Brenley's Suggested Terms

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[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