viral DNA at specific sites to produce 5' protruding ends." [phi:0000022] is_a: GO:0098035 ! viral DNA genome packaging via site-specific sequence recognition created_by: brenley creation_date: 2012-07-20T11:40:47Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098038 name: non-replicative transposition, DNA-mediated namespace: biological_process def: "Process by which a transposable element is excised from the donor site and integrated at the target site without replication of the element. Also referred to as cut-and-paste transposition." [phi:0000137, PMID:2553270] is_a: GO:0006313 ! transposition, DNA-mediated created_by: brenley creation_date: 2012-07-20T16:47:50Z ! remove cut-and-paste transposition synonym from 'transposition, DNA-mediated'. ! ADDED: 6th Aug 2012.
[Term] id: GO:0098039 name: replicative transposition, DNA-mediated namespace: biological_process def: "Process of transposition in which the existing element is replicated and one of the copies is excised and integrated at a new target site. Also referred to as copy-and-paste transposition." [PMID:10540284] synonym: "transpositional DNA genome replication" EXACT [phi:0000037] is_a: GO:0006313 ! transposition, DNA-mediated created_by: brenley creation_date: 2012-07-20T16:52:02Z ! ADDDED: HAS_PART: DNA replication ; GO:0006260 (not a more specific term we can use). ! ADDED: 6th Aug 2012.
[Term] id: GO:0098040 name: transpososome namespace: cellular_component def: "A nucleoprotein complex where DNA cleavage, transfer and resealing occurs during a transposition event." [phi:0000157] comment: Proteins can include transposases and other regulatory proteins. is_a: GO:0044424 ! intracellular part created_by: brenley creation_date: 2012-07-31T14:02:11Z
[Term] id: GO:0098041 name: cointegrate formation, maintenance and resolution namespace: biological_process def: "Processes that result in the formation of a DNA region consisting of two fused replicons/plasmids as a result of replicative transposition event." [phi:0000246] relationship: part_of GO:0098039 ! replicative transposition, DNA-mediated created_by: brenley creation_date: 2012-07-20T17:02:36Z
[Term] id: GO:0098042 name: virus terminase, small subunit namespace: cellular_component def: "Protein component that forms a complex with the terminase large subunit at the base of the virus capsid/head involved in packaging of the genome into the head/capsid." [phi:0000074] is_a: GO:0043493 ! virus terminase complex created_by: brenley creation_date: 2012-07-25T10:16:02Z ! SCRAP- the small subunit is often just one protein.
[Term] id: GO:0098043 name: regulation of holin activity namespace: molecular_function def: "Any process that modulates the activity of a holin." [] xref: phi:0000098 "antiholin activity" relationship: regulates GO:0015267 ! channel activity created_by: brenley creation_date: 2012-07-25T10:24:16Z ! Becky added in via TG: ID: GO:1901217 Label: regulation of holin activity
[Term] id: GO:0098044 name: negative regulation of holin activity namespace: molecular_function def: "Any process that stops or reduces the activity of a holin." [] xref: phi:0000098 "phage antiholin activity inhibits holin." is_a: GO:0098043 ! regulation of holin activity relationship: negatively_regulates GO:0015267 ! channel activity created_by: brenley creation_date: 2012-07-25T10:27:40Z ! Becky added in via TG (synonym = antiholin) : id: GO: GO:1901218 Label: negative regulation of holin activity
[Term] id: GO:0098045 name: virus baseplate assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form a virusbase plate." [phi:0000328, GOC:bm] relationship: part_of GO:0098003 ! virus tail assembly is_a: GO:0022415 ! viral reproductive process created_by: brenley creation_date: 2012-07-25T14:50:32Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098046 name: type V protein secretion system complex namespace: cellular_component def: "A complex of proteins that permits the transfer of proteins into the extracellular milieu or directly into host cells via the type V secretion system." [phi:0000261] is_a: GO:0044464 ! cell part created_by: brenley creation_date: 2012-07-25T15:42:15Z ! ALREADY ADDED BY BECKY. ID kept.
[Term] id: GO:0098047 name: generalized transduction namespace: biological_process def: "When bacteriophages complete their lytic cycle, random bacterial chromosomal DNA segments or plasmid DNA instead of viral DNA may be inserted into the viral capsid. The phage particle loaded with a piece of bacterial DNA may infect another bacterial cell. This newly acquired DNA can fall to one of three fates. It can be recycled. If the DNA was originally a plasmid, it can recircularize inside the new cell and become a plasmid again. If the new DNA matches with a homologous region of the recipient chromosome, it will recombine so that part or most of that DNA material is incorporated into the new host chromosome." [phi:0000247] is_a: GO:0009293 ! transduction created_by: brenley creation_date: 2012-07-27T10:43:53Z
[Term] id: GO:0098048 name: specialized transduction namespace: biological_process def: "While excising from the chromosome incorrectly, a prophage can leave part of its DNA in the chromosome and pick up adjacent bacterial DNA. This DNA may be packaged into a mature phage particle, which can be released and infect a new host. Depending on which part of the phage DNA has been lost, this new genome may or not be able to complete a lytic cycle. If its bacterial DNA moiety is homologous to the recipient cell chromosome, integration can occur by homologous recombination. If the integrase and attachment site components of the phage are still present, integration can also occur by site-specific recombination. In both cases the recipient chromosome will contain two copies of the bacterial DNA segment carried by the transducing genome. The genes most susceptible to transfer by this mechanism are those in the direct vicinity of the original prophage." [phi:0000248] is_a: GO:0009293 ! transduction created_by: brenley creation_date: 2012-07-27T10:46:29Z
[Term] id: GO:0098049 name: tyrosine-based transposase activity namespace: molecular_function def: "Tyrosine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome." [phi:0000149] is_a: GO:0004803 ! transposase activity created_by: brenley creation_date: 2012-07-27T11:18:16Z
[Term] id: GO:0098050 name: serine-based transposase activity namespace: molecular_function def: "Serine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome." [phi:0000152] is_a: GO:0004803 ! transposase activity created_by: brenley creation_date: 2012-07-27T11:21:03Z
[Term] id: GO:0098051 name: Y2 transposase activity namespace: molecular_function def: "Y2-transposases catalyze the rolling circle transposition. They contain several conserved motifs including a pair of tyrosine residues, that are conserved among plasmid and phage rolling-circle replication proteins, which are important for DNA binding, breakage and reunion." [phi:0000159] is_a: GO:0098049 ! tyrosine-based transposase activity created_by: brenley creation_date: 2012-07-27T11:23:18Z
[Term] id: GO:0098052 name: serine-based recombinase activity namespace: molecular_function def: "Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a 5-prime phosphoseryl enzyme intermediate in which the target sequence is first cleaved by nucleophilic attack by a serine in the active site." [phi:0000144] xref: Wikipedia:http\://en.wikipedia.org/wiki/Site-specific_recombination is_a: GO:0009009 ! site-specific recombinase activity created_by: brenley creation_date: 2012-07-27T11:29:04Z
[Term] id: GO:0098053 name: non-site-specific recombinase activity namespace: molecular_function def: "Recombinase activity that is not target site specific or dependent on a pair of short, unique DNA target sequences. They rather use specific sites on the transposable element and random target sites." [] is_a: GO:0000150 ! recombinase activity created_by: brenley creation_date: 2012-07-27T11:32:48Z
[Term] id: GO:0098054 name: DDE-based recombinase activity namespace: molecular_function def: "Recomoinases with aDDE transposase have a related amino-acid motif (the DDE motif), which forms the active site of the transposase and is responsible for coordinating the cleavage and joining steps of transposition. Breakage of the DNA occurs at the end of the element (usually a hydrolysis) and is followed by breakage and integration at the target site (a transesterification reaction)." [phi:0000153] is_a: GO:0098053 ! non-site-specific recombinase activity created_by: brenley creation_date: 2012-07-27T11:33:50Z
[Term] id: GO:0098055 name: intasome namespace: cellular_component def: "A multiprotein complex containing DNA, site-specific tyrosine or serine based integrase and accessory proteins involved in the integration or excision of DNA fragments during recombination." [phi:0000155] is_a: GO:0044424 ! intracellular part created_by: brenley creation_date: 2012-07-31T14:18:59Z
[Term] id: GO:0098056 name: resolvasome namespace: cellular_component def: "A multicomponent protein complex including a tyrosine or serine based resolvase that mediates resolution of chromosome dimers and replicon fusions." [phi:0000158] is_a: GO:0044424 ! intracellular part created_by: brenley creation_date: 2012-07-31T14:20:20Z
[Term] id: GO:0098057 name: relaxosome namespace: cellular_component def: "A multicomponent protein complex including a relaxase, which mediates cleavage and initiation of rolling circle replication on a double stranded DNA molecule during conjugation, phage replication and transposition." [] is_a: GO:0044424 ! intracellular part created_by: brenley creation_date: 2012-07-31T14:23:05Z
[Term] id: GO:0098058 name: terminase activity namespace: molecular_function def: "Enables the directed movement of a single viral genomic DNA particle into the prohead/procapsid after cleavage of the genome from a concatamer." [PMID:17501915] comment: This enzyme includes the ability to cleave concatameric DNA into single genomic units. synonym: "virus terminase motor" RELATED [] is_a: GO:0015616 ! DNA translocase activity created_by: brenley creation_date: 2012-07-31T15:57:32Z ! SCRAP: Multifunctional protein- capture at the annotation level.
[Term] id: GO:0098059 name: virus membrane, internal to capsid namespace: cellular_component def: "The lipid bilayer component of a virion that is contained within the capsid/head." [] is_a: GO:0055036 ! virion membrane created_by: brenley creation_date: 2012-07-31T17:32:55Z
[Term] id: GO:0098060 name: virus membrane, external to capsid namespace: cellular_component def: "The lipid bilayer component of a virion that is external to the capsid/head and surrounds the capsid/head." [] is_a: GO:0055036 ! virion membrane created_by: brenley creation_date: 2012-07-31T17:35:25Z
[Term] id: GO:0098061 name: viral capsid, internal space namespace: cellular_component def: "The region of a virus contained within the capsid shell, and usually containing the viral genome and accessory proteins" [] synonym: "internal head protein" EXACT [] is_a: GO:xxxxxxx ! virion part created_by: brenley creation_date: 2012-08-01T12:12:47Z ! ADDED: 6th Aug 2012.
[Term] id: GO:0098062 name: DNA packaging activity namespace: molecular_function def: "Enables the directed movement of a viral genomic DNA into the prohead/procapsid." [PMID:17501915] comment: Enzyme does NOT have endonuclease activity since each viral genome is synthesized separately. is_a: GO:0015616 ! DNA translocase activity created_by: brenley creation_date: 2012-08-01T15:29:29Z ! ADDED: DNA translocase activity involved in viral DNA genome packaging ; GO:0039631
[Term] id: GO:0098063 name: dsRNA translocation namespace: molecular_function def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a double-stranded RNA molecule." [PMID:16505972] is_a: GO:0003723 ! RNA binding created_by: brenley creation_date: 2012-08-01T15:47:13Z ! ADDED: RNA translocase activity ; GO:0039630
[Term] id: GO:0098064 name: dsRNA packaging activity namespace: molecular_function def: "Enables the directed movement of a viral genomic DNA into the prohead/procapsid." [PMID:16505972] is_a: GO:0098063 ! dsRNA translocation created_by: brenley creation_date: 2012-08-01T15:50:39Z ! ADDED: RNA translocase activity involved in viral RNA genome packaging ; GO:0039632