format-version: 1.2 date: 01:11:2011 15:47 saved-by: ariane auto-generated-by: OBO-Edit 2.1-beta13 default-namespace: Phage ontology [Term] id: phi:0000001 name: phage process def: "All processes related to the phage developmental cycles." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000257 ! bacteriophage [Term] id: phi:0000002 name: phage infectious cycle def: "The set of processes by which a bacteriophage multiplies. Upon infection of a host bacterial cell, virulent phages replicate the viral genome and assemble progeny particles. Temperate phages can either follow that same route or establish as a prophage (lysogeny). Under some circumstances the prophage can be induced and complete a lytic cycle." [PHI:AT, PHI:IM, PHI:SC] synonym: "lytic viral life cycle" EXACT [GO:0030068] synonym: "viral assembly, maturation, egress, and release" RELATED [GO:0019067] synonym: "viral infectious cycle" RELATED [GO:0019058] xref: GO:0019058 xref: GO:0019067 xref: GO:0030068 is_a: phi:0000001 ! phage process [Term] id: phi:0000003 name: phage pre adsorption def: "Any process by which a phage loosely binds to its host surface and scans it for receptors with its fibers, spikes or a baseplate component." [PHI:AT, PHI:IM, PHI:SC] is_obsolete: true [Term] id: phi:0000004 name: phage adsorption def: "Process by which a bacteriophage, using its tail fibers, spikes or a baseplate component, recognizes and binds to its specific receptor on the host cell surface. This process can include enzymatic degradation of the surface polysaccharide of the bacterium." [PHI:AT, PHI:IM, PHI:SC] comment: Often defined by subtraction of the number of unadsorbed phages measured either as the number of plaque forming units (pfu) recovered following chloroform treatment of infected cells, or by co-sedimentation of pfu with cells (with or without dilution before centrifugation). These methods may give different values for the % adsorbed phage. relationship: part_of phi:0000007 ! phage lysogeny relationship: part_of phi:0000372 ! phage lytic cycle [Term] id: phi:0000005 name: phage reversible adsorption 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." [PHI:AT, PHI:IM, PHI:SC] 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. relationship: part_of phi:0000004 ! phage adsorption [Term] id: phi:0000006 name: phage irreversible adsorption def: "The process by which conformational changes of virion proteins or injection of virion proteins into the infected cell initially commit infection. Disruption of the phage:cell complex at this step results in the loss of infective phage virions." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000004 ! phage adsorption [Term] id: phi:0000007 name: phage lysogeny def: "A set of processes by which temperate bacteriophages establish as a prophage either integrated in the host genome at a more or less specific or random location or as a linear or as a circular plasmid in the host cytoplasm. The lytic functions are repressed by a phage encoded lysogeny repressor. The lysogenic bacterium is immune to superinfection by phages related to the prophage and susceptible to that same repressor. Phages that are insensitive to that repressor are called heteroimmune." [PHI:AT, PHI:IM, PHI:SC] synonym: "establishment of viral latency " BROAD [GO:001904] xref: GO:001904 relationship: part_of phi:0000002 ! phage infectious cycle [Term] id: phi:0000008 name: phage DNA translocation def: "Process by which a bacteriophage transfers its DNA in the host cell." [PHI:AT, PHI:IM, PHI:SC] comment: Formerly Ejection/injection. synonym: "viral genome transport in host cell" BROAD [GO:0046796] xref: GO:0046796 relationship: part_of phi:0000007 ! phage lysogeny relationship: part_of phi:0000372 ! phage lytic cycle [Term] id: phi:0000009 name: phage assembly def: "Processes leading to the building of a mature phage particle." [PHI:AT, PHI:IM, PHI:SC] comment: GO:0042963 definition is not appropriate: A late phase of bacteriophage replication during which all the components necessary for the formation of a mature virion collect at a particular site in the bacterial cell and the basic structure of the virus particle is formed. synonym: "phage morphogenesis" EXACT [PHI:AT] relationship: part_of phi:0000372 ! phage lytic cycle [Term] id: phi:0000010 name: phage head/capsid assembly def: "Process by which phage heads/capsids are assembled." [PHI:AT, PHI:IM, PHI:SC] synonym: "viral capsid assembly" BROAD [GO:0019069] xref: GO:0019069 relationship: part_of phi:0000009 ! phage assembly [Term] id: phi:0000011 name: phage tail fiber assembly def: "Process by which phage tail fibers are assembled." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000009 ! phage assembly [Term] id: phi:0000012 name: phage head tail joining def: "Process by which tailed phage heads and tails are put together." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000009 ! phage assembly [Term] id: phi:0000013 name: phage release by lysis def: "Process of dissolution of cells by the action of specific phage encoded enzymes that causes cell rupture and release of the phage progeny." [PHI:AT, PHI:IM, PHI:SC] synonym: "lytic viral release" BROAD [GO:0019077] xref: GO:0019077 is_a: phi:0000014 ! phage release [Term] id: phi:0000014 name: phage release def: "Process of releasing mature phage particles from the host cell." [PHI:AT, PHI:IM, PHI:SC] synonym: "release of virus from host " BROAD [GO:0019076] xref: GO:0019076 relationship: part_of phi:0000372 ! phage lytic cycle [Term] id: phi:0000015 name: phage tail assembly def: "Process by which tailed phage tails are assembled." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000009 ! phage assembly [Term] id: phi:0000016 name: cell wall synthesis inhibition def: "Process used by some phages as part_of the host cell lysis process." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000014 ! phage release [Term] id: phi:0000017 name: phage prohead/capsid assembly def: "Process of building the precursor of the phage head/capsid, which shall later encapsidate the viral genome." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000010 ! phage head/capsid assembly [Term] id: phi:0000018 name: phage genome packaging def: "Process of incorporation of the phage genome into the phage head/capsid." [PHI:AT, PHI:IM, PHI:SC] synonym: "viral DNA genome packaging " BROAD [GO:0019072] synonym: "viral genome packaging" BROAD [GO:0019073] xref: GO:0019072 xref: GO:0019073 relationship: part_of phi:0000010 ! phage head/capsid assembly [Term] id: phi:0000019 name: phage DNA maturation def: "Processing of replicated DNA into a packageable structure, often a linear concatemer." [PHI:AT, PHI:IM, PHI:SC] synonym: "viral DNA cleavage" BROAD [GO:0019070] synonym: "viral genome maturation " BROAD [GO:0019071] xref: GO:0019070 xref: GO:0019071 relationship: part_of phi:0000018 ! phage genome packaging [Term] id: phi:0000020 name: phage headful packaging def: "Mode of packaging of double stranded DNA phage genomes with terminally redundant and possibly circularly permuted ends. These are generated by the activity of the phage-encoded terminase, which as part_of the phage head specifically binds the pac site on tandem arrays of phage DNA copies and is triggered to cut the DNA when the phage head is full." [PHI:AT, PHI:IM, PHI:SC] comment: Generalized transducing phages usually use this mode of packaging. The prohead terminase binds pac-like sites on the host chromosome and processes it as if it was phage DNA. is_a: phi:0000019 ! phage DNA maturation [Term] id: phi:0000021 name: phage 3'extended cos packaging def: "Mode of packaging of double stranded DNA phage genomes with 3' protruding ends. These are generated by the activity of the phage encoded terminase, which, when bound to the phage prohead, specifically binds the cos sites on tandem arrays of phage DNA copies and introduces staggered nicks to generate the 3' protruding 'sticky' ends." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000019 ! phage DNA maturation [Term] id: phi:0000022 name: phage 5'extended cos packaging def: "Mode of packaging of double stranded DNA phage genomes with 5' protruding ends. These are generated by the activity of the phage encoded terminase, which, when bound to the phage prohead, specifically binds the cos sites on tandem arrays of phage DNA copies and introduces staggered nicks to generate the 5' protruding 'sticky' ends." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000019 ! phage DNA maturation [Term] id: phi:0000023 name: phage budding def: "Process of releasing mature enveloped phage particles (Plasmaviridae phages) by formation of a bulge." [PHI:AT, PHI:IM, PHI:SC] synonym: "lytic viral budding" RELATED [GO:0019078] xref: GO:0019078 is_a: phi:0000014 ! phage release [Term] id: phi:0000024 name: phage genome replication def: "Process of replicating the phage genome." [PHI:AT, PHI:IM, PHI:SC] synonym: "viral genome replication " BROAD [GO:0019079] xref: GO:0019079 relationship: part_of phi:0000009 ! phage assembly [Term] id: phi:0000025 name: phage RNA replication def: "Process of replicating a phage RNA genome." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000024 ! phage genome replication [Term] id: phi:0000026 name: phage DNA replication def: "Process of replicating a phage DNA genome." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000024 ! phage genome replication [Term] id: phi:0000027 name: regulation of phage replication def: "Any process that modulates the frequency, rate or extent of the phage genome replication." [PHI:AT, PHI:IM, PHI:SC] synonym: "regulation of viral genome replication " EXACT [GO:0045069] xref: GO:0045069 relationship: part_of phi:0000024 ! phage genome replication [Term] id: phi:0000028 name: protein primed DNA replication def: "Process of DNA-dependent DNA replication primed by a phage encoded protein bound at the ends of its linear genome to produce two linear daughter DNA molecules." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000026 ! phage DNA replication [Term] id: phi:0000029 name: sigma DNA replication def: "Process of DNA-dependent DNA replication proceeding by the rolling circle mode, i.e. on a circular DNA molecule to produce a concatemer." [PHI:AT, PHI:IM, PHI:SC] synonym: "sigma virus replication" EXACT [GO:0008167] xref: GO:0008167 is_a: phi:0000026 ! phage DNA replication [Term] id: phi:0000030 name: theta DNA replication def: "Process of DNA replication proceeding uni or bidirectionally on a circular DNA template to produce two daughter circular DNA molecules ." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000026 ! phage DNA replication [Term] id: phi:0000031 name: transpositional DNA replication def: "Process of DNA-dependent DNA replication proceeding by successive rounds of replicative transposition." [PHI:AT, PHI:IM, PHI:SC] comment: This mode of replication is used by the transposable phages. is_a: phi:0000026 ! phage DNA replication [Term] id: phi:0000032 name: recombination directed DNA replication def: "Process of DNA-dependent DNA replication intiated by homologous recombination." [PHI:AT, PHI:IM, PHI:SC] comment: Typically used by phages of the T4 family. is_a: phi:0000026 ! phage DNA replication [Term] id: phi:0000033 name: phage gene expression def: "Cascade of transcription and translation of the phage genes." [PHI:AT, PHI:IM, PHI:SC] synonym: "viral genome expression" BROAD [GO:0019080] xref: GO:0019080 relationship: part_of phi:0000007 ! phage lysogeny relationship: part_of phi:0000372 ! phage lytic cycle [Term] id: phi:0000034 name: phage gene transcription def: "Cascade of transcription of the phage genes." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000033 ! phage gene expression [Term] id: phi:0000035 name: phage class I gene transcription def: "The transcriptional period of the earliest expressed viral genes mainly encoding transcriptional regulators." [PHI:AT, PHI:IM, PHI:SC] synonym: "immediate early viral mRNA transcription" EXACT [GO:0019085] synonym: "phage early transcription" RELATED [PHI:AT] xref: GO:0019085 is_a: phi:0000034 ! phage gene transcription [Term] id: phi:0000036 name: phage class II gene transcription def: "The second round of viral gene transcription, usually of replication genes." [PHI:AT, PHI:IM, PHI:SC] synonym: "(delayed) early viral mRNA transcription " EXACT [GO:0019084] xref: GO:0019084 is_a: phi:0000034 ! phage gene transcription [Term] id: phi:0000037 name: phage class IIB gene transcription def: "The third round of phage transcription, usually of regulators involved in the progression of induction of the phage late gene expression." [PHI:AT, PHI:IM, PHI:SC] synonym: "middle promoter transcription " EXACT [PHI:AT] is_a: phi:0000034 ! phage gene transcription [Term] id: phi:0000038 name: phage class III gene transcription def: "The transcriptional period of the latest expressed viral genes mainly encoding phage capsid components, morphogenesis proteins and cell wall degradation enzymes." [PHI:AT, PHI:IM, PHI:SC] comment: Typically turned on by phage-encoded transcription factors. synonym: "late viral mRNA transcription" EXACT [GO:0019086] synonym: "phage late transcription" RELATED [PHI:AT] xref: GO:0019086 is_a: phi:0000034 ! phage gene transcription [Term] id: phi:0000039 name: phage transcription termination def: "Process by which phage gene transcription stops and RNA-polymerase is released from the DNA template." [PHI:AT, PHI:IM, PHI:SC] xref: GO:0030401 relationship: part_of phi:0000048 ! negative transcriptional regulation of phage gene expression [Term] id: phi:0000040 name: phage transcription anti termination def: "Functions to prevent the termination of RNA synthesis. Acts as a regulatory device, e.g. in phage lambda, enabling a terminator to be masked from RNA polymerase so that distal genes can be expressed." [GO:0030401] xref: GO:0030401 relationship: part_of phi:0000049 ! positive transcriptional regulation of phage gene expression [Term] id: phi:0000041 name: regulation of phage gene expression def: "Any process that activates or represses phage gene expression." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000033 ! phage gene expression [Term] id: phi:0000042 name: positive regulation of phage replication def: "Any process that stimulates the frequency, rate or extent of the phage genome replication." [PHI:AT, PHI:IM, PHI:SC] synonym: "positive regulation of viral genome replication" BROAD [GO:0045070] xref: GO:0045070 relationship: part_of phi:0000027 ! regulation of phage replication [Term] id: phi:0000043 name: negative regulation of phage replication def: "Any process that decreases the frequency, rate or extent of the phage genome replication." [PHI:AT, PHI:IM, PHI:SC] synonym: "negative regulation of viral genome replication " BROAD [GO:0045071] xref: GO:0045071 relationship: part_of phi:0000027 ! regulation of phage replication [Term] id: phi:0000044 name: transcriptional-regulation of phage gene expression def: "Any process that activates or represses the transcription of phage genes. Typically turned on by phage-encoded transcription factors." [PHI:AT, PHI:IM, PHI:SC] synonym: "regulation of viral transcription " BROAD [GO:0046782] xref: GO:0046782 relationship: part_of phi:0000041 ! regulation of phage gene expression [Term] id: phi:0000045 name: negative post transcriptional regulation of phage gene expression def: "Any process that represses the expression of phage genes at the post-transcriptional level." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000047 ! post-transcriptional regulation of phage gene expression [Term] id: phi:0000046 name: positive post transcriptional regulation of phage gene expression def: "Any process that activates the expression of phage genes at the post-transcriptional level." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000047 ! post-transcriptional regulation of phage gene expression [Term] id: phi:0000047 name: post-transcriptional regulation of phage gene expression def: "Any process that activates or represses the expression of phage genes at a post-trasncriptional level." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000041 ! regulation of phage gene expression [Term] id: phi:0000048 name: negative transcriptional regulation of phage gene expression def: "Any process that represses the expression of phage genes at the transcriptional level." [PHI:AT, PHI:IM, PHI:SC] comment: Typically turned off by phage-encoded transcription factors. synonym: "negative regulation of viral transcription " BROAD [GO:0032897] xref: GO:0032897 relationship: part_of phi:0000049 ! positive transcriptional regulation of phage gene expression [Term] id: phi:0000049 name: positive transcriptional regulation of phage gene expression def: "Any process that activates the expression of phage genes at the transcriptional level." [PHI:AT, PHI:IM, PHI:SC] comment: Typically turned on by phage-encoded transcription factors. synonym: "positive regulation of viral transcription " BROAD [GO:0050434] xref: GO:0050434 relationship: part_of phi:0000044 ! transcriptional-regulation of phage gene expression [Term] id: phi:0000050 name: post-translational regulation of phage gene expression def: "Any process that up or down-regulates protein activity or stability." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000041 ! regulation of phage gene expression [Term] id: phi:0000051 name: establishment as a plasmid prophage def: "A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a plasmid." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000007 ! phage lysogeny [Term] id: phi:0000052 name: phage lysogenic conversion def: "Process through which a prophage induces a hereditary change in the phenotype or fitness of the lysogen." [PHI:AT, PHI:IM, PHI:SC] synonym: "transformation of host cell by virus " RELATED [GO:0019087] xref: GO:0019087 relationship: part_of phi:0000007 ! phage lysogeny [Term] id: phi:0000053 name: establishment as a linear plasmid prophage def: "A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a linear plasmid." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000051 ! establishment as a plasmid prophage [Term] id: phi:0000054 name: establishment as a circular plasmid prophage def: "A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a circular plasmid." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000051 ! establishment as a plasmid prophage [Term] id: phi:0000055 name: establishment as an integrated prophage def: "A process by which the phage integrates in the host genomes and establishes as a stable prophage." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000007 ! phage lysogeny [Term] id: phi:0000056 name: prophage DNA integration def: "Process by which the phage DNA integrates into the host genome by recombination. Integration usually proceeds via site-specific recombination into the host chromosome." [PHI:AT, PHI:IM, PHI:SC] synonym: "provirus integration" EXACT [GO:0019047] xref: GO:0019047 is_a: phi:0000132 ! site-specific DNA integration relationship: part_of phi:0000055 ! establishment as an integrated prophage [Term] id: phi:0000057 name: maintenance of prophage immunity def: "Process by which a latent prophage blocks the expression of its own lytic genes as well as expression of those genes by a related superinfecting phage with the same immunity. The host bacterium is thus \"immune\" to superinfection by such related phages." [PHI:AT, PHI:IM, PHI:SC] synonym: "provirus maintenance" BROAD [GO:0032360] xref: GO:0032360 relationship: part_of phi:0000053 ! establishment as a linear plasmid prophage relationship: part_of phi:0000054 ! establishment as a circular plasmid prophage relationship: part_of phi:0000055 ! establishment as an integrated prophage [Term] id: phi:0000058 name: phage latent infection def: "To be written." [PHI:AT, PHI:IM, PHI:SC] comment: IS this term really necessary? is_a: phi:0000001 ! phage process [Term] id: phi:0000059 name: phage abortive infection def: "Process of infection by a phage, which does not complete the lytic cycle and produces no viable phage burst. It may or may not provoke cell death." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000001 ! phage process [Term] id: phi:0000060 name: phage pseudolysogeny def: "Simulated lysogeny in a mixed population of phage-infected bacteria, non-infected phage-sensitive bacteria, and free phages." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000002 ! phage infectious cycle [Term] id: phi:0000061 name: phage component def: "All macromolecules, proteins, nucleic acids, sugars, lipids etc. that are part or participate in the assembly of the mature virion particle." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000257 ! bacteriophage [Term] id: phi:0000062 name: prophage induction def: "Process by which a prophage is made to switch from the latent/lysogenic state to the lytic cycle and production of phage progeny." [PHI:AT, PHI:IM, PHI:SC] synonym: "reactivation of latent virus" BROAD [GO:0019046] xref: GO:0019046 relationship: part_of phi:0000002 ! phage infectious cycle [Term] id: phi:0000063 name: prophage DNA excision def: "Process by which a prophage DNA is excised from the host genome." [PHI:AT] synonym: "provirus excision" EXACT [GO:0032359] xref: GO:0032359 is_a: phi:0000134 ! site-specific DNA excision relationship: part_of phi:0000062 ! prophage induction [Term] id: phi:0000064 name: phage head/capsid protein def: "Component of the closed shell (head or capsid) of the phage." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000161 ! head/capsid [Term] id: phi:0000065 name: capsid scaffolding protein def: "Transient internal component of the phage prohead, which allows for its assembly. It is degraded or leaves the prohead without being degraded and is replaced by the phage DNA upon maturation." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000177 ! prohead/procapsid [Term] id: phi:0000066 name: phage head/capsid major protein def: "Abbreviated MHP, the major subunit component that forms the closed shell (capsid) of the phage head." [PHI:AT, PHI:IM, PHI:SC] synonym: "capsomer" EXACT [GO:0046727] xref: GO:0046727 is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000067 name: phage portal associated protein def: "Also called gate keepers, these proteins close the head after packaging and maturation of the phage genome, are part of the completed head, allow for the binding of the tail and are part of the complete phage particle." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000068 name: phage portal protein def: "Protein component that forms the junction between the Caudovirales phage head and tail and serves as a gate through which DNA passes during packaging and translocation." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000069 name: phage head/capsid decoration protein def: "Component of the phage head/capsid. Located on the outer head surface they are involved in the stabilization of the head structure and, usually, are not essential." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000070 name: phage head/capsid fiber protein def: "Protein component of fiber structures, which decorate the head/capsid of some phages." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000176 ! phage head/capsid fiber [Term] id: phi:0000071 name: phage terminal protein def: "Protein covalently linked to the ends of dsDNA phages that use protein primed DNA replication." [PHI:AT, PHI:IM, PHI:MS, PHI:SC] comment: The protein primes DNA replication and may have other functions including cell wall hydrolase. is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000072 name: phage terminase complex def: "A complex of large and small terminase subunits. It is responsible for binding to and thereby choosing the DNA that will be packaged; it also carries the ATPase motor (DNA translocase) that drives the DNA into the prohead during packaging and has the nuclease activity that cleaves virion-length DNA from overlength or circular replicating DNA. The name refers to the nuclease activity that creates the termini of the virion DNA. Some phage terminases exist as single polypeptides and some terminase complexes include an RNA component." [GO:0043493, PHI:AT, PHI:IM, PHI:SC] xref: GO:0043493 is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000073 name: phage terminase large subunit def: "Phage component that forms a complex with the terminase small subunit at the base of the phage head." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000072 ! phage terminase complex [Term] id: phi:0000074 name: phage terminase small subunit def: "Phage component that forms a complex with the terminase large subunit at the base of the phage head." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000072 ! phage terminase complex [Term] id: phi:0000075 name: capsid neck fiber protein def: "Protein component of fiber structures appended at the neck at the base of some phage heads." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000187 ! capsid structural protein relationship: part_of phi:0000310 ! capsid neck fiber [Term] id: phi:0000076 name: injected protein def: "Protein component of a phage, which is injected into the host cytoplasm upon phage infection." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000061 ! phage component is_a: phi:0000187 ! capsid structural protein [Term] id: phi:0000077 name: pre DNA injected protein def: "Protein component of a phage, which is injected into the host cytoplasm upon phage infection prior to phage DNA translocation." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000076 ! injected protein [Term] id: phi:0000078 name: post DNA injected protein def: "Protein component of a phage, which is injected into the host cytoplasm upon phage infection after phage DNA translocation." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000076 ! injected protein [Term] id: phi:0000079 name: translocation protein def: "Protein component of a phage, which is injected into the host membrane upon phage infection, creating a channel for phage DNA translocation." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000076 ! injected protein [Term] id: phi:0000080 name: phage inner vesicle def: "Biochemical assembly that contains both proteins and lipids and is part_of some (Tectiviridae) phage capsids." [PHI:AT, PHI:HWA] is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000081 name: phage tail protein def: "Protein component of the assembled tail of tailed phages (caudovirale)." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000187 ! capsid structural protein relationship: part_of phi:0000174 ! capsid tail [Term] id: phi:0000082 name: phage major tail protein def: "Abbreviated MTP, the term refers to protein component found in large amount, easily detectable upon electrophoresis of tailed phage particles of the types Myoviridae and Siphoviridae." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000081 ! phage tail protein [Term] id: phi:0000083 name: phage tail tube protein def: "Protein that forms the internal tube of the contractile tails of Myovirirdae phages. It is the channel for DNA ejection into the host cytoplasm." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000081 ! phage tail protein [Term] id: phi:0000084 name: phage tail sheath protein def: "Protein that forms the external contractile envelope of the tails of Myoviridae phages. Its contraction ensures ejection of the phage DNA into the host cytoplasm." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000081 ! phage tail protein [Term] id: phi:0000085 name: phage tail shaft protein def: "Protein that forms the tube of the non-contractile tails of Siphoviridae phages. It is the channel for DNA translocation into the host cytoplasm." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000081 ! phage tail protein [Term] id: phi:0000086 name: phage tail tape measure protein def: "Protein TMP that controls the tail tube length in Myoviridae and tail shaft length in Siphoviridae. The protein is part of the finished tail. Some phages inject their TMP with their DNA in the host cytoplasm." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000081 ! phage tail protein [Term] id: phi:0000087 name: phage tail tip protein def: "Protein structure that forms the basal tip of the phage tail and is used by the phage to adsorb to the host cell." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000081 ! phage tail protein relationship: part_of phi:0000088 ! phage base plate protein [Term] id: phi:0000088 name: phage base plate protein def: "Multiprotein component at the head-distal end of the tail and to which fibers of tailed phages may be attached (Caudovirales). Sometimes referred to as the tail tip or tip structure in Siphoviridae." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000081 ! phage tail protein [Term] id: phi:0000089 name: phage tail fiber protein def: "Protein component of the fiber, structure appended to the phage tail and used to scan, recognize and attach to the host cell." [PHI:AT, PHI:IM, PHI:SC] comment: Fibers typically bind to particular LPS, polysaccharide or protein receptors on the cell surface is_obsolete: true replaced_by: phi:0000175 [Term] id: phi:0000090 name: prophage def: "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated island." [SO:0001006] xref: SO:0001006 is_a: phi:0000235 ! genomic island [Term] id: phi:0000091 name: phage concatemer def: "Tandem array or branched complex of DNA bacteriophage genomes generated in the bacterial host cytoplasm during phage replication and which is the substrate for DNA packaging." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000172 ! SO term [Term] id: phi:0000092 name: cryptic prophage def: "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." [SO:0001007] synonym: "defective prophage" RELATED [SO:0001007] xref: SO:0001007 is_a: phi:0000090 ! prophage [Term] id: phi:0000093 name: phage related bacterial component def: "A bacterial component to be added in GO that had to do with the phage life cycle." [PHI:AT, PHI:IM, PHI:SC] comment: This is a temporary term. relationship: part_of phi:0000257 ! bacteriophage [Term] id: phi:0000094 name: phage receptor def: "A bacterial component located on the cell surface and which is specifically recognized and used by the phage for adsorption." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000093 ! phage related bacterial component [Term] id: phi:0000095 name: phage tail fiber minor protein def: "Minor protein component of the phage tail fiber." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000175 ! capsid tail fiber [Term] id: phi:0000096 name: phage tail fiber major protein def: "Major protein component of the phage tail fiber." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000175 ! capsid tail fiber [Term] id: phi:0000097 name: phage activity def: "Molecular functions of phage components." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000257 ! bacteriophage [Term] id: phi:0000098 name: anti holin activity def: "Inhibits holin activity." [PHI:AT, PHI:IM, PHI:SC] comment: Some anti-holins differ from their cognate holins by only a few terminal amino acids. is_a: phi:0000097 ! phage activity [Term] id: phi:0000099 name: holin activity def: "Catalysis of the temporally regulated formation of a transmembrane protein hole that directly or indirectly allows murein hydrolyases to access their cell wall substrate." [PHI:AT, PHI:IM, PHI:SC] xref: GO:0034290 xref: XX: is_a: phi:0000097 ! phage activity [Term] id: phi:0000100 name: anti repressor activity def: "Inhibition, inactivation or degradation of a transcriptional repressor." [PHI:AT, PHI:IM, PHI:SC] comment: An activity as that of the lambda Cro repressor that has opposing effects on gene expression than another repressor, here lambda CI by operator binding is NOT considered an anti-repressor. is_a: phi:0000097 ! phage activity [Term] id: phi:0000101 name: ATPase activity def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate. May or may not be coupled to another reaction." [GO:0016887] xref: GO:0016887 is_a: phi:0000097 ! phage activity [Term] id: phi:0000102 name: CI/Cro transcriptional repressor activity def: "Transcriptional repressor activity involved in switching between lytic and lysogenic transcription." [PHI:AT, PHI:IM, PHI:SC] is_obsolete: true [Term] id: phi:0000103 name: endolysin activity def: "Cell wall degradation enzyme synthesized by a phage during its lytic cycle and responsible for host cell lysis." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] is_a: phi:0000097 ! phage activity [Term] id: phi:0000104 name: exolysin activity def: "Cell wall hydrolase activity associated with phage structures (usually the tail or the base plate) and which helps DNA translocation by damaging the host cell envelope after adsorption." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000097 ! phage activity [Term] id: phi:0000105 name: peptidase activity def: "Catalysis of the hydrolysis of peptide bonds." [GO:0008233] xref: GO:0008233 is_a: phi:0000097 ! phage activity [Term] id: phi:0000106 name: coat chaperon activity def: "Chaperon activity required for the assembly of the phage coat." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000181 ! capsid protein chaperon activity [Term] id: phi:0000107 name: tail chaperon activity def: "Chaperon activity required for the assembly of the phage tail." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000181 ! capsid protein chaperon activity [Term] id: phi:0000108 name: tail fiber chaperon activity def: "Chaperon activity required for the assembly of the phage fibers." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000181 ! capsid protein chaperon activity [Term] id: phi:0000109 name: DNA binding activity def: "Interacting selectively with DNA (deoxyribonucleic acid)." [GO:0003677] xref: GO:0003677 is_a: phi:0000097 ! phage activity [Term] id: phi:0000110 name: single stranded DNA binding activity def: "Interacting selectively with single stranded DNA (deoxyribonucleic acid)." [GO:0003697] xref: GO:0003697 is_a: phi:0000109 ! DNA binding activity [Term] id: phi:0000111 name: double stranded DNA binding activity def: "Interacting selectively with double stranded DNA (deoxyribonucleic acid)." [GO:0003690] xref: GO:0003690 is_a: phi:0000109 ! DNA binding activity [Term] id: phi:0000112 name: DNA topoisomerase activity def: "Catalysis of a topological transformation in double-stranded DNA by a covalent or non-covalent mechanism." [GO:0003916] xref: GO:0003916 is_a: phi:0000097 ! phage activity [Term] id: phi:0000113 name: DNA polymerase processivity factor activity def: "An accessory subunit of DNA polymerase that acts to increase the processivity of polymerization." [GO:0030337] xref: GO:0030337 is_a: phi:0000097 ! phage activity [Term] id: phi:0000114 name: DNA helicase activity def: "Catalysis of the hydrolysis of ATP to unwind the DNA helix at the replication fork, allowing the resulting single strands to be copied." [GO:0003678] xref: GO:0003678 is_a: phi:0000097 ! phage activity [Term] id: phi:0000115 name: DNA directed DNA polymerase activity def: "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from DNA replication." [GO:0003887] xref: GO:0003887 is_a: phi:0000097 ! phage activity [Term] id: phi:0000116 name: DNA directed RNA polymerase activity def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GO:0003899] xref: GO:0003899 is_a: phi:0000097 ! phage activity [Term] id: phi:0000117 name: DNA methyltransferase activity def: "Catalysis of the transfer of a methyl group to a DNA molecule." [GO:0009008] xref: GO:0009008 is_a: phi:0000097 ! phage activity [Term] id: phi:0000118 name: DNA primase activity def: "Catalysis of the synthesis of short RNA primers for the Okazaki fragments on both DNA template strands at the replication fork. A DNA-directed RNA polymerase that forms a complex with alpha DNA polymerase." [GO:0003896] xref: GO:0003896 is_a: phi:0000097 ! phage activity [Term] id: phi:0000119 name: DNA exonuclease activity def: "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end." [GO:0004527] xref: GO:0004527 is_a: phi:0000097 ! phage activity [Term] id: phi:0000120 name: DNA 3'-5' exonuclease activity def: "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end." [GO:0008408] xref: GO:0008408 is_a: phi:0000119 ! DNA exonuclease activity [Term] id: phi:0000121 name: DNA 5'-3' exonuclease activity def: "Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end." [GO:0008409] xref: GO:0008409 is_a: phi:0000119 ! DNA exonuclease activity [Term] id: phi:0000122 name: excisionase activity def: "DNA-binding activity that activates excision by a serine or tyrosine based integrase, of a DNA segment from another, usually larger, DNA molecule such as a chromosome." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000097 ! phage activity [Term] id: phi:0000123 name: prohead protease activity def: "Protease activity involved in head maturation. Usually degrades the scaffolding or remove portions of coat or portal proteins in an assembly dependent manner. May be part_of the scaffolding protein or encoded by the same gene." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000105 ! peptidase activity [Term] id: phi:0000124 name: cell-wall peptidase activity def: "Protease activity involved in breaking down of the cell wall as part of the phage lysis process." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000105 ! peptidase activity [Term] id: phi:0000125 name: phage terminase activity def: "Catalysis of DNA cleavage involved in the packaging of DNA into phage heads." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000126 ! DNA endonuclease activity [Term] id: phi:0000126 name: DNA endonuclease activity def: "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GO:0004519] xref: GO:0004519 is_a: phi:0000097 ! phage activity [Term] id: phi:0000127 name: transcriptional repressor activity def: "Any transcription regulator activity that prevents or downregulates transcription." [GO:0016564] xref: GO:0016564 is_a: phi:0000184 ! transcription factor activity [Term] id: phi:0000128 name: translation repressor activity def: "Antagonizes ribosome-mediated translation of mRNA into a polypeptide." [GO:0030371] xref: GO:0030371 is_a: phi:0000097 ! phage activity [Term] id: phi:0000129 name: DNA recombination def: "The processes by which a new genotype is formed by reassortment of genes resulting in gene combinations. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur between chromosome and plasmid or those and horizontally acquired DNA introduced in the cell via genetic transformation, conjugation or transduction." [GO:0006310] comment: This definition differs from that in GO. xref: GO:0006310 is_a: phi:0000141 ! recombination process [Term] id: phi:0000130 name: homologous DNA recombination def: "The formation and repair of double strand breaks through a double Holliday junction intermediate that results in the equal exchange of genetic material between a pair of homologous DNA fragments (chromosome, plasmid, phage)." [GO:0007131] comment: This definition differs from that in GO. xref: GO:0007131 is_a: phi:0000129 ! DNA recombination [Term] id: phi:0000131 name: site-specific DNA recombination def: "Recombination between two DNA sites begins by the recognition and binding of these sites by the recombinase protein. This is followed by the synapsis i.e. bringing the sites together to form the synaptic complex. It is within this synaptic complex that the strand exchange takes place, as the DNA is cleaved and rejoined by controlled transesterification reactions. During strand exchange, the DNA cut at fixed points within crossover region of the site releases a deoxyribose hydroxyl group, while recombinase protein forms a transient covalent bond to a DNA backbone phosphate. This phosphodiester bond between hydroxyl group of the nucleophilic, serine or tyrosine residue conserves the energy that was expended in cleaving the DNA. Energy stored in this bond is subsequently used for the rejoining of the DNA to the corresponding deoxyribose hydroxyl group on the other site. The entire process therefore goes through without the need for external energy rich cofactors such as ATP." [XX:] xref: XX: "http://en.wikipedia.org/wiki/Site-specific_recombination" is_a: phi:0000129 ! DNA recombination [Term] id: phi:0000132 name: site-specific DNA integration def: "The process by which a segment of DNA is incorporated into another by a site-specific recombination event." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000131 ! site-specific DNA recombination [Term] id: phi:0000133 name: DNA integration def: "The process by which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome." [GO:0015074] xref: GO:0015074 is_a: phi:0000129 ! DNA recombination [Term] id: phi:0000134 name: site-specific DNA excision def: "The process by which a segment of DNA is separated from another by a site-specific recombination event. The process occurs during prophage excision, the resolution of a cointegrate DNA molecule resulting from a process of replicative transposition into finished transposition products, the resolution of multimeric plasmids into monomers and the separation of entangled circular bacterial chromosomes prior to cell division." [PHI:AT] is_a: phi:0000131 ! site-specific DNA recombination [Term] id: phi:0000135 name: replicative transpositional recombination def: "A process of transpositional recombination, which involves the replication of the transposed DNA segment." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000136 ! transpositional DNA recombination [Term] id: phi:0000136 name: transpositional DNA recombination def: "A process that moves a DNA region from one to another location in a genome via a DNA intermediate." [GO:0006313] comment: Synonyms recently associated with the GO term do not apply here. These are in fact much too specific. xref: GO:0006313 is_a: phi:0000129 ! DNA recombination [Term] id: phi:0000137 name: conservative transpositional recombination def: "A process of transpositional recombination, which does not involve the replication of the transposed DNA segment. This process can however lead to the duplication of the transposed DNA segment by recombinational repair." [PHI:AL, PHI:AT, PHI:GC] is_a: phi:0000136 ! transpositional DNA recombination [Term] id: phi:0000138 name: recombinational repair def: "The repair of damaged DNA that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GO:0000725] xref: GO:0000725 is_a: phi:0000129 ! DNA recombination [Term] id: phi:0000139 name: telomere resolution def: "A process involving DNA breakage and reunion that converts replicated telomeres into covalently closed hairpin telomeres on the ends of linear DNA molecules." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000053 ! establishment as a linear plasmid prophage [Term] id: phi:0000140 name: recombinase activity def: "Activities related to bacteria, phage, plasmid and transposon recombination." [PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] relationship: part_of phi:0000097 ! phage activity relationship: part_of phi:0000314 ! MeGO [Term] id: phi:0000141 name: recombination process def: "Processes related to bacteria, phage, plasmid and transposon recombination." [PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] relationship: part_of phi:0000314 ! MeGO [Term] id: phi:0000142 name: DNA breakage and rejoining enzymes def: "Catalysis of cleavage and formation of new phosphodiester bonds between a pair of DNA target sequences." [PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] is_a: phi:0000140 ! recombinase activity [Term] id: phi:0000143 name: tyrosine-based recombinase activity def: "Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequence by cleavage of one DNA strand and formation of a covalent phosphotyrosyl enzyme intermediate. Depending on the enzyme families, this bond can be a 3' or 5',phosphotyrosyl, liberating a 5' or a 3'OH nucleophile involved in the reunion part of the reaction." [GO:0009037] comment: Def different form existing GO. xref: GO:0009037 is_a: phi:0000142 ! DNA breakage and rejoining enzymes [Term] id: phi:0000144 name: serine-based recombinase activity 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:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM, XX: "http://en.wikipedia.org/wiki/Site-specific_recombination"] xref: XX: "http://en.wikipedia.org/wiki/Site-specific_recombination" is_a: phi:0000142 ! DNA breakage and rejoining enzymes [Term] id: phi:0000145 name: tyrosine based integrase activity def: "Tyrosine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another." [GO:0009037] comment: Definition differs from GO:0009037 xref: GO:0009037 is_obsolete: true consider: phi:0000132 consider: phi:0000143 [Term] id: phi:0000146 name: tyrosine based resolvase activity def: "Tyrosine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two." [PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] is_obsolete: true consider: phi:0000134 consider: phi:0000143 [Term] id: phi:0000147 name: tyrosine based topoisomerase IB activity def: "Catalysis of a topological transformation in DNA through the cleavage of one DNA strand and formation of a covalent 3-prime-phosphotyrosyl enzyme intermediate to allow passage of another strand; changes the linking number by +1 per catalytic cycle." [PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] is_a: phi:0000143 ! tyrosine-based recombinase activity [Term] id: phi:0000148 name: protelomerase activity def: "Catalysis of a site-specific breakage and reunion reaction that generates two hairpin telomeres from a replicated telomere substrate. Occurs via a two-step transesterification with a protein-DNA intermediate similar to that used by topoisomerases and site-specific recombinases." [GO:0043336, PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] xref: GO:0043336 xref: PHI:AT xref: PMID:11804598 is_a: phi:0000143 ! tyrosine-based recombinase activity [Term] id: phi:0000149 name: tyrosine-based transposase activity def: "Tyrosine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome." [PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] is_obsolete: true [Term] id: phi:0000150 name: serine based integrase activity def: "Serine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another." [PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] is_obsolete: true consider: phi:0000132 consider: phi:0000144 [Term] id: phi:0000151 name: serine based resolvase activity def: "Serine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two." [PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] is_obsolete: true consider: phi:0000134 consider: phi:0000144 [Term] id: phi:0000152 name: serine based transposase activity def: "Serine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome." [PHI:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] is_obsolete: true [Term] id: phi:0000153 name: DDE-based recombinase activity 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:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] is_a: phi:0000142 ! DNA breakage and rejoining enzymes relationship: part_of phi:0000157 ! transpososome [Term] id: phi:0000154 name: recombination component def: "Any multiprotein recombinogenic complex containing DNA, recombinase and accessory proteins." [PHI:AT] relationship: part_of phi:0000314 ! MeGO [Term] id: phi:0000155 name: intasome def: "Any multiprotein recombinogenic complex containing DNA, site-specific tyrosine or serine based integrase and accessory proteins and involved in the intgeration or ecision of DNA fragments." [PHI:AT] is_a: phi:0000061 ! phage component is_a: phi:0000154 ! recombination component [Term] id: phi:0000156 name: relaxosome def: "A multi-component enzymatic machine including a relaxase, which mediates cleavage and initiation of rolling circle replication on a doubles stranded DNA molecule during conjugation, phage replication and transposition." [PHI:AT] is_a: phi:0000154 ! recombination component is_a: phi:0000258 ! plasmid component [Term] id: phi:0000157 name: transpososome def: "A multi-component enzymatic machine, which mediates DNA transposition; it Includes the DDE (DDD?) transposase and accessory proteins including nucleoid associated proteins such as HU or IHF." [PHI:AT] is_a: phi:0000061 ! phage component is_a: phi:0000154 ! recombination component is_a: phi:0000258 ! plasmid component [Term] id: phi:0000158 name: resolvasome def: "A multi-component enzymatic machine including a tyrosine or serine based resolvase, which mediates resolution of chromosome dimers and replicon fusions." [PHI:AT] is_a: phi:0000258 ! plasmid component [Term] id: phi:0000159 name: Y2 transposase activity 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:AL, PHI:AT, PHI:GC, PHI:GH, PHI:IM] is_a: phi:0000142 ! DNA breakage and rejoining enzymes [Term] id: phi:0000160 name: rolling circle transposition def: "Movement of a DNA segment form one to another location in a genome by a mechanism that resembles rolling-circle replication carried out by many bacterial plasmids and phage." [PHI:A, PHI:IM, PHI:SC] is_a: phi:0000136 ! transpositional DNA recombination [Term] id: phi:0000161 name: head/capsid def: "The protein coat that surrounds the infective nucleic acid in phage particles. It comprises numerous regularly arranged subunits." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000061 ! phage component [Term] id: phi:0000162 name: inhibitor of RNA polymerase def: "Activity that represses RNA polymerase activity." [PHI:AT, PHI:IM, PHI:SC] comment: Typically expressed by phages to turn off host egne expression. is_a: phi:0000097 ! phage activity [Term] id: phi:0000163 name: inhibitor of RecBCD nuclease def: "Activity that inhibits DNA degradation by the phage host protein complex RecBCD." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000097 ! phage activity [Term] id: phi:0000164 name: plasmid mediated regulation of host gene expression def: "Any process that modulates host gene expression as a result of phage gene expression." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000335 ! phage mediated modulation of host functions is_a: phi:0000336 ! plasmid mediated modulation of host functions [Term] id: phi:0000165 name: plasmid mediated positive regulation of host gene expression def: "Any process that up-regulates host gene expression as a result of phage gene expression." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000164 ! plasmid mediated regulation of host gene expression [Term] id: phi:0000166 name: plasmid mediated negative regulation of host gene expression def: "Any process that down-regulates host gene expression as a result of phage gene expression." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000164 ! plasmid mediated regulation of host gene expression [Term] id: phi:0000167 name: inhibitor of FtsH protease activity def: "Activity that inhibits protein breakdown by the phage host protease FtsH." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000097 ! phage activity [Term] id: phi:0000168 name: modulator of nucleoid associated protein HNS def: "Activity that modulates the nucleoid associated protein/DNA chaperon HNS." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000097 ! phage activity [Term] id: phi:0000169 name: inhibitor-of deoxyguanosine triphospho hydrolase def: "Activity that decreases deoxyguanosine triphospho-hydrolase activity." [PHI:AT, PHI:IM, PHI:SC] comment: Typically expressed by phages to turn off host egne expression. is_a: phi:0000097 ! phage activity [Term] id: phi:0000170 name: plasmid mediated modulation of host protein activity def: "Any process that activates or represses the activity of a host protein." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000335 ! phage mediated modulation of host functions is_a: phi:0000336 ! plasmid mediated modulation of host functions [Term] id: phi:0000171 name: host cell killing activity def: "Activity that provokes host cell kiling independently of any other phage lytic or plasmid activity." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000097 ! phage activity is_a: phi:0000325 ! plasmid activity [Term] id: phi:0000172 name: SO term def: "To be (or already) transferred to SO" [PHI:AT, PHI:IM, PHI:SC] [Term] id: phi:0000173 name: major capsid structural protein def: "Protein that is a major component of the phage particle." [PHI:AT] xref: GO:0042001 is_a: phi:0000187 ! capsid structural protein [Term] id: phi:0000174 name: capsid tail def: "Component of the tailed phages i.e. the 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." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000061 ! phage component [Term] id: phi:0000175 name: capsid tail fiber def: "Tail fibers are appended at the phage tail tip and serve to scan, recognize and attach to the cognate receptor on bacterial host cell surface. Tail fibers typically bind to particular LPS, polysaccharide, protein or other components of the cell surface." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000061 ! phage component [Term] id: phi:0000176 name: phage head/capsid fiber def: "Fiber structures, which decorate the head of some phages." [PHI:AT, PHI:IM, PHI:SC] relationship: part_of phi:0000064 ! phage head/capsid protein [Term] id: phi:0000177 name: prohead/procapsid def: "The precursor protein complex that will evolve into the coat that surrounds the infective nucleic acid in phage particles. It builds up around the scaffolding, which assembles on top of the portal complex and is later degraded or leaves the prohead without degradation to be replaced by DNA." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000061 ! phage component [Term] id: phi:0000178 name: phage minor tail protein def: "Protein component found in low number of copies in the tail of phage particles of the types myoviridae and siphoviridae." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000081 ! phage tail protein [Term] id: phi:0000179 name: phage head/capsid internal protein def: "Phage head/capsid protein component located inside the finished head." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000180 name: inhibitor of RecA protease activity def: "Activity that inhibits the protease activity of the host RecA protein." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000097 ! phage activity [Term] id: phi:0000181 name: capsid protein chaperon activity def: "Chaperon activity required for the assembly of phage components." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000097 ! phage activity [Term] id: phi:0000182 name: DNA excision def: "The process by which a segment of DNA is separated from another, usually larger, DNA molecule such as a chromosome." [PHI:AT] synonym: "DNA resolution" EXACT [GO:0007131] xref: GO:0007131 is_a: phi:0000129 ! DNA recombination [Term] id: phi:0000183 name: RNA directed RNA polymerase activity def: "Catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template." [GO:0003968] xref: GO:0003899 is_a: phi:0000097 ! phage activity [Term] id: phi:0000184 name: transcription factor activity def: "Any transcription regulator activity that prevents or downregulates transcription." [GO:0003700] xref: GO:0003700 is_a: phi:0000109 ! DNA binding activity [Term] id: phi:0000185 name: phage head/capsid minor protein def: "Protein component found in low number of copies in the shell/head/capsid of phage particles." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000186 name: minor capsid structural protein def: "Protein that is a minor component of the phage particle." [PHI:AT] xref: GO:0042001 is_a: phi:0000187 ! capsid structural protein [Term] id: phi:0000187 name: capsid structural protein def: "Protein component of the phage virion." [PHI:AT] xref: GO:0042001 is_a: phi:0000061 ! phage component [Term] id: phi:0000188 name: shiga toxin activity def: "Usually taken in with food or water contaminated with bacteria that express it, the Shiga toxin is composed of two subunits, A and B. It acts on the lining of the blood vessels, the vascular endothelium. After it enters the cell, the toxin inhibits the ribosomes, leading to cell death." [PHI:AT] xref: CBWInfo:Verotox.html#0003 is_a: phi:0000321 ! intracellular AB toxin activity [Term] id: phi:0000189 name: shiga toxin subunit A def: "One of the two subunits. The A subunit of the Shiga toxin is an N-glycosidase that modifies the RNA component of the ribosome to inactivate it and so brings a halt to protein synthesis leading to cell death." [PHI:AT] xref: CBWInfo:Verotox.html#0003 relationship: part_of phi:0000188 ! shiga toxin activity [Term] id: phi:0000190 name: shiga toxin subunit B def: "Shiga toxin subunit B binds to a component of the cell membrane known as Gb3 allowing the complex AB toxin to enter the cell." [PHI:AT] xref: CBWInfo:Verotox.html#0003 relationship: part_of phi:0000188 ! shiga toxin activity [Term] id: phi:0000191 name: unclassified def: "Yet..." [PHI:AT, PHI:IM, PHI:MS, PHI:SC] [Term] id: phi:0000192 name: thioredoxin def: "Thioredoxins are proteins that act as antioxidants by facilitating the reduction of other proteins by cysteine thiol-disulfide exchange. Thioredoxins are found in nearly all known organisms and are essential for life in mammals. Thioredoxin is a co-factor of some phage DNA-polymerases." [PHI:AT] synonym: "thiol-disulfide exchange intermediate activity " EXACT [GO:0030508] xref: GO:0030508 xref: Wikipedia:thioredoxin is_a: phi:0000097 ! phage activity [Term] id: phi:0000193 name: restriction alleviation def: "Any process that results into the inhibition of a host restriction." [PHI:AT] is_a: phi:0000335 ! phage mediated modulation of host functions is_a: phi:0000336 ! plasmid mediated modulation of host functions [Term] id: phi:0000194 name: plasmid maintenance def: "The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division." [GO:0006276] xref: GO:n0006276 is_a: phi:0000259 ! plasmid process relationship: part_of phi:0000053 ! establishment as a linear plasmid prophage relationship: part_of phi:0000054 ! establishment as a circular plasmid prophage [Term] id: phi:0000195 name: phage translation repressor activity def: "Phage encoded protein that antagonizes ribosome-mediated translation of mRNA into a polypeptide." [PHI:AT] xref: GO:0030371 is_a: phi:0000128 ! translation repressor activity [Term] id: phi:0000196 name: plasmid copy number control def: "Any process that controls the number of copies of a plasmid per host cell." [PHI:AT] relationship: part_of phi:0000053 ! establishment as a linear plasmid prophage relationship: part_of phi:0000054 ! establishment as a circular plasmid prophage relationship: part_of phi:0000268 ! plasmid vegetative DNA replication [Term] id: phi:0000197 name: virulent phage def: "Phage which upon infection has no other choice than entering the lytic cycle." [PHI:AT] relationship: part_of phi:0000314 ! MeGO [Term] id: phi:0000198 name: temperate phage def: "Phage which upon infection has the choice between going lytic or lysogenic." [PHI:AT] comment: Needs revision xref: Wikipedia:thioredoxin relationship: part_of phi:0000314 ! MeGO [Term] id: phi:0000199 name: hyaluronidase activity def: "Activity resulting in the degradation of hyaluronic acid." [PHI:AT] xref: KEGG:EC 3.2.1.35 xref: Wikipedia:http\://en.wikipedia.org/wiki/Hyaluronidase is_a: phi:0000097 ! phage activity is_a: phi:0000262 ! toxin [Term] id: phi:0000200 name: leukocidin cativity def: "Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes, and macrophages." [PHI:AT] comment: Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes and macrophages. xref: PMID:16794307 is_a: phi:0000097 ! phage activity is_a: phi:0000262 ! toxin [Term] id: phi:0000201 name: superantigen activity def: "Family of potent immunostimulators able to simultaneously bind to the MHC class 2 molecules and the T cell receptor bacterial, resulting in alpha-beta T cell activation." [PHI:AT] xref: Wikipedia:http\://en.wikipedia.org/wiki/Superantigen is_a: phi:0000097 ! phage activity is_a: phi:0000262 ! toxin [Term] id: phi:0000202 name: staphylokinase def: "Staphylokinases (SAK) are enzymes, which activate plasminogen, which in turn can degrade various host proteins during infection." [PHI:AT] xref: Wikipedia:http\://en.wikipedia.org/wiki/Staphylokinase is_a: phi:0000097 ! phage activity is_a: phi:0000262 ! toxin [Term] id: phi:0000203 name: streptodornase def: "Streptodornases are DNases secreted by S. pyogenes and which protect the bacteria from being trapped in neutrophil extracellular traps (NETs) by digesting the NET's web of DNA, to which are bound neutrophil serine proteases that can kill the bacteria." [PHI:AT] synonym: "streptokinase" EXACT [] xref: Wikipedia:http\://en.wikipedia.org/wiki/Streptococcus_pyogenes is_a: phi:0000097 ! phage activity is_a: phi:0000262 ! toxin [Term] id: phi:0000204 name: exfoliative toxin A def: "Exfoliative toxin A is a Staphylococcus aureus protease activity, which causes peeling of the skin observed in staphylococcal scalded-skin syndrome." [PHI:AT] xref: Wikipedia:http\://en.wikipedia.org/wiki/Staphylococcus_aureus is_a: phi:0000097 ! phage activity is_a: phi:0000262 ! toxin [Term] id: phi:0000205 name: capsid neck protein def: "Protein component of a constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae)." [PHI:AT, PHI:HWA] is_a: phi:0000187 ! capsid structural protein relationship: part_of phi:0000309 ! capsid neck [Term] id: phi:0000206 name: capsid collar protein def: "Protein component of a small disk located below some phage heads." [PHI:AT, PHI:HWA] is_a: phi:0000187 ! capsid structural protein relationship: part_of phi:0000308 ! capsid collar [Term] id: phi:0000207 name: capsid collar fiber protein def: "Protein component of the fibers attached to the collar structure of some phages." [PHI:AT, PHI:HWA] is_a: phi:0000187 ! capsid structural protein relationship: part_of phi:0000307 ! capsid collar fiber [Term] id: phi:0000208 name: phage spike def: "Short stuctures (generally 30 nm long) at the tail tip of some phages and used for attachment." [PHI:AT, PHI:HWA] is_a: phi:0000064 ! phage head/capsid protein [Term] id: phi:0000209 name: pathogenicity island def: "Genomic island which carries genes encoding proteins related to pathogenicity such as attachment, invasion of the host, other virulence factors, toxins, etc." [SO:0000773] comment: SO definition: Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species. synonym: "pathogenic island" EXACT [] xref: SO:0000773 is_a: phi:0000235 ! genomic island [Term] id: phi:0000210 name: phage capsid triangulation number def: "Number of triangles into which an icosahedral virus capsid can be subdivided." [PHI:AT, PHI:HWA] is_a: phi:0000191 ! unclassified [Term] id: phi:0000211 name: attachment site def: "Short DNA sequence, which is a target region for site-specific integration and/or excision and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase." [PHI:AT, PHI:GC] synonym: "site specific recombination target region " EXACT [SO:0000342] xref: SO:0000342 is_a: phi:0000172 ! SO term [Term] id: phi:0000212 name: attB site def: "Integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:0000943] xref: SO:0000943 is_a: phi:0000211 ! attachment site [Term] id: phi:0000213 name: attP site def: "Attachment site located on the on the phage genome." [PHI:AT, PHI:GC, SO:0000942] xref: SO:0000942 is_a: phi:0000211 ! attachment site relationship: part_of phi:0000091 ! phage concatemer [Term] id: phi:0000214 name: attL site def: "Attachment site located on the bacterial chromosome at the left of a prophage region and which is used for prophage site-specific excision." [PHI:AT, PHI:GC, SO:0000944] synonym: "attBP'" EXACT [PHI:AT] xref: SO:0000944 is_a: phi:0000211 ! attachment site relationship: part_of phi:0000090 ! prophage relationship: part_of phi:0000311 ! transposable prophage [Term] id: phi:0000215 name: attR site def: "A region that results from recombination between attP site and attB site, composed of the 5' portion of attP site and the 3' portion of attB site." [SO:0000945] synonym: "attPB'" EXACT [PHI:AT] xref: SO:0000945 is_a: phi:0000211 ! attachment site relationship: part_of phi:0000090 ! prophage relationship: part_of phi:0000311 ! transposable prophage [Term] id: phi:0000216 name: attCTn site def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [SO:0001043] xref: SO:0001043 is_a: phi:0000211 ! attachment site relationship: part_of phi:0000242 ! conjugative transposon relationship: part_of phi:0000243 ! defective conjugative transposon [Term] id: phi:0000217 name: attI site def: "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:0000367] xref: SO:0000367 is_a: phi:0000211 ! attachment site relationship: part_of phi:0000237 ! integron platform [Term] id: phi:0000218 name: attC site def: "Attachment site located on a gene cassette (sensu integron) and used for site-specific integration in an integron." [PHI:AT, PHI:GC] comment: Exists in SO but I prefer my definition, because SO's does not mention the cassette. synonym: "59 base pairs sequence" EXACT [] xref: SO:0000950 is_a: phi:0000211 ! attachment site relationship: part_of phi:0000238 ! gene cassette (sensu integrons) [Term] id: phi:0000219 name: resolution site def: "Target region for site-specific recombination leading to the resolution of a chromosome or plasmid dimer or a cointegrate resulting from replicative transposition." [PHI:AT, PHI:GC, SO:0000947] synonym: "cer site" RELATED [] synonym: "dif site" RELATED [] synonym: "loxP site" RELATED [] synonym: "res site" EXACT [] xref: SO:0000947 relationship: part_of phi:0000240 ! unitary transposon relationship: part_of phi:0000246 ! cointegrate [Term] id: phi:0000220 name: transposon end def: "Region located at either end of an integrated transposon; it includes binding sites for the cognate transposase enzyme, which nicks the transposon at its last base pair." [PHI:AT, PHI:GC] is_a: phi:0000302 ! inverted repeat [Term] id: phi:0000221 name: IRLI def: "The left transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence." [PHI:AT, PHI:GC] is_a: phi:0000220 ! transposon end relationship: part_of phi:0000241 ! composite transposon [Term] id: phi:0000222 name: IRL def: "The left end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRR." [PHI:AT, PHI:GC] comment: In the case of transposable (pro)phages it is called attL and includes several subsites, attL1, attL2 and attL3. synonym: "inverted repeat" RELATED [SO:0000294] is_a: phi:0000220 ! transposon end relationship: part_of phi:0000240 ! unitary transposon relationship: part_of phi:0000245 ! insertion sequence [Term] id: phi:0000223 name: IRR def: "The right end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRL." [PHI:AT, PHI:GC] comment: In the case of transposable (pro)phages it is called attR and includes several subsites, attR1, attR2 and attR3. synonym: "inverted repeat" RELATED [SO:0000294] is_a: phi:0000220 ! transposon end relationship: part_of phi:0000240 ! unitary transposon relationship: part_of phi:0000245 ! insertion sequence [Term] id: phi:0000224 name: IRLO def: "The left transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence." [PHI:AT, PHI:GC] is_a: phi:0000220 ! transposon end relationship: part_of phi:0000241 ! composite transposon [Term] id: phi:0000225 name: IRRO def: "The right transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence." [PHI:AT, PHI:GC] is_a: phi:0000220 ! transposon end relationship: part_of phi:0000241 ! composite transposon [Term] id: phi:0000226 name: IRRI def: "The right transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence." [PHI:AT, PHI:GC] is_a: phi:0000220 ! transposon end relationship: part_of phi:0000241 ! composite transposon [Term] id: phi:0000227 name: type I secretion membrane fusion protein activity def: "To be added." [PHI:AT] relationship: part_of phi:0000265 ! type I protein secretion system complex [Term] id: phi:0000228 name: inversion site def: "A region specifically recognized by a recombinase, which inverts the region flanked by a pair of sites." [SO:0000948] synonym: "ftr site" RELATED [] synonym: "inv site" EXACT [] xref: SO:0000948 is_a: phi:0000302 ! inverted repeat [Term] id: phi:0000229 name: IRLinv site def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [PHI:AT, PHI:GC] is_a: phi:0000228 ! inversion site [Term] id: phi:0000230 name: IRRinv site def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [SO:0001047] xref: SO:0001047 is_a: phi:0000228 ! inversion site [Term] id: phi:0000231 name: pac site def: "DNA region recognized by the terminase small subunit as the first step in synapsis of the double stranded DNA phage full head packaging complex." [PHI:AT, PHI:GC] relationship: part_of phi:0000090 ! prophage relationship: part_of phi:0000091 ! phage concatemer relationship: part_of phi:0000311 ! transposable prophage [Term] id: phi:0000232 name: cos site def: "DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex that generates double stranded DNA phage genomes with sticky ends." [PHI:AT, PHI:GC] relationship: part_of phi:0000090 ! prophage relationship: part_of phi:0000091 ! phage concatemer [Term] id: phi:0000233 name: 3'extended cos site def: "DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex that generates phage genomes with 3'-extended protruding sticky ends." [PHI:AT] is_a: phi:0000232 ! cos site [Term] id: phi:0000234 name: 5'extended cos site def: "DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex, which generates phage genomes with 5'-extended protruding sticky ends." [PHI:AT] is_a: phi:0000232 ! cos site [Term] id: phi:0000235 name: genomic island def: "Chromosomal DNA region that has features suggesting a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [SO:0000772] comment: revise SO definition. xref: SO:0000772 is_a: phi:0000300 ! integrated mobile genetic element [Term] id: phi:0000236 name: integron def: "A DNA region encoding an integrase, which acts at an adjacent attI site to insert a gene cassette with an attC site through attI-attC recombination. The integron also carries a promoter that controls expression of the gene on the cassette." [SO:0000365] comment: A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. DEF in SO not really complete. xref: SO:0000365 is_a: phi:0000235 ! genomic island [Term] id: phi:0000237 name: integron platform def: "DNA region that contains a tyrosine based recombinase gene, a primary recombination site attI and a strong outward promoter Pc." [PHI:AT, PHI:GC] relationship: part_of phi:0000236 ! integron [Term] id: phi:0000238 name: gene cassette (sensu integrons) def: "Discrete DNA region which can exist either as discrete circular region with an attC site, or integrated after attI by attC recombination, downstream of the integron Pc promoter, which controls the expression of its usually single encoded gene." [PHI:AT, PHI:GC] relationship: part_of phi:0000236 ! integron [Term] id: phi:0000239 name: transposable element def: "Transposable DNA region that encodes mobility and its regulatory functions and other phenotypic traits such as antibiotic resistance, catabolic enzymes etc." [SO:0000101] comment: SO definition: A transposon or insertion sequence. An element that can insert in a variety of DNA sequence. xref: SO:0000101 is_a: phi:0000235 ! genomic island [Term] id: phi:0000240 name: unitary transposon def: "Transposon in which mobility genes and phenotypic genes are surrounded by imperfect inverted repeats." [PHI:AT, PHI:GC] is_a: phi:0000301 ! DNA transposon [Term] id: phi:0000241 name: composite transposon def: "Transposon composed of two identical IS sequences in the same or opposite orientation flanking a region containing the phenotypic genes." [PHI:AT, PHI:GC] is_a: phi:0000301 ! DNA transposon [Term] id: phi:0000242 name: conjugative transposon def: "A genomic island which contains genes for integration/excision and intercellular transfer by conjugation." [SO:0000371] comment: Diiferes fro OS def (A transposon that encodes function required for conjugation). synonym: "CTn" EXACT [] synonym: "ICE" EXACT [] xref: SO:0000371 is_a: phi:0000301 ! DNA transposon [Term] id: phi:0000243 name: defective conjugative transposon def: "A genomic island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [SO:0001049] xref: SO:0001049 is_a: phi:0000242 ! conjugative transposon [Term] id: phi:0000244 name: transfer agent def: "DNA region that contains genes for phage head and tail formation but no replication genes. The produced heads only encapsidate host DNA, generating defective generalized transducing particles." [PHI:AT, PHI:GC] is_a: phi:0000092 ! cryptic prophage [Term] id: phi:0000245 name: insertion sequence def: "DNA region flanked by inverted repeats and containing genes coding for transposition enzymes and regulators of transposition." [PHI:AT, PHI:GC, SO:0000973] xref: SO:0000973 is_a: phi:0000301 ! DNA transposon [Term] id: phi:0000246 name: cointegrate def: "A DNA region consisting of two fused replicons/plasmids resulting from a replicative transposition event." [PHI:AT, PHI:GC] comment: SO definition for cointegrate replicon: A MGE region consisting of two fused replicons/plasmids resulting from a replicative transposition event. synonym: "cointegrate replicon" RELATED [SO:0001045] xref: SO:0001045 is_a: phi:0000172 ! SO term [Term] id: phi:0000247 name: generalized transduction 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:AT] comment: This definition differs from that in GO:0009293. xref: GO:0007131 xref: Wiki:http\://en.wikipedia.org/wiki/Transduction_(genetics)#Generalized_transduction is_a: phi:0000249 ! transduction [Term] id: phi:0000248 name: specialized transduction 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:AT] comment: This definition differs from that in GO:0009293. xref: GO:0007131 is_a: phi:0000249 ! transduction [Term] id: phi:0000249 name: transduction def: "Transfer of a DNA segment from one to another cell by a virus (usually a bacteriophage)." [Phi:AT] comment: This definition differs from that in GO:0009293. xref: GO:0007131 xref: Wiki:http\://en.wikipedia.org/wiki/Transduction_(genetics) is_a: phi:0000001 ! phage process is_a: phi:0000130 ! homologous DNA recombination [Term] id: phi:0000250 name: phage extrusion def: "Process of releasing mature phage particles (filamentous phages) by passing through bacterial membranes." [PHI:AT, PHI:IM, PHI:SC] synonym: "non-lytic viral release " BROAD [GO:0046753] synonym: "phage excretion" EXACT [Phi:AT] xref: GO:0046753 is_a: phi:0000014 ! phage release [Term] id: phi:0000251 name: catabolic island def: "Genomic island which carries genes encoding proteins involved in catabolism, usually of man-made toxic compounds (chlorinated aromatic and aliphatic compounds for instance)." [PHI:AT, PHI:GC] synonym: "metabolic island" RELATED [SO:0000774] is_a: phi:0000235 ! genomic island [Term] id: phi:0000252 name: symbiosis island def: "Genomic island that carries genes encoding proteins involved in symbiosis, usually with plants." [SO:0000776] comment: SO definition: A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria. xref: SO:0000776 is_a: phi:0000235 ! genomic island [Term] id: phi:0000253 name: fitness island def: "Genomic island whose presence increases the fitness of the host." [PHI:AT, PHI:GC] synonym: "adaptive island" EXACT [SO:0000775] xref: SO:0000775 is_a: phi:0000235 ! genomic island [Term] id: phi:0000254 name: integrative conjugative transposon def: "Genomic island that carries determinants for integration and excision of the host genome and for inter-cellular transfer by conjugation. The former include an integrase of the tyrosine or serine base integrase and cognate att sites. The latter can or not be related to plasmid encoded conjugation machinery." [PHI:AT, PHI:GC] is_obsolete: true [Term] id: phi:0000255 name: phage genome def: "The nucleotide sequence of a virus that infects bacteria." [SO:0001042] synonym: "phage sequence" EXACT [SO:0001042] xref: SO:0001042 is_a: phi:0000172 ! SO term [Term] id: phi:0000256 name: transposable phage def: "A DS DNA phage that integrates and replicates by transpositional recombination." [PHI:AT, PHI:GC] relationship: part_of phi:0000314 ! MeGO [Term] id: phi:0000257 name: bacteriophage def: "Virus that infect bacteria." [PHI:AT, PHI:GC] synonym: "phage" EXACT [PHI:AT] synonym: "phage particle" EXACT [PHI:AT] relationship: part_of phi:0000314 ! MeGO [Term] id: phi:0000258 name: plasmid component def: "Components associated with plasmids." [PHI:AT] xref: Wikipedia:thioredoxin relationship: part_of phi:0000359 ! plasmid [Term] id: phi:0000259 name: plasmid process alt_id: phi:0000362 def: "Any process that changes the level of transcription of plasmid genes." [PHI:AT] xref: Wikipedia:thioredoxin relationship: part_of phi:0000359 ! plasmid [Term] id: phi:0000260 name: transposable phage genome def: "Genome of a DS DNA phage that integrates and replicates by transpositional recombination." [PHI:AT, PHI:GC] is_a: phi:0000255 ! phage genome [Term] id: phi:0000261 name: type V protein secretion system complex 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:AT] is_a: phi:0000316 ! protein secretion [Term] id: phi:0000262 name: toxin def: "Poisonous activity, especially of proteins or conjugated proteins produced by certain animals, higher plants, and pathogenic bacteria." [PHI:AT] synonym: "effector" NARROW [] xref: : "Dorland's Medical Dictionary" is_a: phi:0000191 ! unclassified [Term] id: phi:0000263 name: type IV protein secretion/mating pair formation system complex def: "A complex of proteins that permits the transfer of nucleoprotein DNA conjugation intermediates or proteins directly into host cells or into the extracellular milieu In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s)." [GO:0043684] comment: Term and definition differ from those in GO. xref: GO:0043684 is_a: phi:0000258 ! plasmid component is_a: phi:0000316 ! protein secretion [Term] id: phi:0000264 name: nucleoid associated protein def: "Protein associated with the bacterial nucleoid." [PHI:AT] is_a: phi:0000191 ! unclassified [Term] id: phi:0000265 name: type I protein secretion system complex def: "A complex of three secretory proteins that carry out secretion in the type I secretion system: an inner membrane transport ATPase (termed ABC protein for ATP-binding cassette), which provides the energy for protein secretion; an outer membrane protein, which is exported via the sec pathway; and a membrane fusion protein, which is anchored in the inner membrane and spans the periplasmic space." [GO:0030256] xref: GO:0030256 is_a: phi:0000316 ! protein secretion [Term] id: phi:0000266 name: type II protein secretion system complex def: "A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of secreted proteins from the cytoplasm into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane." [GO:0015627] xref: GO:0015627 is_a: phi:0000316 ! protein secretion [Term] id: phi:0000267 name: type III protein secretion system complex def: "A complex nanomachine of approximately 20 proteins that carries out protein secretion in the type III secretion system. It contains an ATPase, spans the inner membrane, the peptidoglycan layer and the outer membrane and secretes a stiff needle like structure of a defined length. The needle is thought to function as the conduit for protein translocation into the target eukaryotic host cell. In some T3S the needle is not complete and the structure serves as the conduit for protein secretion." [GO:0030257] comment: Definition differs from GO. synonym: "injectisome" RELATED [] xref: GO:0030257 is_a: phi:0000316 ! protein secretion [Term] id: phi:0000268 name: plasmid vegetative DNA replication def: "Process of bidirectional (theta) vegetative replication of a plasmid DNA genome." [PHI:AT] is_a: phi:0000259 ! plasmid process [Term] id: phi:0000269 name: plasmid conjugative DNA replication def: "Process of sigma-type replication of a plasmid DNA genome from the origin of transfer oriT, during conjugation." [PHI:AT] relationship: part_of phi:0000271 ! intercellular transfer by conjugation [Term] id: phi:0000270 name: oriT def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [SO:0000724] xref: SO:0000724 is_a: phi:0000299 ! origin of replication relationship: part_of phi:0000242 ! conjugative transposon relationship: part_of phi:0000298 ! plasmid genome [Term] id: phi:0000271 name: intercellular transfer by conjugation def: "The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells; some or all of the chromosome(s) of one cell (donor) is then transferred into the other cell (recipient) unidirectional conjugation occurs between cells of different mating types." [GO:0009291] comment: It is essential NOT to use 'male' and female' because any bacterium can be donor and recipient even at the same time. synonym: "unidirectional conjugation" RELATED [GO:0009291] xref: GO:0009291 is_a: phi:0000259 ! plasmid process [Term] id: phi:0000272 name: type IV secretion system coupling protein def: "Inner membrane ATPase (TraG/VirD4) that recruits the DNA substrate including the conjugative relaxase to the T4SS and powers the intercellular transfer of DNA by conjugation." [PHI:AT] relationship: part_of phi:0000277 ! type IV secretion system motor [Term] id: phi:0000273 name: pilin def: "Alpha-beta fibrous proteins found in pilus structures in bacteria. Bacterial pili are used in partner recognition and exchange of genetic material during bacterial conjugation. Pili are more common in gram-negative bacteria, where, individual pilin molecules are linked by noncovalent protein-protein interactions. Gram-positive bacteria often have polymerized pilin." [PHI:AT] comment: Several terms associated to pilus and flagllum as components and their biogenesis are in GO. synonym: "flagellin" RELATED [] is_a: phi:0000191 ! unclassified relationship: part_of phi:0000266 ! type II protein secretion system complex [Term] id: phi:0000274 name: fimbrium def: "A proteinaceous hair-like appendage on the surface of bacteria; range from 2-8 nm in diameter." [GO:0009289] xref: GO:0009289 relationship: part_of phi:0000263 ! type IV protein secretion/mating pair formation system complex [Term] id: phi:0000275 name: type IV secretion system pilin def: "Structural subunit of the T4SS Secretion pilus of the T4SS formed or VirB2/TrbC/TraA/TraX structural subunits, some of which when mature assumes a circular configuration. The pilus is involved in mating pair formation prior to unidirectional conjugation." [PHI:AT] is_a: phi:0000273 ! pilin relationship: part_of phi:0000263 ! type IV protein secretion/mating pair formation system complex [Term] id: phi:0000276 name: VirB3 related outer membrane protein def: "Outer membrane component (TrbD/TraL) of the T4SS also involved in mating pair formation prior to unidirectional conjugation. VirB3 interacts with T4SS VirB6 and VirB4 related proteins." [PHI:AT] is_obsolete: true [Term] id: phi:0000277 name: type IV secretion system motor def: "Heart of the T4SS, this complex consists of a Walker A- Walker B hexameric ATPase (VirB4/TrwK/TrbE/TraC/TraU), possibly cytosolic and anchored to the inner membrane through interaction with the integral inner membrane protein (VirB3/TrwM/?), an hexameric ATP dependent chaperon (VirB11/TrwD/?) and a third ATPase devoted to DNA trasnfer (TraG/VirD4) also called coupling protein. VirB4 and alike are supposed to power transfer of the pilin protein, VirB11 and alike to power unfolding of the secreted pilin, and TraG and alike to power DNA transfer." [PHI:AT] relationship: part_of phi:0000263 ! type IV protein secretion/mating pair formation system complex [Term] id: phi:0000278 name: type IV secretion system minor pilus component def: "Component (TrbJ/TraE) of the T4SS pilus that may be involved in adhesion." [PHI:AT] relationship: part_of phi:0000263 ! type IV protein secretion/mating pair formation system complex [Term] id: phi:0000279 name: VirB1 related cell wall hydrolase activity def: "Protein of the T4SS, also involved in mating pair formation prior to unidirectional conjugation and that perforates the peptidoglycan cell wall." [PHI:AT] is_obsolete: true [Term] id: phi:0000280 name: type IV secretion system-Mpf stabilizer def: "Polytopic inner membrane protein (VirB6/TrbL/TraG/), which is part of the lumen of the T4SS-Mating pair formation channel." [PHI:AT] relationship: part_of phi:0000263 ! type IV protein secretion/mating pair formation system complex [Term] id: phi:0000281 name: type IV secretion system pilus associated lipoprotein def: "Lipoprotein component (VirB7/TrbH/TraV/TraI) that connects the pilus to the core of the T4SS-Mating pair formation complex." [PHI:AT] relationship: part_of phi:0000263 ! type IV protein secretion/mating pair formation system complex [Term] id: phi:0000282 name: VirB8 related inner-outer membrane bridging protein def: "Protein that forms a bridge over the periplasm connecting the inner membrane and outer membrane components of the T4SS-Mating pair formation complex. Interacts with VirB1, VirB3, VirB4, VirB9 and VirB10." [PHI:AT] relationship: part_of phi:0000263 ! type IV protein secretion/mating pair formation system complex [Term] id: phi:0000283 name: type IV secretion system secretin def: "Periplasm spanning and outer membrane component of T4SS formed of the VirB9/TrbG/TraK/TraN subunit." [PHI:AT] relationship: part_of phi:0000263 ! type IV protein secretion/mating pair formation system complex [Term] id: phi:0000284 name: type IV secretion system bridging component def: "A nodal point connecting the inner and outer membrane components of the T4SS formed of VirB10/TrbI/TraB/TraO subunits." [PHI:AT] relationship: part_of phi:0000263 ! type IV protein secretion/mating pair formation system complex [Term] id: phi:0000285 name: VirB11 typeII/IV secretion NTPase activity def: "Hexameric ring shaped NTPase similar to the F1-ATPase molecular motors and that fuels the T4SS and TIISS." [PHI:AT] xref: GO:0015219 is_obsolete: true [Term] id: phi:0000286 name: type III secretion system needle ruler def: "Protein involved in the determination of the length of the needle from the injectisome. This protein (YscP, Spa32, InvJ) is thought to operate as a molecular ruler coupled to a substrate-specificity switch." [PHI:AT, PHI:GC] xref: PMID:16458574 relationship: part_of phi:0000267 ! type III protein secretion system complex [Term] id: phi:0000287 name: type III secretion outer membrane ring def: "Located in the outer membrane of the bacterial cell this part of the injectisome contains the pilotin (YscW, MxiA), a lipoprotein ancillary to the secretin (YscW) and the secretin ( YscC ) ." [PHI:AT, PHI:GC] relationship: part_of phi:0000267 ! type III protein secretion system complex [Term] id: phi:0000288 name: type III secretion system extracellular needle def: "Needle component of the TIIISS system, which is formed of YscF (MxiH, EscF) proteins and protrudes outside from the bacterial surface by about 60 nm." [PHI:AT, PHI:GC] relationship: part_of phi:0000267 ! type III protein secretion system complex [Term] id: phi:0000289 name: type III secretion system needle tip def: "Terminal structure of the needle made of protein LcrV (PcrV, AcrV, IpaD) serving as a scaffold for the translocation pore YopBD." [PHI:AT, PHI:GC] relationship: part_of phi:0000291 ! type III secretion system translocator [Term] id: phi:0000290 name: type III secretion system secretin def: "Component of the injectisome that spans the outer membrane and contains YscC subunits." [PHI:AT, PHI:GC] relationship: part_of phi:0000287 ! type III secretion outer membrane ring [Term] id: phi:0000291 name: type III secretion system translocator def: "A set of two hydrophobic (YopB/YopD in Yersinia, PopB/PopD in Pseudomonas aeruginosa) and one hydrophilic (LcrV in Yersinia, PcrV in P.aeruginosa) proteins, exported by the injectisome and which form a pore in the host cell membrane to allow effector translocation." [PHI:AT, PHI:GC] synonym: "translocation pore" EXACT [] relationship: part_of phi:0000267 ! type III protein secretion system complex [Term] id: phi:0000292 name: type II secretion T2SO protein activity def: "Peptidase component of the TIISS system." [PHI:AT] is_obsolete: true [Term] id: phi:0000293 name: type II secretion system outer membrane component def: "T2SF Out etc?" [PHI:AT] relationship: part_of phi:0000266 ! type II protein secretion system complex [Term] id: phi:0000294 name: type II secretion envelope protein def: "Envelope protein component of TIISS. PulD, Out? etc." [PHI:AT] synonym: "secretin" RELATED [] relationship: part_of phi:0000266 ! type II protein secretion system complex [Term] id: phi:0000295 name: type III secretion inner membrane ring def: "Inner membrane ring component of the type III secretion machine, which includes lipoprotein YscJ (PrgK, EscJ), YscS, T, U and V and probably the YscR and D subunits." [PHI:AT, PHI:GC] synonym: "MS ring" EXACT [PHI:GC] relationship: part_of phi:0000267 ! type III protein secretion system complex [Term] id: phi:0000296 name: type III secretion system cytoplasmic ring component def: "Cytoplasmic ring component of the type III secretion machine, which includes YscQ subunits and probably YScK and YscL and the YscN ATpase." [PHI:AT, PHI:GC] relationship: part_of phi:0000267 ! type III protein secretion system complex [Term] id: phi:0000297 name: oriV def: "An origin of vegetative replication in plasmids and phages." [SO:0000952] xref: SO:0000952 is_a: phi:0000299 ! origin of replication relationship: part_of phi:0000091 ! phage concatemer relationship: part_of phi:0000255 ! phage genome relationship: part_of phi:0000298 ! plasmid genome [Term] id: phi:0000298 name: plasmid genome def: "A self-replicating linear or circular DNA molecule that is distinct from a chromosome in the organism." [SO:0000155] comment: "Plasmid" in SO. Add "linear" in SO definition as it is. synonym: "plasmid" EXACT [] xref: SO:00155 is_a: phi:0000172 ! SO term [Term] id: phi:0000299 name: origin of replication def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [SO:0000296] xref: SO:0000296 is_a: phi:0000172 ! SO term relationship: part_of phi:0000298 ! plasmid genome [Term] id: phi:0000300 name: integrated mobile genetic element def: "An MGE that is integrated into the host chromosome." [SO:0001039] xref: SO:0001039 is_a: phi:0000172 ! SO term [Term] id: phi:0000301 name: DNA transposon def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:0000182] xref: SO:0000182 is_a: phi:0000239 ! transposable element [Term] id: phi:0000302 name: inverted repeat def: "The sequence is complementary and repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:0000294] xref: SO:0000294 is_a: phi:0000172 ! SO term relationship: part_of phi:0000241 ! composite transposon [Term] id: phi:0000303 name: plasmid partitioning def: "Any process by which plasmids are segregated or distributed into daughter cells upon cell division. As in, but not restricted to, the taxon Bacteria." [GO:0030542] comment: Should be connected to chromsome segregation? GO:0007059? xref: GO:0030542 relationship: part_of phi:0000194 ! plasmid maintenance [Term] id: phi:0000304 name: plasmid dimer resolution def: "The recombination process that separates plasmid dimers or higher multimers into monomers." [PHI:AT] is_a: phi:0000134 ! site-specific DNA excision relationship: part_of phi:0000194 ! plasmid maintenance [Term] id: phi:0000305 name: regulation of vegetative plasmid DNA replication def: "Any process that controls the initiation of bidirectional (theta) vegetative replication of a plasmid DNA genome." [PHI:AT] synonym: "copy number control" RELATED [PHI:AT] relationship: part_of phi:0000268 ! plasmid vegetative DNA replication [Term] id: phi:0000306 name: regulation of plasmid DNA conjugation def: "Any process that controls plasmid DNA conjugation." [PHI:AT] is_a: phi:0000259 ! plasmid process [Term] id: phi:0000307 name: capsid collar fiber def: "Fiber attached to the collar structure of some phages." [PHI:AT, PHI:HWA] is_a: phi:0000061 ! phage component [Term] id: phi:0000308 name: capsid collar def: "Small disk located below some phage heads." [PHI:AT, PHI:HWA] is_a: phi:0000061 ! phage component [Term] id: phi:0000309 name: capsid neck def: "A constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae)." [PHI:AT, PHI:HWA] is_a: phi:0000061 ! phage component [Term] id: phi:0000310 name: capsid neck fiber def: "Fiber appended at the neck at the base of some phage heads." [PHI:AT, PHI:IM, PHI:SC] synonym: "wisker" EXACT [PHI:AT] is_a: phi:0000061 ! phage component [Term] id: phi:0000311 name: transposable prophage def: "Integrated genome of a transposable phage." [PHI:AT, PHI:GC] is_a: phi:0000090 ! prophage is_a: phi:0000301 ! DNA transposon [Term] id: phi:0000312 name: IAS def: "Internal activating sequence for transposition in transposable phages. It transiently binds transposase to stimulate transpososome synapsis." [PHI:AT, PHI:GC] relationship: part_of phi:0000311 ! transposable prophage [Term] id: phi:0000313 name: type IV secretion system pilin maturation def: "Process that during assembly of the T4SS removes the C-terminal aa from the pilin and generates the final cyclic pilin product by introducing a new peptide bond. This process requires the TraF/TrhI component of the T4SS." [PHI:AT] relationship: part_of phi:0000271 ! intercellular transfer by conjugation [Term] id: phi:0000314 name: MeGO def: "Ontology for non-phage prokaryotic mobile genetic elements." [PHI:AT] [Term] id: phi:0000315 name: plasmid entry exclusion def: "Definition?" [PHI:AT] relationship: part_of phi:0000271 ! intercellular transfer by conjugation [Term] id: phi:0000316 name: protein secretion def: "The regulated release of proteins from a cell or group of cells." [GO:0009306] xref: GO:0009306 is_a: phi:0000191 ! unclassified [Term] id: phi:0000317 name: relaxase activity def: "Relaxase is an enzyme in prokaryotes that is involved bacterial conjugation. It forms part of the relaxosome multi protein complex and nicks double-stranded DNA at the OriT origin of transfer on a bacterial plasmid forming a covalent 5'phosphotyrosyl bond." [Wiki: "http://en.wikipedia.org/wiki/Relaxase"] xref: PMID:19396961 xref: XX: is_a: phi:0000325 ! plasmid activity [Term] id: phi:0000318 name: plasmid fertility inhibition def: "Def?" [PHI:AT] relationship: part_of phi:0000271 ! intercellular transfer by conjugation [Term] id: phi:0000319 name: autoinducer synthesis def: "Any step required for the synthesis of an autoinducer (AI) molecule, otherwise called a pheromone, a signaling molecule used by bacteria participating in quorum sensing. One common type of autoinducer is an acyl homoserine lactone (AHL)." [PHI:AT] xref: http://en.wikipedia.org/wiki/Autoinducer is_a: phi:0000191 ! unclassified [Term] id: phi:0000320 name: lantibiotic biosynthesis def: "Lantibiotics are a class of peptide antibiotics that contain polycyclic thioether amino acids as well as the unsaturated amino acids dehydroalanine and 2-aminoisobutyric acid. These characteristic cyclic thioether amino acids are composed of either lanthionine or methyllanthionine. Lantibiotics are produced by a large number of Gram positive bacteria such as Streptococcus and Streptomyces to attack other gram positive bacteria and as such they are considered a member of the bacteriocins. They are synthesised with a leader polypeptide sequence that is only removed during the transport of the molecule out of the synthesizing cell." [PHI:AT] xref: http://en.wikipedia.org/wiki/Lantibiotics is_a: phi:0000191 ! unclassified [Term] id: phi:0000321 name: intracellular AB toxin activity def: "Toxin that exerts its activity within the target eukaryotic cell. The B subunit attaches to target regions on cell membranes, the A subunit enters through the membrane and possesses enzymatic function that affects internal cellular bio-mechanisms." [PHI:AT] xref: http://en.wikipedia.org/wiki/Exotoxin#Injected_toxins is_a: phi:0000323 ! cytotoxin [Term] id: phi:0000322 name: post-segregational killing def: "Plasmid-sensu, process of increased plasmid prevalence (number of plasmid-containing cells/total number of cells) in growing bacterial populations by selective elimination of daughter cells that did not inherit a plasmid copy at cell division." [PHI:AT] comment: Needs to be checked by Laurence. xref: PMID:19325885 is_a: phi:0000259 ! plasmid process relationship: part_of phi:0000194 ! plasmid maintenance [Term] id: phi:0000323 name: cytotoxin def: "A molecular entity with a toxin disposition\\, the realization of which damages host cells." [IDO:0000584] xref: IDO:0000584 is_a: phi:0000262 ! toxin [Term] id: phi:0000324 name: plasmid mobilization def: "Def to be provided." [PHI:AT] synonym: "copy number control" RELATED [] is_a: phi:0000259 ! plasmid process [Term] id: phi:0000325 name: plasmid activity def: "Molecular functions associated with plasmids." [PHI:AT] relationship: part_of phi:0000359 ! plasmid [Term] id: phi:0000326 name: phage function unknown def: "No process, component or activity can yet be assigned to this phage function." [PHI:AT] relationship: part_of phi:0000257 ! bacteriophage [Term] id: phi:0000327 name: PhiGO def: "Phage ontoloy" [PHI:AT] is_obsolete: true [Term] id: phi:0000328 name: phage base plate assembly def: "Process by which tailed phage base plates are assembled." [PHI:AT] relationship: part_of phi:0000009 ! phage assembly [Term] id: phi:0000329 name: DNA inversion def: "The process by which a segment of DNA is inverted from its original orientation." [PHI:AT] is_a: phi:0000129 ! DNA recombination [Term] id: phi:0000330 name: site-specific DNA inversion def: "The process by which a segment of DNA is inverted from its original orientation through the action of a site-specific recombinase." [PHI:AT] is_a: phi:0000131 ! site-specific DNA recombination [Term] id: phi:0000331 name: phage genome circularization def: "The process that converts a linear double stranded DNA phage genome into the circular form, either by homologous recombination between redundant ends or by association of complementary single stranded ends (sticky ends). The circular form is the template for genome replication and for most temperate phages it is also necessary for lysogenisation, either as a circular plasmid or as an integrated prophage." [PHI:AT] relationship: part_of phi:0000024 ! phage genome replication relationship: part_of phi:0000054 ! establishment as a circular plasmid prophage relationship: part_of phi:0000055 ! establishment as an integrated prophage [Term] id: phi:0000332 name: prophage mediated phage exclusion def: "Any process through which a prophage inhibits the development of an unrelated, usually virulent superinfecting phage." [PHI:AT, PHI:IM] relationship: part_of phi:0000007 ! phage lysogeny [Term] id: phi:0000333 name: plasmid function unknown def: "No process, component or activity can yet be assigned to this plasmid function." [PHI:AT] relationship: part_of phi:0000359 ! plasmid [Term] id: phi:0000334 name: plasmid mediated phage exclusion def: "Any process through which a plasmid inhibits the development of an infecting phage." [PHI:AT, PHI:IM] is_a: phi:0000259 ! plasmid process [Term] id: phi:0000335 name: phage mediated modulation of host functions def: "Any process by which a phage activates or represses the expression or the activity of one or more of its host proteins." [PHI:AT] synonym: "modification by virus of host cellular process" RELATED [GO:001905] synonym: "modulation by virus of host transcription " RELATED [GO:0043921] synonym: "regulation of host mRNA translation by virus " NARROW [GO:0019057] xref: GO:0019054 xref: GO:0019057 xref: GO:0043921 relationship: part_of phi:0000033 ! phage gene expression [Term] id: phi:0000336 name: plasmid mediated modulation of host functions def: "Any process by which a plasmid activates or represses the expression or the activity of one or more of its host proteins." [PHI:AT] relationship: part_of phi:0000259 ! plasmid process [Term] id: phi:0000337 name: plasmid mediated inhibition of host SOS repsonse def: "Any process that results in preventing or decreasing the SOS response of the bacterial host." [PHI:AT] is_a: phi:0000335 ! phage mediated modulation of host functions is_a: phi:0000336 ! plasmid mediated modulation of host functions [Term] id: phi:0000338 name: chaperon activity def: "A protein activity necessary for the correct non-covalent folding or unfolding of another protein." [PHI:AT] xref: http://en.wikipedia.org/wiki/Autoinducer is_a: phi:0000191 ! unclassified [Term] id: phi:0000339 name: cell wall degrading lysozyme activity def: "Cell wall transglycosylase synthesized by a phage during its lytic cycle and responsible for host cell lysis." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] is_a: phi:0000103 ! endolysin activity [Term] id: phi:0000340 name: cell wall degrading amidase activity def: "Cell wall amidase synthesized by a phage during its lytic cycle and responsible for host cell lysis." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] is_a: phi:0000103 ! endolysin activity [Term] id: phi:0000341 name: cell wall degrading endopeptidase activity def: "Cell wall endopeptidase synthesized by a phage during its lytic cycle and responsible for host cell lysis." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] is_a: phi:0000103 ! endolysin activity [Term] id: phi:0000342 name: spanin def: "Nearly ubiquitous among phages of Gram-negative hosts, these proteins are predicted to span the bacterial host periplasm providing a physical connection between the inner and outer membranes. They are required for phage release by lysis." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] xref: PMID:17900620 is_a: phi:0000061 ! phage component [Term] id: phi:0000343 name: Rz/Rz1-type spanin def: "Rz/Rz1 type spanins are two component spanins. The Rz protein has a predicted N-terminal transmembrane domain that spans the bacterial host inner membrane. The Rz1 protein is tethered to the inner leaflet of the host outer membrane by the fatty acid and lipid moeities of the N-terminal cysteine." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] xref: PMID:17900620 is_a: phi:0000342 ! spanin [Term] id: phi:0000344 name: phage T1-type spanin def: "T1 type spanins are one component spanins tethered to the bacterial host outer membrane by the fatty acid and lipid moieties of the N-terminal cysteine and to the host inner membrane by a predicted C-terminal transmembrane domain." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] xref: PMID:17900620 is_a: phi:0000342 ! spanin [Term] id: phi:0000345 name: Rz-type spanin component def: "The Rz proteins have a predicted N-terminal transmembrane domain, which spans the bacterial host inner membrane. There C-terminal domain interact with the C-terminal domain of cognate Rz1 spanin components." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] xref: PMID:17900620 relationship: part_of phi:0000343 ! Rz/Rz1-type spanin [Term] id: phi:0000346 name: Rz1-type spanin component def: "Rz1-like proteins are tethered to the inner leaflet of the host outer membrane by the fatty acid and lipid moieties of their N-terminal cysteine and interact with the Rz-like C-terminal domains through their C-terminal domain. The Rz1 coding sequence is either embedded within or adjacent to the Rz gene." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] xref: PMID:17900620 relationship: part_of phi:0000343 ! Rz/Rz1-type spanin [Term] id: phi:0000347 name: phage tail needle def: "Tail fiber component, which during infection is injected into the host, likely piercing a hole in the host cell envelope." [PHI:AT, PHI:IM, PHI:SC] xref: PMID:18059287 relationship: part_of phi:0000175 ! capsid tail fiber [Term] id: phi:0000348 name: cell wall degrading transglycosylase activity def: "Cell wall transglycosylase synthesized by a phage during its lytic cycle and responsible for host cell lysis." [PHI:AT, PHI:IM, PHI:RY, PHI:SC] is_a: phi:0000103 ! endolysin activity [Term] id: phi:0000349 name: target site selection protein def: "Component of the transpososme, this protein contributes to target site selction. Some proteins in the family select specific sites (as the Tn7 TnsE protein) others more or less random sites (as the Tn7 TnsD protein)." [PHI:AT] relationship: part_of phi:0000157 ! transpososome [Term] id: phi:0000350 name: regulation of DNA transposition def: "Any process that controls the process of DNA transposition." [PHI:AT] relationship: part_of phi:0000031 ! transpositional DNA replication relationship: part_of phi:0000136 ! transpositional DNA recombination [Term] id: phi:0000351 name: positive regulation of DNA transposition def: "Any process that stimulates the process of DNA transposition." [PHI:AT] is_a: phi:0000350 ! regulation of DNA transposition [Term] id: phi:0000352 name: negative regulation of DNA transposition def: "Any process that inhibits the process of DNA transposition." [PHI:AT] is_a: phi:0000350 ! regulation of DNA transposition [Term] id: phi:0000353 name: host nucleoid disruption activity def: "Any phage activity that provokes the disruption of the host bacterial nuceloid." [PHI:AT] is_a: phi:0000171 ! host cell killing activity [Term] id: phi:0000354 name: genome segregation def: "The process by which genetic material is organized and physically separated and apportioned to two daughter bacterial cells." [PHI:AT] synonym: "chromosome segregation" RELATED [GO:0007059] is_a: phi:0000191 ! unclassified [Term] id: phi:0000355 name: phage entry exclusion def: "A phage or plasmid-mediated process that prevents entry of an infecting phage into the host cell." [PHI:AT] comment: This process differs from immunity established by a prophage through the synthesis of a repressor protein that blocks gene expression by a superinfecting phage with the same immunity region. synonym: "abortive infection" RELATED [phi:0000059] is_a: phi:0000001 ! phage process [Term] id: phi:0000356 name: site-specific endoribonuclease activity def: "Definition?" [PHI:AT] xref: PMID:17046813 is_a: phi:0000097 ! phage activity [Term] id: phi:0000357 name: type III secretion complex injectisome def: "Structure found in many T3S nanomachines that possess a stiff needlelike structure of a defined length. The needle is thought to function as the conduit for protein translocation into the target eukaryotic host cell. In other T3S the needle is not complete and the structure serves as the conduit for protein secretion." [PHI:AT, PHI:GC] comment: Is a synonym of type III secretion complex is_obsolete: true [Term] id: phi:0000358 name: relaxosome assembly def: "The process that leads to the assembly of the relaxosome, a multi-component enzymatic machine, which mediates cleavage and initiation of rolling circle replication on a doubles stranded DNA molecule during conjugation, phage replication and transposition." [PHI:AT] relationship: part_of phi:0000271 ! intercellular transfer by conjugation [Term] id: phi:0000359 name: plasmid def: "This is a temporary term: parent to all functions related to plasmid processes, components and molecular activities." [PHI:AT] relationship: part_of phi:0000314 ! MeGO [Term] id: phi:0000360 name: negative regulation of plasmid gene expression def: "Any process that inhibits the process of transcription of plasmid genes." [PHI:AT] is_a: phi:0000363 ! regulation of plasmid gene expression [Term] id: phi:0000361 name: positive regulation of plasmid gene expression def: "Any process that stimulates the process of transcription of plasmid genes." [PHI:AT] is_a: phi:0000363 ! regulation of plasmid gene expression [Term] id: phi:0000363 name: regulation of plasmid gene expression def: "Any process that influences the level of plasmid gene transcription." [PHI:AT] is_a: phi:0000259 ! plasmid process [Term] id: phi:0000364 name: bacteriocin def: "Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s)." [PH:AT] xref: Wiki:http\://en.wikipedia.org/wiki/Bacteriocin is_a: phi:0000325 ! plasmid activity is_a: phi:0000374 ! exotoxin [Term] id: phi:0000365 name: cobalamin biosynthesis def: "Any step required for the synthesis of cobalamin, a term that may refer to several substances depending on the upper axial ligand of the cobalt ion." [PHI:AT] is_a: phi:0000191 ! unclassified [Term] id: phi:0000366 name: establishment as a prophage def: "Process by which a phage genome reaches a latent state, becoming a component of its host genome." [PHI:AT, PHI:IM, PHI:SC] synonym: "establishment of viral latency " BROAD [GO:0019043] xref: GO:0019043 is_a: phi:0000132 ! site-specific DNA integration relationship: part_of phi:0000055 ! establishment as an integrated prophage [Term] id: phi:0000367 name: negative regulation by host of phage transcription def: "Any process by which a host bacterium stops, prevents or reduces the frequency, rate or extent of phage transcription, the synthesis of RNA on either a DNA or an RNA template." [PHI:AT] synonym: "negative regulation by host of viral transcription " BROAD [GO:0043922] xref: GO:0043922 relationship: part_of phi:0000048 ! negative transcriptional regulation of phage gene expression [Term] id: phi:0000368 name: positive regulation by host of phage transcription def: "Any process by which a host bacterium activates the frequency, rate or extent of phage transcription, the synthesis of RNA on either a DNA or an RNA template." [PHI:AT] synonym: "positive regulation by host of viral transcription " BROAD [] xref: GO:0043923 relationship: part_of phi:0000041 ! regulation of phage gene expression [Term] id: phi:0000369 name: phage capsid envelopment def: "The process by which a capsid acquires a membrane envelope." [PHI:AT] synonym: "viral capsid envelopment " BROAD [GO:0046744] xref: GO:0046744 relationship: part_of phi:0000010 ! phage head/capsid assembly [Term] id: phi:0000370 name: lysis-inhibition def: "Lysis inhibition (LIN) refers to a highly adaptive attribute of the T4-related phages, which delay lysis for several hours in response to sensing the presence of external related phages attacking the cell. A block in expressing LIN results in large-plaque morphology." [PHI:AT, PHI:IM, PHI:SC] is_a: phi:0000001 ! phage process created_by: Ariane creation_date: 2009-06-02T04:00:05Z [Term] id: phi:0000371 name: antibiotic resistance def: "A resistance to drug that mitigates the damaging effects of an antibiotic." [IDO:0000581] comment: is_a response to drug, GO:0042493. xref: IDO:0000581 is_a: phi:0000191 ! unclassified created_by: Ariane creation_date: 2009-06-02T04:47:24Z [Term] id: phi:0000372 name: phage lytic cycle def: "The set of processes by which a bacteriophage produces infectious progeny." [PHI:AT, PHI:IM, PHI:SC] comment: Formerly Ejection/injection. relationship: part_of phi:0000002 ! phage infectious cycle created_by: Ariane creation_date: 2010-04-21T05:45:42Z [Term] id: phi:0000373 name: endotoxin def: "A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis." [IDO:0000552] synonym: "effector" NARROW [] xref: : "http://en.wikipedia.org/wiki/Endotoxin" is_a: phi:0000262 ! toxin created_by: Ariane creation_date: 2010-04-23T02:50:09Z [Term] id: phi:0000374 name: exotoxin def: "A toxin excreted by a microorganism, including bacteria, fungi, algae, and protozoa. Exotoxins can cause damage by destroying host cells or disrupting normal host cellular metabolism. Exotoxins are either secreted, or, similar to endotoxins, released during lysis of the cell." [IDO:0000550, PHI:AT] synonym: "effector" NARROW [] xref: : "http://en.wikipedia.org/wiki/Exotoxin" xref: IDO:0000550 is_a: phi:0000262 ! toxin created_by: Ariane creation_date: 2010-04-23T02:52:50Z [Term] id: phi:0000375 name: predicted prophage function unknown def: "No process, component or activity can yet be assigned to this predicted prophage function." [PHI:AT] relationship: part_of phi:0000257 ! bacteriophage created_by: ariane creation_date: 2011-07-12T01:43:27Z [Typedef] id: part_of name: part_of namespace: default_namespace is_transitive: true created_by: jane creation_date: 2009-04-23T02:02:33Z