OBO-Edit 2.1-beta13 01:11:2011 15:47 Phage ontology 1.2 ariane definition term replaced by consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym jane 2009-04-23T02:02:33Z default_namespace part_of part_of All processes related to the phage developmental cycles. Phage ontology phi:0000001 phage process phi:0000001 All processes related to the phage developmental cycles. PHI:AT PHI:IM PHI:SC 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. GO:0019058 GO:0019067 GO:0030068 lytic viral life cycle Phage ontology viral assembly, maturation, egress, and release viral infectious cycle phi:0000002 phage infectious cycle phi:0000002 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 lytic viral life cycle GO:0030068 viral assembly, maturation, egress, and release GO:0019067 viral infectious cycle GO:0019058 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. Phage ontology phi:0000003 phage pre adsorption true phi:0000003 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 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. Phage ontology phi:0000004 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. phage adsorption phi:0000004 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 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. Phage ontology phi:0000005 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. phage reversible adsorption phi:0000005 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 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. Phage ontology phi:0000006 phage irreversible adsorption phi:0000006 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 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. establishment of viral latency GO:001904 Phage ontology phi:0000007 phage lysogeny phi:0000007 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 establishment of viral latency GO:001904 Process by which a bacteriophage transfers its DNA in the host cell. viral genome transport in host cell GO:0046796 Phage ontology phi:0000008 Formerly Ejection/injection. phage DNA translocation phi:0000008 Process by which a bacteriophage transfers its DNA in the host cell. PHI:AT PHI:IM PHI:SC viral genome transport in host cell GO:0046796 Processes leading to the building of a mature phage particle. phage morphogenesis Phage ontology phi:0000009 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. phage assembly phi:0000009 Processes leading to the building of a mature phage particle. PHI:AT PHI:IM PHI:SC phage morphogenesis PHI:AT Process by which phage heads/capsids are assembled. viral capsid assembly GO:0019069 Phage ontology phi:0000010 phage head/capsid assembly phi:0000010 Process by which phage heads/capsids are assembled. PHI:AT PHI:IM PHI:SC viral capsid assembly GO:0019069 Process by which phage tail fibers are assembled. Phage ontology phi:0000011 phage tail fiber assembly phi:0000011 Process by which phage tail fibers are assembled. PHI:AT PHI:IM PHI:SC Process by which tailed phage heads and tails are put together. Phage ontology phi:0000012 phage head tail joining phi:0000012 Process by which tailed phage heads and tails are put together. PHI:AT PHI:IM PHI:SC Process of dissolution of cells by the action of specific phage encoded enzymes that causes cell rupture and release of the phage progeny. lytic viral release GO:0019077 Phage ontology phi:0000013 phage release by lysis phi:0000013 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 lytic viral release GO:0019077 Process of releasing mature phage particles from the host cell. release of virus from host GO:0019076 Phage ontology phi:0000014 phage release phi:0000014 Process of releasing mature phage particles from the host cell. PHI:AT PHI:IM PHI:SC release of virus from host GO:0019076 Process by which tailed phage tails are assembled. Phage ontology phi:0000015 phage tail assembly phi:0000015 Process by which tailed phage tails are assembled. PHI:AT PHI:IM PHI:SC Process used by some phages as part_of the host cell lysis process. Phage ontology phi:0000016 cell wall synthesis inhibition phi:0000016 Process used by some phages as part_of the host cell lysis process. PHI:AT PHI:IM PHI:SC Process of building the precursor of the phage head/capsid, which shall later encapsidate the viral genome. Phage ontology phi:0000017 phage prohead/capsid assembly phi:0000017 Process of building the precursor of the phage head/capsid, which shall later encapsidate the viral genome. PHI:AT PHI:IM PHI:SC Process of incorporation of the phage genome into the phage head/capsid. viral DNA genome packaging viral genome packaging GO:0019072 GO:0019073 Phage ontology phi:0000018 phage genome packaging phi:0000018 Process of incorporation of the phage genome into the phage head/capsid. PHI:AT PHI:IM PHI:SC viral DNA genome packaging GO:0019072 viral genome packaging GO:0019073 Processing of replicated DNA into a packageable structure, often a linear concatemer. viral DNA cleavage viral genome maturation GO:0019070 GO:0019071 Phage ontology phi:0000019 phage DNA maturation phi:0000019 Processing of replicated DNA into a packageable structure, often a linear concatemer. PHI:AT PHI:IM PHI:SC viral DNA cleavage GO:0019070 viral genome maturation GO:0019071 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. Phage ontology phi:0000020 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. phage headful packaging phi:0000020 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 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. Phage ontology phi:0000021 phage 3'extended cos packaging phi:0000021 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 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. Phage ontology phi:0000022 phage 5'extended cos packaging phi:0000022 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 Process of releasing mature enveloped phage particles (Plasmaviridae phages) by formation of a bulge. GO:0019078 Phage ontology lytic viral budding phi:0000023 phage budding phi:0000023 Process of releasing mature enveloped phage particles (Plasmaviridae phages) by formation of a bulge. PHI:AT PHI:IM PHI:SC lytic viral budding GO:0019078 Process of replicating the phage genome. viral genome replication GO:0019079 Phage ontology phi:0000024 phage genome replication phi:0000024 Process of replicating the phage genome. PHI:AT PHI:IM PHI:SC viral genome replication GO:0019079 Process of replicating a phage RNA genome. Phage ontology phi:0000025 phage RNA replication phi:0000025 Process of replicating a phage RNA genome. PHI:AT PHI:IM PHI:SC Process of replicating a phage DNA genome. Phage ontology phi:0000026 phage DNA replication phi:0000026 Process of replicating a phage DNA genome. PHI:AT PHI:IM PHI:SC Any process that modulates the frequency, rate or extent of the phage genome replication. GO:0045069 regulation of viral genome replication Phage ontology phi:0000027 regulation of phage replication phi:0000027 Any process that modulates the frequency, rate or extent of the phage genome replication. PHI:AT PHI:IM PHI:SC regulation of viral genome replication GO:0045069 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. Phage ontology phi:0000028 protein primed DNA replication phi:0000028 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 Process of DNA-dependent DNA replication proceeding by the rolling circle mode, i.e. on a circular DNA molecule to produce a concatemer. GO:0008167 sigma virus replication Phage ontology phi:0000029 sigma DNA replication phi:0000029 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 sigma virus replication GO:0008167 Process of DNA replication proceeding uni or bidirectionally on a circular DNA template to produce two daughter circular DNA molecules . Phage ontology phi:0000030 theta DNA replication phi:0000030 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 Process of DNA-dependent DNA replication proceeding by successive rounds of replicative transposition. Phage ontology phi:0000031 This mode of replication is used by the transposable phages. transpositional DNA replication phi:0000031 Process of DNA-dependent DNA replication proceeding by successive rounds of replicative transposition. PHI:AT PHI:IM PHI:SC Process of DNA-dependent DNA replication intiated by homologous recombination. Phage ontology phi:0000032 Typically used by phages of the T4 family. recombination directed DNA replication phi:0000032 Process of DNA-dependent DNA replication intiated by homologous recombination. PHI:AT PHI:IM PHI:SC Cascade of transcription and translation of the phage genes. viral genome expression GO:0019080 Phage ontology phi:0000033 phage gene expression phi:0000033 Cascade of transcription and translation of the phage genes. PHI:AT PHI:IM PHI:SC viral genome expression GO:0019080 Cascade of transcription of the phage genes. Phage ontology phi:0000034 phage gene transcription phi:0000034 Cascade of transcription of the phage genes. PHI:AT PHI:IM PHI:SC The transcriptional period of the earliest expressed viral genes mainly encoding transcriptional regulators. GO:0019085 immediate early viral mRNA transcription Phage ontology phage early transcription phi:0000035 phage class I gene transcription phi:0000035 The transcriptional period of the earliest expressed viral genes mainly encoding transcriptional regulators. PHI:AT PHI:IM PHI:SC immediate early viral mRNA transcription GO:0019085 phage early transcription PHI:AT The second round of viral gene transcription, usually of replication genes. GO:0019084 (delayed) early viral mRNA transcription Phage ontology phi:0000036 phage class II gene transcription phi:0000036 The second round of viral gene transcription, usually of replication genes. PHI:AT PHI:IM PHI:SC (delayed) early viral mRNA transcription GO:0019084 The third round of phage transcription, usually of regulators involved in the progression of induction of the phage late gene expression. middle promoter transcription Phage ontology phi:0000037 phage class IIB gene transcription phi:0000037 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 middle promoter transcription PHI:AT The transcriptional period of the latest expressed viral genes mainly encoding phage capsid components, morphogenesis proteins and cell wall degradation enzymes. GO:0019086 late viral mRNA transcription Phage ontology phage late transcription phi:0000038 Typically turned on by phage-encoded transcription factors. phage class III gene transcription phi:0000038 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 late viral mRNA transcription GO:0019086 phage late transcription PHI:AT Process by which phage gene transcription stops and RNA-polymerase is released from the DNA template. GO:0030401 Phage ontology phi:0000039 phage transcription termination phi:0000039 Process by which phage gene transcription stops and RNA-polymerase is released from the DNA template. PHI:AT PHI:IM PHI:SC 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 Phage ontology phi:0000040 phage transcription anti termination phi:0000040 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 Any process that activates or represses phage gene expression. Phage ontology phi:0000041 regulation of phage gene expression phi:0000041 Any process that activates or represses phage gene expression. PHI:AT PHI:IM PHI:SC Any process that stimulates the frequency, rate or extent of the phage genome replication. positive regulation of viral genome replication GO:0045070 Phage ontology phi:0000042 positive regulation of phage replication phi:0000042 Any process that stimulates the frequency, rate or extent of the phage genome replication. PHI:AT PHI:IM PHI:SC positive regulation of viral genome replication GO:0045070 Any process that decreases the frequency, rate or extent of the phage genome replication. negative regulation of viral genome replication GO:0045071 Phage ontology phi:0000043 negative regulation of phage replication phi:0000043 Any process that decreases the frequency, rate or extent of the phage genome replication. PHI:AT PHI:IM PHI:SC negative regulation of viral genome replication GO:0045071 Any process that activates or represses the transcription of phage genes. Typically turned on by phage-encoded transcription factors. regulation of viral transcription GO:0046782 Phage ontology phi:0000044 transcriptional-regulation of phage gene expression phi:0000044 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 regulation of viral transcription GO:0046782 Any process that represses the expression of phage genes at the post-transcriptional level. Phage ontology phi:0000045 negative post transcriptional regulation of phage gene expression phi:0000045 Any process that represses the expression of phage genes at the post-transcriptional level. PHI:AT PHI:IM PHI:SC Any process that activates the expression of phage genes at the post-transcriptional level. Phage ontology phi:0000046 positive post transcriptional regulation of phage gene expression phi:0000046 Any process that activates the expression of phage genes at the post-transcriptional level. PHI:AT PHI:IM PHI:SC Any process that activates or represses the expression of phage genes at a post-trasncriptional level. Phage ontology phi:0000047 post-transcriptional regulation of phage gene expression phi:0000047 Any process that activates or represses the expression of phage genes at a post-trasncriptional level. PHI:AT PHI:IM PHI:SC Any process that represses the expression of phage genes at the transcriptional level. negative regulation of viral transcription GO:0032897 Phage ontology phi:0000048 Typically turned off by phage-encoded transcription factors. negative transcriptional regulation of phage gene expression phi:0000048 Any process that represses the expression of phage genes at the transcriptional level. PHI:AT PHI:IM PHI:SC negative regulation of viral transcription GO:0032897 Any process that activates the expression of phage genes at the transcriptional level. positive regulation of viral transcription GO:0050434 Phage ontology phi:0000049 Typically turned on by phage-encoded transcription factors. positive transcriptional regulation of phage gene expression phi:0000049 Any process that activates the expression of phage genes at the transcriptional level. PHI:AT PHI:IM PHI:SC positive regulation of viral transcription GO:0050434 Any process that up or down-regulates protein activity or stability. Phage ontology phi:0000050 post-translational regulation of phage gene expression phi:0000050 Any process that up or down-regulates protein activity or stability. PHI:AT PHI:IM PHI:SC A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a plasmid. Phage ontology phi:0000051 establishment as a plasmid prophage phi:0000051 A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a plasmid. PHI:AT PHI:IM PHI:SC Process through which a prophage induces a hereditary change in the phenotype or fitness of the lysogen. GO:0019087 Phage ontology transformation of host cell by virus phi:0000052 phage lysogenic conversion phi:0000052 Process through which a prophage induces a hereditary change in the phenotype or fitness of the lysogen. PHI:AT PHI:IM PHI:SC transformation of host cell by virus GO:0019087 A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a linear plasmid. Phage ontology phi:0000053 establishment as a linear plasmid prophage phi:0000053 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 A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a circular plasmid. Phage ontology phi:0000054 establishment as a circular plasmid prophage phi:0000054 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 A process by which the phage integrates in the host genomes and establishes as a stable prophage. Phage ontology phi:0000055 establishment as an integrated prophage phi:0000055 A process by which the phage integrates in the host genomes and establishes as a stable prophage. PHI:AT PHI:IM PHI:SC Process by which the phage DNA integrates into the host genome by recombination. Integration usually proceeds via site-specific recombination into the host chromosome. GO:0019047 provirus integration Phage ontology phi:0000056 prophage DNA integration phi:0000056 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 provirus integration GO:0019047 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. provirus maintenance GO:0032360 Phage ontology phi:0000057 maintenance of prophage immunity phi:0000057 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 provirus maintenance GO:0032360 To be written. Phage ontology phi:0000058 IS this term really necessary? phage latent infection phi:0000058 To be written. PHI:AT PHI:IM PHI:SC 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. Phage ontology phi:0000059 phage abortive infection phi:0000059 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 Simulated lysogeny in a mixed population of phage-infected bacteria, non-infected phage-sensitive bacteria, and free phages. Phage ontology phi:0000060 phage pseudolysogeny phi:0000060 Simulated lysogeny in a mixed population of phage-infected bacteria, non-infected phage-sensitive bacteria, and free phages. PHI:AT PHI:IM PHI:SC All macromolecules, proteins, nucleic acids, sugars, lipids etc. that are part or participate in the assembly of the mature virion particle. Phage ontology phi:0000061 phage component phi:0000061 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 Process by which a prophage is made to switch from the latent/lysogenic state to the lytic cycle and production of phage progeny. reactivation of latent virus GO:0019046 Phage ontology phi:0000062 prophage induction phi:0000062 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 reactivation of latent virus GO:0019046 Process by which a prophage DNA is excised from the host genome. GO:0032359 provirus excision Phage ontology phi:0000063 prophage DNA excision phi:0000063 Process by which a prophage DNA is excised from the host genome. PHI:AT provirus excision GO:0032359 Component of the closed shell (head or capsid) of the phage. Phage ontology phi:0000064 phage head/capsid protein phi:0000064 Component of the closed shell (head or capsid) of the phage. PHI:AT PHI:IM PHI:SC 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. Phage ontology phi:0000065 capsid scaffolding protein phi:0000065 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 Abbreviated MHP, the major subunit component that forms the closed shell (capsid) of the phage head. GO:0046727 capsomer Phage ontology phi:0000066 phage head/capsid major protein phi:0000066 Abbreviated MHP, the major subunit component that forms the closed shell (capsid) of the phage head. PHI:AT PHI:IM PHI:SC capsomer GO:0046727 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. Phage ontology phi:0000067 phage portal associated protein phi:0000067 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 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. Phage ontology phi:0000068 phage portal protein phi:0000068 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 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. Phage ontology phi:0000069 phage head/capsid decoration protein phi:0000069 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 Protein component of fiber structures, which decorate the head/capsid of some phages. Phage ontology phi:0000070 phage head/capsid fiber protein phi:0000070 Protein component of fiber structures, which decorate the head/capsid of some phages. PHI:AT PHI:IM PHI:SC Protein covalently linked to the ends of dsDNA phages that use protein primed DNA replication. Phage ontology phi:0000071 The protein primes DNA replication and may have other functions including cell wall hydrolase. phage terminal protein phi:0000071 Protein covalently linked to the ends of dsDNA phages that use protein primed DNA replication. PHI:AT PHI:IM PHI:MS PHI:SC 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 Phage ontology phi:0000072 phage terminase complex phi:0000072 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 Phage component that forms a complex with the terminase small subunit at the base of the phage head. Phage ontology phi:0000073 phage terminase large subunit phi:0000073 Phage component that forms a complex with the terminase small subunit at the base of the phage head. PHI:AT PHI:IM PHI:SC Phage component that forms a complex with the terminase large subunit at the base of the phage head. Phage ontology phi:0000074 phage terminase small subunit phi:0000074 Phage component that forms a complex with the terminase large subunit at the base of the phage head. PHI:AT PHI:IM PHI:SC Protein component of fiber structures appended at the neck at the base of some phage heads. Phage ontology phi:0000075 capsid neck fiber protein phi:0000075 Protein component of fiber structures appended at the neck at the base of some phage heads. PHI:AT PHI:IM PHI:SC Protein component of a phage, which is injected into the host cytoplasm upon phage infection. Phage ontology phi:0000076 injected protein phi:0000076 Protein component of a phage, which is injected into the host cytoplasm upon phage infection. PHI:AT PHI:IM PHI:SC Protein component of a phage, which is injected into the host cytoplasm upon phage infection prior to phage DNA translocation. Phage ontology phi:0000077 pre DNA injected protein phi:0000077 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 Protein component of a phage, which is injected into the host cytoplasm upon phage infection after phage DNA translocation. Phage ontology phi:0000078 post DNA injected protein phi:0000078 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 Protein component of a phage, which is injected into the host membrane upon phage infection, creating a channel for phage DNA translocation. Phage ontology phi:0000079 translocation protein phi:0000079 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 Biochemical assembly that contains both proteins and lipids and is part_of some (Tectiviridae) phage capsids. Phage ontology phi:0000080 phage inner vesicle phi:0000080 Biochemical assembly that contains both proteins and lipids and is part_of some (Tectiviridae) phage capsids. PHI:AT PHI:HWA Protein component of the assembled tail of tailed phages (caudovirale). Phage ontology phi:0000081 phage tail protein phi:0000081 Protein component of the assembled tail of tailed phages (caudovirale). PHI:AT PHI:IM PHI:SC 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. Phage ontology phi:0000082 phage major tail protein phi:0000082 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 Protein that forms the internal tube of the contractile tails of Myovirirdae phages. It is the channel for DNA ejection into the host cytoplasm. Phage ontology phi:0000083 phage tail tube protein phi:0000083 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 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. Phage ontology phi:0000084 phage tail sheath protein phi:0000084 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 Protein that forms the tube of the non-contractile tails of Siphoviridae phages. It is the channel for DNA translocation into the host cytoplasm. Phage ontology phi:0000085 phage tail shaft protein phi:0000085 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 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. Phage ontology phi:0000086 phage tail tape measure protein phi:0000086 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 Protein structure that forms the basal tip of the phage tail and is used by the phage to adsorb to the host cell. Phage ontology phi:0000087 phage tail tip protein phi:0000087 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 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. Phage ontology phi:0000088 phage base plate protein phi:0000088 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 Protein component of the fiber, structure appended to the phage tail and used to scan, recognize and attach to the host cell. phi:0000175 Phage ontology phi:0000089 Fibers typically bind to particular LPS, polysaccharide or protein receptors on the cell surface phage tail fiber protein true phi:0000089 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 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 Phage ontology phi:0000090 prophage phi:0000090 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 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. Phage ontology phi:0000091 phage concatemer phi:0000091 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 A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes. SO:0001007 Phage ontology defective prophage phi:0000092 cryptic prophage phi:0000092 A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes. SO:0001007 defective prophage SO:0001007 A bacterial component to be added in GO that had to do with the phage life cycle. Phage ontology phi:0000093 This is a temporary term. phage related bacterial component phi:0000093 A bacterial component to be added in GO that had to do with the phage life cycle. PHI:AT PHI:IM PHI:SC A bacterial component located on the cell surface and which is specifically recognized and used by the phage for adsorption. Phage ontology phi:0000094 phage receptor phi:0000094 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 Minor protein component of the phage tail fiber. Phage ontology phi:0000095 phage tail fiber minor protein phi:0000095 Minor protein component of the phage tail fiber. PHI:AT PHI:IM PHI:SC Major protein component of the phage tail fiber. Phage ontology phi:0000096 phage tail fiber major protein phi:0000096 Major protein component of the phage tail fiber. PHI:AT PHI:IM PHI:SC Molecular functions of phage components. Phage ontology phi:0000097 phage activity phi:0000097 Molecular functions of phage components. PHI:AT PHI:IM PHI:SC Inhibits holin activity. Phage ontology phi:0000098 Some anti-holins differ from their cognate holins by only a few terminal amino acids. anti holin activity phi:0000098 Inhibits holin activity. PHI:AT PHI:IM PHI:SC Catalysis of the temporally regulated formation of a transmembrane protein hole that directly or indirectly allows murein hydrolyases to access their cell wall substrate. GO:0034290 XX:<new dbxref> Phage ontology phi:0000099 holin activity phi:0000099 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 Inhibition, inactivation or degradation of a transcriptional repressor. Phage ontology phi:0000100 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. anti repressor activity phi:0000100 Inhibition, inactivation or degradation of a transcriptional repressor. PHI:AT PHI:IM PHI:SC Catalysis of the reaction: ATP + H2O = ADP + phosphate. May or may not be coupled to another reaction. GO:0016887 Phage ontology phi:0000101 ATPase activity phi:0000101 Catalysis of the reaction: ATP + H2O = ADP + phosphate. May or may not be coupled to another reaction. GO:0016887 Transcriptional repressor activity involved in switching between lytic and lysogenic transcription. Phage ontology phi:0000102 CI/Cro transcriptional repressor activity true phi:0000102 Transcriptional repressor activity involved in switching between lytic and lysogenic transcription. PHI:AT PHI:IM PHI:SC Cell wall degradation enzyme synthesized by a phage during its lytic cycle and responsible for host cell lysis. Phage ontology phi:0000103 endolysin activity phi:0000103 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 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. Phage ontology phi:0000104 exolysin activity phi:0000104 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 Catalysis of the hydrolysis of peptide bonds. GO:0008233 Phage ontology phi:0000105 peptidase activity phi:0000105 Catalysis of the hydrolysis of peptide bonds. GO:0008233 Chaperon activity required for the assembly of the phage coat. Phage ontology phi:0000106 coat chaperon activity phi:0000106 Chaperon activity required for the assembly of the phage coat. PHI:AT PHI:IM PHI:SC Chaperon activity required for the assembly of the phage tail. Phage ontology phi:0000107 tail chaperon activity phi:0000107 Chaperon activity required for the assembly of the phage tail. PHI:AT PHI:IM PHI:SC Chaperon activity required for the assembly of the phage fibers. Phage ontology phi:0000108 tail fiber chaperon activity phi:0000108 Chaperon activity required for the assembly of the phage fibers. PHI:AT PHI:IM PHI:SC Interacting selectively with DNA (deoxyribonucleic acid). GO:0003677 Phage ontology phi:0000109 DNA binding activity phi:0000109 Interacting selectively with DNA (deoxyribonucleic acid). GO:0003677 Interacting selectively with single stranded DNA (deoxyribonucleic acid). GO:0003697 Phage ontology phi:0000110 single stranded DNA binding activity phi:0000110 Interacting selectively with single stranded DNA (deoxyribonucleic acid). GO:0003697 Interacting selectively with double stranded DNA (deoxyribonucleic acid). GO:0003690 Phage ontology phi:0000111 double stranded DNA binding activity phi:0000111 Interacting selectively with double stranded DNA (deoxyribonucleic acid). GO:0003690 Catalysis of a topological transformation in double-stranded DNA by a covalent or non-covalent mechanism. GO:0003916 Phage ontology phi:0000112 DNA topoisomerase activity phi:0000112 Catalysis of a topological transformation in double-stranded DNA by a covalent or non-covalent mechanism. GO:0003916 An accessory subunit of DNA polymerase that acts to increase the processivity of polymerization. GO:0030337 Phage ontology phi:0000113 DNA polymerase processivity factor activity phi:0000113 An accessory subunit of DNA polymerase that acts to increase the processivity of polymerization. GO:0030337 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 Phage ontology phi:0000114 DNA helicase activity phi:0000114 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 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from DNA replication. GO:0003887 Phage ontology phi:0000115 DNA directed DNA polymerase activity phi:0000115 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from DNA replication. GO:0003887 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 Phage ontology phi:0000116 DNA directed RNA polymerase activity phi:0000116 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 Catalysis of the transfer of a methyl group to a DNA molecule. GO:0009008 Phage ontology phi:0000117 DNA methyltransferase activity phi:0000117 Catalysis of the transfer of a methyl group to a DNA molecule. GO:0009008 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 Phage ontology phi:0000118 DNA primase activity phi:0000118 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 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end. GO:0004527 Phage ontology phi:0000119 DNA exonuclease activity phi:0000119 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end. GO:0004527 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end. GO:0008408 Phage ontology phi:0000120 DNA 3'-5' exonuclease activity phi:0000120 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end. GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end. GO:0008409 Phage ontology phi:0000121 DNA 5'-3' exonuclease activity phi:0000121 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end. GO:0008409 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. Phage ontology phi:0000122 excisionase activity phi:0000122 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 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. Phage ontology phi:0000123 prohead protease activity phi:0000123 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 Protease activity involved in breaking down of the cell wall as part of the phage lysis process. Phage ontology phi:0000124 cell-wall peptidase activity phi:0000124 Protease activity involved in breaking down of the cell wall as part of the phage lysis process. PHI:AT PHI:IM PHI:SC Catalysis of DNA cleavage involved in the packaging of DNA into phage heads. Phage ontology phi:0000125 phage terminase activity phi:0000125 Catalysis of DNA cleavage involved in the packaging of DNA into phage heads. PHI:AT PHI:IM PHI:SC Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. GO:0004519 Phage ontology phi:0000126 DNA endonuclease activity phi:0000126 Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks. GO:0004519 Any transcription regulator activity that prevents or downregulates transcription. GO:0016564 Phage ontology phi:0000127 transcriptional repressor activity phi:0000127 Any transcription regulator activity that prevents or downregulates transcription. GO:0016564 Antagonizes ribosome-mediated translation of mRNA into a polypeptide. GO:0030371 Phage ontology phi:0000128 translation repressor activity phi:0000128 Antagonizes ribosome-mediated translation of mRNA into a polypeptide. GO:0030371 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 Phage ontology phi:0000129 This definition differs from that in GO. DNA recombination phi:0000129 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 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 Phage ontology phi:0000130 This definition differs from that in GO. homologous DNA recombination phi:0000130 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 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:<new xref> Phage ontology phi:0000131 site-specific DNA recombination phi:0000131 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:<new dbxref> XX:<new xref> http://en.wikipedia.org/wiki/Site-specific_recombination The process by which a segment of DNA is incorporated into another by a site-specific recombination event. Phage ontology phi:0000132 site-specific DNA integration phi:0000132 The process by which a segment of DNA is incorporated into another by a site-specific recombination event. PHI:AT PHI:IM PHI:SC The process by which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome. GO:0015074 Phage ontology phi:0000133 DNA integration phi:0000133 The process by which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome. GO:0015074 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. Phage ontology phi:0000134 site-specific DNA excision phi:0000134 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 A process of transpositional recombination, which involves the replication of the transposed DNA segment. Phage ontology phi:0000135 replicative transpositional recombination phi:0000135 A process of transpositional recombination, which involves the replication of the transposed DNA segment. PHI:AT PHI:IM PHI:SC A process that moves a DNA region from one to another location in a genome via a DNA intermediate. GO:0006313 Phage ontology phi:0000136 Synonyms recently associated with the GO term do not apply here. These are in fact much too specific. transpositional DNA recombination phi:0000136 A process that moves a DNA region from one to another location in a genome via a DNA intermediate. GO:0006313 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. Phage ontology phi:0000137 conservative transpositional recombination phi:0000137 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 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 Phage ontology phi:0000138 recombinational repair phi:0000138 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 A process involving DNA breakage and reunion that converts replicated telomeres into covalently closed hairpin telomeres on the ends of linear DNA molecules. Phage ontology phi:0000139 telomere resolution phi:0000139 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 Activities related to bacteria, phage, plasmid and transposon recombination. Phage ontology phi:0000140 recombinase activity phi:0000140 Activities related to bacteria, phage, plasmid and transposon recombination. PHI:AL PHI:AT PHI:GC PHI:GH PHI:IM Processes related to bacteria, phage, plasmid and transposon recombination. Phage ontology phi:0000141 recombination process phi:0000141 Processes related to bacteria, phage, plasmid and transposon recombination. PHI:AL PHI:AT PHI:GC PHI:GH PHI:IM Catalysis of cleavage and formation of new phosphodiester bonds between a pair of DNA target sequences. Phage ontology phi:0000142 DNA breakage and rejoining enzymes phi:0000142 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 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 Phage ontology phi:0000143 Def different form existing GO. tyrosine-based recombinase activity phi:0000143 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 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. XX:<new xref> Phage ontology phi:0000144 serine-based recombinase activity phi:0000144 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:<new dbxref> XX:<new xref> http://en.wikipedia.org/wiki/Site-specific_recombination Tyrosine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another. phi:0000132 phi:0000143 GO:0009037 Phage ontology phi:0000145 Definition differs from GO:0009037 tyrosine based integrase activity true phi:0000145 Tyrosine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another. GO:0009037 Tyrosine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two. phi:0000134 phi:0000143 Phage ontology phi:0000146 tyrosine based resolvase activity true phi:0000146 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 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. Phage ontology phi:0000147 tyrosine based topoisomerase IB activity phi:0000147 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 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:AT PMID:11804598 Phage ontology phi:0000148 protelomerase activity phi:0000148 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 Tyrosine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome. Phage ontology phi:0000149 tyrosine-based transposase activity true phi:0000149 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 Serine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another. phi:0000132 phi:0000144 Phage ontology phi:0000150 serine based integrase activity true phi:0000150 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 Serine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two. phi:0000134 phi:0000144 Phage ontology phi:0000151 serine based resolvase activity true phi:0000151 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 Serine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome. Phage ontology phi:0000152 serine based transposase activity true phi:0000152 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 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). Phage ontology phi:0000153 DDE-based recombinase activity phi:0000153 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 Any multiprotein recombinogenic complex containing DNA, recombinase and accessory proteins. Phage ontology phi:0000154 recombination component phi:0000154 Any multiprotein recombinogenic complex containing DNA, recombinase and accessory proteins. PHI:AT 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. Phage ontology phi:0000155 intasome phi:0000155 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 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. Phage ontology phi:0000156 relaxosome phi:0000156 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 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. Phage ontology phi:0000157 transpososome phi:0000157 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 A multi-component enzymatic machine including a tyrosine or serine based resolvase, which mediates resolution of chromosome dimers and replicon fusions. Phage ontology phi:0000158 resolvasome phi:0000158 A multi-component enzymatic machine including a tyrosine or serine based resolvase, which mediates resolution of chromosome dimers and replicon fusions. PHI:AT 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. Phage ontology phi:0000159 Y2 transposase activity phi:0000159 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 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. Phage ontology phi:0000160 rolling circle transposition phi:0000160 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 The protein coat that surrounds the infective nucleic acid in phage particles. It comprises numerous regularly arranged subunits. Phage ontology phi:0000161 head/capsid phi:0000161 The protein coat that surrounds the infective nucleic acid in phage particles. It comprises numerous regularly arranged subunits. PHI:AT PHI:IM PHI:SC Activity that represses RNA polymerase activity. Phage ontology phi:0000162 Typically expressed by phages to turn off host egne expression. inhibitor of RNA polymerase phi:0000162 Activity that represses RNA polymerase activity. PHI:AT PHI:IM PHI:SC Activity that inhibits DNA degradation by the phage host protein complex RecBCD. Phage ontology phi:0000163 inhibitor of RecBCD nuclease phi:0000163 Activity that inhibits DNA degradation by the phage host protein complex RecBCD. PHI:AT PHI:IM PHI:SC Any process that modulates host gene expression as a result of phage gene expression. Phage ontology phi:0000164 plasmid mediated regulation of host gene expression phi:0000164 Any process that modulates host gene expression as a result of phage gene expression. PHI:AT PHI:IM PHI:SC Any process that up-regulates host gene expression as a result of phage gene expression. Phage ontology phi:0000165 plasmid mediated positive regulation of host gene expression phi:0000165 Any process that up-regulates host gene expression as a result of phage gene expression. PHI:AT PHI:IM PHI:SC Any process that down-regulates host gene expression as a result of phage gene expression. Phage ontology phi:0000166 plasmid mediated negative regulation of host gene expression phi:0000166 Any process that down-regulates host gene expression as a result of phage gene expression. PHI:AT PHI:IM PHI:SC Activity that inhibits protein breakdown by the phage host protease FtsH. Phage ontology phi:0000167 inhibitor of FtsH protease activity phi:0000167 Activity that inhibits protein breakdown by the phage host protease FtsH. PHI:AT PHI:IM PHI:SC Activity that modulates the nucleoid associated protein/DNA chaperon HNS. Phage ontology phi:0000168 modulator of nucleoid associated protein HNS phi:0000168 Activity that modulates the nucleoid associated protein/DNA chaperon HNS. PHI:AT PHI:IM PHI:SC Activity that decreases deoxyguanosine triphospho-hydrolase activity. Phage ontology phi:0000169 Typically expressed by phages to turn off host egne expression. inhibitor-of deoxyguanosine triphospho hydrolase phi:0000169 Activity that decreases deoxyguanosine triphospho-hydrolase activity. PHI:AT PHI:IM PHI:SC Any process that activates or represses the activity of a host protein. Phage ontology phi:0000170 plasmid mediated modulation of host protein activity phi:0000170 Any process that activates or represses the activity of a host protein. PHI:AT PHI:IM PHI:SC Activity that provokes host cell kiling independently of any other phage lytic or plasmid activity. Phage ontology phi:0000171 host cell killing activity phi:0000171 Activity that provokes host cell kiling independently of any other phage lytic or plasmid activity. PHI:AT PHI:IM PHI:SC To be (or already) transferred to SO Phage ontology phi:0000172 SO term phi:0000172 To be (or already) transferred to SO PHI:AT PHI:IM PHI:SC Protein that is a major component of the phage particle. GO:0042001 Phage ontology phi:0000173 major capsid structural protein phi:0000173 Protein that is a major component of the phage particle. PHI:AT 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. Phage ontology phi:0000174 capsid tail phi:0000174 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 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. Phage ontology phi:0000175 capsid tail fiber phi:0000175 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 Fiber structures, which decorate the head of some phages. Phage ontology phi:0000176 phage head/capsid fiber phi:0000176 Fiber structures, which decorate the head of some phages. PHI:AT PHI:IM PHI:SC 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. Phage ontology phi:0000177 prohead/procapsid phi:0000177 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 Protein component found in low number of copies in the tail of phage particles of the types myoviridae and siphoviridae. Phage ontology phi:0000178 phage minor tail protein phi:0000178 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 Phage head/capsid protein component located inside the finished head. Phage ontology phi:0000179 phage head/capsid internal protein phi:0000179 Phage head/capsid protein component located inside the finished head. PHI:AT PHI:IM PHI:SC Activity that inhibits the protease activity of the host RecA protein. Phage ontology phi:0000180 inhibitor of RecA protease activity phi:0000180 Activity that inhibits the protease activity of the host RecA protein. PHI:AT PHI:IM PHI:SC Chaperon activity required for the assembly of phage components. Phage ontology phi:0000181 capsid protein chaperon activity phi:0000181 Chaperon activity required for the assembly of phage components. PHI:AT PHI:IM PHI:SC The process by which a segment of DNA is separated from another, usually larger, DNA molecule such as a chromosome. GO:0007131 DNA resolution Phage ontology phi:0000182 DNA excision phi:0000182 The process by which a segment of DNA is separated from another, usually larger, DNA molecule such as a chromosome. PHI:AT DNA resolution GO:0007131 Catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template. GO:0003899 Phage ontology phi:0000183 RNA directed RNA polymerase activity phi:0000183 Catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template. GO:0003968 Any transcription regulator activity that prevents or downregulates transcription. GO:0003700 Phage ontology phi:0000184 transcription factor activity phi:0000184 Any transcription regulator activity that prevents or downregulates transcription. GO:0003700 Protein component found in low number of copies in the shell/head/capsid of phage particles. Phage ontology phi:0000185 phage head/capsid minor protein phi:0000185 Protein component found in low number of copies in the shell/head/capsid of phage particles. PHI:AT PHI:IM PHI:SC Protein that is a minor component of the phage particle. GO:0042001 Phage ontology phi:0000186 minor capsid structural protein phi:0000186 Protein that is a minor component of the phage particle. PHI:AT Protein component of the phage virion. GO:0042001 Phage ontology phi:0000187 capsid structural protein phi:0000187 Protein component of the phage virion. PHI:AT 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. CBWInfo:Verotox.html#0003 Phage ontology phi:0000188 shiga toxin activity phi:0000188 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 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. CBWInfo:Verotox.html#0003 Phage ontology phi:0000189 shiga toxin subunit A phi:0000189 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 Shiga toxin subunit B binds to a component of the cell membrane known as Gb3 allowing the complex AB toxin to enter the cell. CBWInfo:Verotox.html#0003 Phage ontology phi:0000190 shiga toxin subunit B phi:0000190 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 Yet... Phage ontology phi:0000191 unclassified phi:0000191 Yet... PHI:AT PHI:IM PHI:MS PHI:SC 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. GO:0030508 Wikipedia:thioredoxin thiol-disulfide exchange intermediate activity Phage ontology phi:0000192 thioredoxin phi:0000192 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 thiol-disulfide exchange intermediate activity GO:0030508 Any process that results into the inhibition of a host restriction. Phage ontology phi:0000193 restriction alleviation phi:0000193 Any process that results into the inhibition of a host restriction. PHI:AT The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division. GO:n0006276 Phage ontology phi:0000194 plasmid maintenance phi:0000194 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 Phage encoded protein that antagonizes ribosome-mediated translation of mRNA into a polypeptide. GO:0030371 Phage ontology phi:0000195 phage translation repressor activity phi:0000195 Phage encoded protein that antagonizes ribosome-mediated translation of mRNA into a polypeptide. PHI:AT Any process that controls the number of copies of a plasmid per host cell. Phage ontology phi:0000196 plasmid copy number control phi:0000196 Any process that controls the number of copies of a plasmid per host cell. PHI:AT Phage which upon infection has no other choice than entering the lytic cycle. Phage ontology phi:0000197 virulent phage phi:0000197 Phage which upon infection has no other choice than entering the lytic cycle. PHI:AT Phage which upon infection has the choice between going lytic or lysogenic. Wikipedia:thioredoxin Phage ontology phi:0000198 Needs revision temperate phage phi:0000198 Phage which upon infection has the choice between going lytic or lysogenic. PHI:AT Activity resulting in the degradation of hyaluronic acid. KEGG:EC 3.2.1.35 Wikipedia:http://en.wikipedia.org/wiki/Hyaluronidase Phage ontology phi:0000199 hyaluronidase activity phi:0000199 Activity resulting in the degradation of hyaluronic acid. PHI:AT Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes, and macrophages. PMID:16794307 Phage ontology phi:0000200 Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes and macrophages. leukocidin cativity phi:0000200 Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes, and macrophages. PHI:AT 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. Wikipedia:http://en.wikipedia.org/wiki/Superantigen Phage ontology phi:0000201 superantigen activity phi:0000201 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 Staphylokinases (SAK) are enzymes, which activate plasminogen, which in turn can degrade various host proteins during infection. Wikipedia:http://en.wikipedia.org/wiki/Staphylokinase Phage ontology phi:0000202 staphylokinase phi:0000202 Staphylokinases (SAK) are enzymes, which activate plasminogen, which in turn can degrade various host proteins during infection. PHI:AT 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. Wikipedia:http://en.wikipedia.org/wiki/Streptococcus_pyogenes streptokinase Phage ontology phi:0000203 streptodornase phi:0000203 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 Exfoliative toxin A is a Staphylococcus aureus protease activity, which causes peeling of the skin observed in staphylococcal scalded-skin syndrome. Wikipedia:http://en.wikipedia.org/wiki/Staphylococcus_aureus Phage ontology phi:0000204 exfoliative toxin A phi:0000204 Exfoliative toxin A is a Staphylococcus aureus protease activity, which causes peeling of the skin observed in staphylococcal scalded-skin syndrome. PHI:AT Protein component of a constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae). Phage ontology phi:0000205 capsid neck protein phi:0000205 Protein component of a constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae). PHI:AT PHI:HWA Protein component of a small disk located below some phage heads. Phage ontology phi:0000206 capsid collar protein phi:0000206 Protein component of a small disk located below some phage heads. PHI:AT PHI:HWA Protein component of the fibers attached to the collar structure of some phages. Phage ontology phi:0000207 capsid collar fiber protein phi:0000207 Protein component of the fibers attached to the collar structure of some phages. PHI:AT PHI:HWA Short stuctures (generally 30 nm long) at the tail tip of some phages and used for attachment. Phage ontology phi:0000208 phage spike phi:0000208 Short stuctures (generally 30 nm long) at the tail tip of some phages and used for attachment. PHI:AT PHI:HWA Genomic island which carries genes encoding proteins related to pathogenicity such as attachment, invasion of the host, other virulence factors, toxins, etc. SO:0000773 pathogenic island Phage ontology phi:0000209 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. pathogenicity island phi:0000209 Genomic island which carries genes encoding proteins related to pathogenicity such as attachment, invasion of the host, other virulence factors, toxins, etc. SO:0000773 Number of triangles into which an icosahedral virus capsid can be subdivided. Phage ontology phi:0000210 phage capsid triangulation number phi:0000210 Number of triangles into which an icosahedral virus capsid can be subdivided. PHI:AT PHI:HWA 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. SO:0000342 site specific recombination target region Phage ontology phi:0000211 attachment site phi:0000211 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 site specific recombination target region SO:0000342 Integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site. SO:0000943 Phage ontology phi:0000212 attB site phi:0000212 Integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site. SO:0000943 Attachment site located on the on the phage genome. SO:0000942 Phage ontology phi:0000213 attP site phi:0000213 Attachment site located on the on the phage genome. PHI:AT PHI:GC SO:0000942 Attachment site located on the bacterial chromosome at the left of a prophage region and which is used for prophage site-specific excision. SO:0000944 attBP' Phage ontology phi:0000214 attL site phi:0000214 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 attBP' PHI:AT 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 attPB' Phage ontology phi:0000215 attR site phi:0000215 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 attPB' PHI:AT An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon. SO:0001043 Phage ontology phi:0000216 attCTn site phi:0000216 An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon. SO:0001043 A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place. SO:0000367 Phage ontology phi:0000217 attI site phi:0000217 A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place. SO:0000367 Attachment site located on a gene cassette (sensu integron) and used for site-specific integration in an integron. SO:0000950 59 base pairs sequence Phage ontology phi:0000218 Exists in SO but I prefer my definition, because SO's does not mention the cassette. attC site phi:0000218 Attachment site located on a gene cassette (sensu integron) and used for site-specific integration in an integron. PHI:AT PHI:GC Target region for site-specific recombination leading to the resolution of a chromosome or plasmid dimer or a cointegrate resulting from replicative transposition. SO:0000947 res site Phage ontology cer site dif site loxP site phi:0000219 resolution site phi:0000219 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 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. Phage ontology phi:0000220 transposon end phi:0000220 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 The left transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence. Phage ontology phi:0000221 IRLI phi:0000221 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 The left end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRR. Phage ontology inverted repeat phi:0000222 In the case of transposable (pro)phages it is called attL and includes several subsites, attL1, attL2 and attL3. IRL phi:0000222 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 inverted repeat SO:0000294 The right end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRL. Phage ontology inverted repeat phi:0000223 In the case of transposable (pro)phages it is called attR and includes several subsites, attR1, attR2 and attR3. IRR phi:0000223 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 inverted repeat SO:0000294 The left transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence. Phage ontology phi:0000224 IRLO phi:0000224 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 The right transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence. Phage ontology phi:0000225 IRRO phi:0000225 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 The right transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence. Phage ontology phi:0000226 IRRI phi:0000226 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 To be added. Phage ontology phi:0000227 type I secretion membrane fusion protein activity phi:0000227 To be added. PHI:AT A region specifically recognized by a recombinase, which inverts the region flanked by a pair of sites. SO:0000948 inv site Phage ontology ftr site phi:0000228 inversion site phi:0000228 A region specifically recognized by a recombinase, which inverts the region flanked by a pair of sites. SO:0000948 Component of the inversion site located at the left of a region susceptible to site-specific inversion. Phage ontology phi:0000229 IRLinv site phi:0000229 Component of the inversion site located at the left of a region susceptible to site-specific inversion. PHI:AT PHI:GC Component of the inversion site located at the right of a region susceptible to site-specific inversion. SO:0001047 Phage ontology phi:0000230 IRRinv site phi:0000230 Component of the inversion site located at the right of a region susceptible to site-specific inversion. SO:0001047 DNA region recognized by the terminase small subunit as the first step in synapsis of the double stranded DNA phage full head packaging complex. Phage ontology phi:0000231 pac site phi:0000231 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 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. Phage ontology phi:0000232 cos site phi:0000232 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 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. Phage ontology phi:0000233 3'extended cos site phi:0000233 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 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. Phage ontology phi:0000234 5'extended cos site phi:0000234 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 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 Phage ontology phi:0000235 revise SO definition. genomic island phi:0000235 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 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 Phage ontology phi:0000236 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. integron phi:0000236 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 DNA region that contains a tyrosine based recombinase gene, a primary recombination site attI and a strong outward promoter Pc. Phage ontology phi:0000237 integron platform phi:0000237 DNA region that contains a tyrosine based recombinase gene, a primary recombination site attI and a strong outward promoter Pc. PHI:AT PHI:GC 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. Phage ontology phi:0000238 gene cassette (sensu integrons) phi:0000238 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 Transposable DNA region that encodes mobility and its regulatory functions and other phenotypic traits such as antibiotic resistance, catabolic enzymes etc. SO:0000101 Phage ontology phi:0000239 SO definition: A transposon or insertion sequence. An element that can insert in a variety of DNA sequence. transposable element phi:0000239 Transposable DNA region that encodes mobility and its regulatory functions and other phenotypic traits such as antibiotic resistance, catabolic enzymes etc. SO:0000101 Transposon in which mobility genes and phenotypic genes are surrounded by imperfect inverted repeats. Phage ontology phi:0000240 unitary transposon phi:0000240 Transposon in which mobility genes and phenotypic genes are surrounded by imperfect inverted repeats. PHI:AT PHI:GC Transposon composed of two identical IS sequences in the same or opposite orientation flanking a region containing the phenotypic genes. Phage ontology phi:0000241 composite transposon phi:0000241 Transposon composed of two identical IS sequences in the same or opposite orientation flanking a region containing the phenotypic genes. PHI:AT PHI:GC A genomic island which contains genes for integration/excision and intercellular transfer by conjugation. SO:0000371 CTn ICE Phage ontology phi:0000242 Diiferes fro OS def (A transposon that encodes function required for conjugation). conjugative transposon phi:0000242 A genomic island which contains genes for integration/excision and intercellular transfer by conjugation. SO:0000371 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 Phage ontology phi:0000243 defective conjugative transposon phi:0000243 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 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. Phage ontology phi:0000244 transfer agent phi:0000244 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 DNA region flanked by inverted repeats and containing genes coding for transposition enzymes and regulators of transposition. SO:0000973 Phage ontology phi:0000245 insertion sequence phi:0000245 DNA region flanked by inverted repeats and containing genes coding for transposition enzymes and regulators of transposition. PHI:AT PHI:GC SO:0000973 A DNA region consisting of two fused replicons/plasmids resulting from a replicative transposition event. SO:0001045 Phage ontology cointegrate replicon phi:0000246 SO definition for cointegrate replicon: A MGE region consisting of two fused replicons/plasmids resulting from a replicative transposition event. cointegrate phi:0000246 A DNA region consisting of two fused replicons/plasmids resulting from a replicative transposition event. PHI:AT PHI:GC cointegrate replicon SO:0001045 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. GO:0007131 Wiki:http://en.wikipedia.org/wiki/Transduction_(genetics)#Generalized_transduction Phage ontology phi:0000247 This definition differs from that in GO:0009293. generalized transduction phi:0000247 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 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. GO:0007131 Phage ontology phi:0000248 This definition differs from that in GO:0009293. specialized transduction phi:0000248 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 Transfer of a DNA segment from one to another cell by a virus (usually a bacteriophage). GO:0007131 Wiki:http://en.wikipedia.org/wiki/Transduction_(genetics) Phage ontology phi:0000249 This definition differs from that in GO:0009293. transduction phi:0000249 Transfer of a DNA segment from one to another cell by a virus (usually a bacteriophage). Phi:AT Process of releasing mature phage particles (filamentous phages) by passing through bacterial membranes. non-lytic viral release GO:0046753 phage excretion Phage ontology phi:0000250 phage extrusion phi:0000250 Process of releasing mature phage particles (filamentous phages) by passing through bacterial membranes. PHI:AT PHI:IM PHI:SC non-lytic viral release GO:0046753 phage excretion Phi:AT Genomic island which carries genes encoding proteins involved in catabolism, usually of man-made toxic compounds (chlorinated aromatic and aliphatic compounds for instance). Phage ontology metabolic island phi:0000251 catabolic island phi:0000251 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 metabolic island SO:0000774 Genomic island that carries genes encoding proteins involved in symbiosis, usually with plants. SO:0000776 Phage ontology phi:0000252 SO definition: A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria. symbiosis island phi:0000252 Genomic island that carries genes encoding proteins involved in symbiosis, usually with plants. SO:0000776 Genomic island whose presence increases the fitness of the host. SO:0000775 adaptive island Phage ontology phi:0000253 fitness island phi:0000253 Genomic island whose presence increases the fitness of the host. PHI:AT PHI:GC adaptive island SO:0000775 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. Phage ontology phi:0000254 integrative conjugative transposon true phi:0000254 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 The nucleotide sequence of a virus that infects bacteria. SO:0001042 phage sequence Phage ontology phi:0000255 phage genome phi:0000255 The nucleotide sequence of a virus that infects bacteria. SO:0001042 phage sequence SO:0001042 A DS DNA phage that integrates and replicates by transpositional recombination. Phage ontology phi:0000256 transposable phage phi:0000256 A DS DNA phage that integrates and replicates by transpositional recombination. PHI:AT PHI:GC Virus that infect bacteria. phage phage particle Phage ontology phi:0000257 bacteriophage phi:0000257 Virus that infect bacteria. PHI:AT PHI:GC phage PHI:AT phage particle PHI:AT Components associated with plasmids. Wikipedia:thioredoxin Phage ontology phi:0000258 plasmid component phi:0000258 Components associated with plasmids. PHI:AT Any process that changes the level of transcription of plasmid genes. phi:0000362 Wikipedia:thioredoxin Phage ontology phi:0000259 plasmid process phi:0000259 Any process that changes the level of transcription of plasmid genes. PHI:AT Genome of a DS DNA phage that integrates and replicates by transpositional recombination. Phage ontology phi:0000260 transposable phage genome phi:0000260 Genome of a DS DNA phage that integrates and replicates by transpositional recombination. PHI:AT PHI:GC 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. Phage ontology phi:0000261 type V protein secretion system complex phi:0000261 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 Poisonous activity, especially of proteins or conjugated proteins produced by certain animals, higher plants, and pathogenic bacteria. : effector Phage ontology phi:0000262 toxin phi:0000262 Poisonous activity, especially of proteins or conjugated proteins produced by certain animals, higher plants, and pathogenic bacteria. PHI:AT : Dorland's Medical Dictionary 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 Phage ontology phi:0000263 Term and definition differ from those in GO. type IV protein secretion/mating pair formation system complex phi:0000263 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 Protein associated with the bacterial nucleoid. Phage ontology phi:0000264 nucleoid associated protein phi:0000264 Protein associated with the bacterial nucleoid. PHI:AT 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 Phage ontology phi:0000265 type I protein secretion system complex phi:0000265 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 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 Phage ontology phi:0000266 type II protein secretion system complex phi:0000266 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 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 Phage ontology injectisome phi:0000267 Definition differs from GO. type III protein secretion system complex phi:0000267 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 Process of bidirectional (theta) vegetative replication of a plasmid DNA genome. Phage ontology phi:0000268 plasmid vegetative DNA replication phi:0000268 Process of bidirectional (theta) vegetative replication of a plasmid DNA genome. PHI:AT Process of sigma-type replication of a plasmid DNA genome from the origin of transfer oriT, during conjugation. Phage ontology phi:0000269 plasmid conjugative DNA replication phi:0000269 Process of sigma-type replication of a plasmid DNA genome from the origin of transfer oriT, during conjugation. PHI:AT A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. SO:0000724 Phage ontology phi:0000270 oriT phi:0000270 A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. SO:0000724 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 Phage ontology unidirectional conjugation phi:0000271 It is essential NOT to use 'male' and female' because any bacterium can be donor and recipient even at the same time. intercellular transfer by conjugation phi:0000271 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 unidirectional conjugation GO:0009291 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. Phage ontology phi:0000272 type IV secretion system coupling protein phi:0000272 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 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. Phage ontology flagellin phi:0000273 Several terms associated to pilus and flagllum as components and their biogenesis are in GO. pilin phi:0000273 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 A proteinaceous hair-like appendage on the surface of bacteria; range from 2-8 nm in diameter. GO:0009289 Phage ontology phi:0000274 fimbrium phi:0000274 A proteinaceous hair-like appendage on the surface of bacteria; range from 2-8 nm in diameter. GO:0009289 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. Phage ontology phi:0000275 type IV secretion system pilin phi:0000275 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 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. Phage ontology phi:0000276 VirB3 related outer membrane protein true phi:0000276 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 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. Phage ontology phi:0000277 type IV secretion system motor phi:0000277 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 Component (TrbJ/TraE) of the T4SS pilus that may be involved in adhesion. Phage ontology phi:0000278 type IV secretion system minor pilus component phi:0000278 Component (TrbJ/TraE) of the T4SS pilus that may be involved in adhesion. PHI:AT Protein of the T4SS, also involved in mating pair formation prior to unidirectional conjugation and that perforates the peptidoglycan cell wall. Phage ontology phi:0000279 VirB1 related cell wall hydrolase activity true phi:0000279 Protein of the T4SS, also involved in mating pair formation prior to unidirectional conjugation and that perforates the peptidoglycan cell wall. PHI:AT Polytopic inner membrane protein (VirB6/TrbL/TraG/), which is part of the lumen of the T4SS-Mating pair formation channel. Phage ontology phi:0000280 type IV secretion system-Mpf stabilizer phi:0000280 Polytopic inner membrane protein (VirB6/TrbL/TraG/), which is part of the lumen of the T4SS-Mating pair formation channel. PHI:AT Lipoprotein component (VirB7/TrbH/TraV/TraI) that connects the pilus to the core of the T4SS-Mating pair formation complex. Phage ontology phi:0000281 type IV secretion system pilus associated lipoprotein phi:0000281 Lipoprotein component (VirB7/TrbH/TraV/TraI) that connects the pilus to the core of the T4SS-Mating pair formation complex. PHI:AT 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. Phage ontology phi:0000282 VirB8 related inner-outer membrane bridging protein phi:0000282 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 Periplasm spanning and outer membrane component of T4SS formed of the VirB9/TrbG/TraK/TraN subunit. Phage ontology phi:0000283 type IV secretion system secretin phi:0000283 Periplasm spanning and outer membrane component of T4SS formed of the VirB9/TrbG/TraK/TraN subunit. PHI:AT A nodal point connecting the inner and outer membrane components of the T4SS formed of VirB10/TrbI/TraB/TraO subunits. Phage ontology phi:0000284 type IV secretion system bridging component phi:0000284 A nodal point connecting the inner and outer membrane components of the T4SS formed of VirB10/TrbI/TraB/TraO subunits. PHI:AT Hexameric ring shaped NTPase similar to the F1-ATPase molecular motors and that fuels the T4SS and TIISS. GO:0015219 Phage ontology phi:0000285 VirB11 typeII/IV secretion NTPase activity true phi:0000285 Hexameric ring shaped NTPase similar to the F1-ATPase molecular motors and that fuels the T4SS and TIISS. PHI:AT 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. PMID:16458574 Phage ontology phi:0000286 type III secretion system needle ruler phi:0000286 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 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 ) . Phage ontology phi:0000287 type III secretion outer membrane ring phi:0000287 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 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. Phage ontology phi:0000288 type III secretion system extracellular needle phi:0000288 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 Terminal structure of the needle made of protein LcrV (PcrV, AcrV, IpaD) serving as a scaffold for the translocation pore YopBD. Phage ontology phi:0000289 type III secretion system needle tip phi:0000289 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 Component of the injectisome that spans the outer membrane and contains YscC subunits. Phage ontology phi:0000290 type III secretion system secretin phi:0000290 Component of the injectisome that spans the outer membrane and contains YscC subunits. PHI:AT PHI:GC 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. translocation pore Phage ontology phi:0000291 type III secretion system translocator phi:0000291 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 Peptidase component of the TIISS system. Phage ontology phi:0000292 type II secretion T2SO protein activity true phi:0000292 Peptidase component of the TIISS system. PHI:AT T2SF Out etc? Phage ontology phi:0000293 type II secretion system outer membrane component phi:0000293 T2SF Out etc? PHI:AT Envelope protein component of TIISS. PulD, Out? etc. Phage ontology secretin phi:0000294 type II secretion envelope protein phi:0000294 Envelope protein component of TIISS. PulD, Out? etc. PHI:AT 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. MS ring Phage ontology phi:0000295 type III secretion inner membrane ring phi:0000295 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 MS ring PHI:GC Cytoplasmic ring component of the type III secretion machine, which includes YscQ subunits and probably YScK and YscL and the YscN ATpase. Phage ontology phi:0000296 type III secretion system cytoplasmic ring component phi:0000296 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 An origin of vegetative replication in plasmids and phages. SO:0000952 Phage ontology phi:0000297 oriV phi:0000297 An origin of vegetative replication in plasmids and phages. SO:0000952 A self-replicating linear or circular DNA molecule that is distinct from a chromosome in the organism. SO:00155 plasmid Phage ontology phi:0000298 "Plasmid" in SO. Add "linear" in SO definition as it is. plasmid genome phi:0000298 A self-replicating linear or circular DNA molecule that is distinct from a chromosome in the organism. SO:0000155 The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. SO:0000296 Phage ontology phi:0000299 origin of replication phi:0000299 The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. SO:0000296 An MGE that is integrated into the host chromosome. SO:0001039 Phage ontology phi:0000300 integrated mobile genetic element phi:0000300 An MGE that is integrated into the host chromosome. SO:0001039 A transposon where the mechanism of transposition is via a DNA intermediate. SO:0000182 Phage ontology phi:0000301 DNA transposon phi:0000301 A transposon where the mechanism of transposition is via a DNA intermediate. SO:0000182 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 Phage ontology phi:0000302 inverted repeat phi:0000302 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 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 Phage ontology phi:0000303 Should be connected to chromsome segregation? GO:0007059? plasmid partitioning phi:0000303 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 The recombination process that separates plasmid dimers or higher multimers into monomers. Phage ontology phi:0000304 plasmid dimer resolution phi:0000304 The recombination process that separates plasmid dimers or higher multimers into monomers. PHI:AT Any process that controls the initiation of bidirectional (theta) vegetative replication of a plasmid DNA genome. Phage ontology copy number control phi:0000305 regulation of vegetative plasmid DNA replication phi:0000305 Any process that controls the initiation of bidirectional (theta) vegetative replication of a plasmid DNA genome. PHI:AT copy number control PHI:AT Any process that controls plasmid DNA conjugation. Phage ontology phi:0000306 regulation of plasmid DNA conjugation phi:0000306 Any process that controls plasmid DNA conjugation. PHI:AT Fiber attached to the collar structure of some phages. Phage ontology phi:0000307 capsid collar fiber phi:0000307 Fiber attached to the collar structure of some phages. PHI:AT PHI:HWA Small disk located below some phage heads. Phage ontology phi:0000308 capsid collar phi:0000308 Small disk located below some phage heads. PHI:AT PHI:HWA A constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae). Phage ontology phi:0000309 capsid neck phi:0000309 A constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae). PHI:AT PHI:HWA Fiber appended at the neck at the base of some phage heads. wisker Phage ontology phi:0000310 capsid neck fiber phi:0000310 Fiber appended at the neck at the base of some phage heads. PHI:AT PHI:IM PHI:SC wisker PHI:AT Integrated genome of a transposable phage. Phage ontology phi:0000311 transposable prophage phi:0000311 Integrated genome of a transposable phage. PHI:AT PHI:GC Internal activating sequence for transposition in transposable phages. It transiently binds transposase to stimulate transpososome synapsis. Phage ontology phi:0000312 IAS phi:0000312 Internal activating sequence for transposition in transposable phages. It transiently binds transposase to stimulate transpososome synapsis. PHI:AT PHI:GC 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. Phage ontology phi:0000313 type IV secretion system pilin maturation phi:0000313 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 Ontology for non-phage prokaryotic mobile genetic elements. Phage ontology phi:0000314 MeGO phi:0000314 Ontology for non-phage prokaryotic mobile genetic elements. PHI:AT Definition? Phage ontology phi:0000315 plasmid entry exclusion phi:0000315 Definition? PHI:AT The regulated release of proteins from a cell or group of cells. GO:0009306 Phage ontology phi:0000316 protein secretion phi:0000316 The regulated release of proteins from a cell or group of cells. GO:0009306 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. PMID:19396961 XX:<new dbxref> Phage ontology phi:0000317 relaxase activity phi:0000317 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: Def? Phage ontology phi:0000318 plasmid fertility inhibition phi:0000318 Def? PHI:AT 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). http://en.wikipedia.org/wiki/Autoinducer Phage ontology phi:0000319 autoinducer synthesis phi:0000319 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 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. http://en.wikipedia.org/wiki/Lantibiotics Phage ontology phi:0000320 lantibiotic biosynthesis phi:0000320 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 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. http://en.wikipedia.org/wiki/Exotoxin#Injected_toxins Phage ontology phi:0000321 intracellular AB toxin activity phi:0000321 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 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. PMID:19325885 Phage ontology phi:0000322 Needs to be checked by Laurence. post-segregational killing phi:0000322 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 A molecular entity with a toxin disposition\, the realization of which damages host cells. IDO:0000584 Phage ontology phi:0000323 cytotoxin phi:0000323 A molecular entity with a toxin disposition\, the realization of which damages host cells. IDO:0000584 Def to be provided. Phage ontology copy number control phi:0000324 plasmid mobilization phi:0000324 Def to be provided. PHI:AT Molecular functions associated with plasmids. Phage ontology phi:0000325 plasmid activity phi:0000325 Molecular functions associated with plasmids. PHI:AT No process, component or activity can yet be assigned to this phage function. Phage ontology phi:0000326 phage function unknown phi:0000326 No process, component or activity can yet be assigned to this phage function. PHI:AT Phage ontoloy Phage ontology phi:0000327 PhiGO true phi:0000327 Phage ontoloy PHI:AT Process by which tailed phage base plates are assembled. Phage ontology phi:0000328 phage base plate assembly phi:0000328 Process by which tailed phage base plates are assembled. PHI:AT The process by which a segment of DNA is inverted from its original orientation. Phage ontology phi:0000329 DNA inversion phi:0000329 The process by which a segment of DNA is inverted from its original orientation. PHI:AT The process by which a segment of DNA is inverted from its original orientation through the action of a site-specific recombinase. Phage ontology phi:0000330 site-specific DNA inversion phi:0000330 The process by which a segment of DNA is inverted from its original orientation through the action of a site-specific recombinase. PHI:AT 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. Phage ontology phi:0000331 phage genome circularization phi:0000331 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 Any process through which a prophage inhibits the development of an unrelated, usually virulent superinfecting phage. Phage ontology phi:0000332 prophage mediated phage exclusion phi:0000332 Any process through which a prophage inhibits the development of an unrelated, usually virulent superinfecting phage. PHI:AT PHI:IM No process, component or activity can yet be assigned to this plasmid function. Phage ontology phi:0000333 plasmid function unknown phi:0000333 No process, component or activity can yet be assigned to this plasmid function. PHI:AT Any process through which a plasmid inhibits the development of an infecting phage. Phage ontology phi:0000334 plasmid mediated phage exclusion phi:0000334 Any process through which a plasmid inhibits the development of an infecting phage. PHI:AT PHI:IM Any process by which a phage activates or represses the expression or the activity of one or more of its host proteins. GO:0019054 GO:0019057 GO:0043921 regulation of host mRNA translation by virus Phage ontology modification by virus of host cellular process modulation by virus of host transcription phi:0000335 phage mediated modulation of host functions phi:0000335 Any process by which a phage activates or represses the expression or the activity of one or more of its host proteins. PHI:AT regulation of host mRNA translation by virus GO:0019057 modification by virus of host cellular process GO:001905 modulation by virus of host transcription GO:0043921 Any process by which a plasmid activates or represses the expression or the activity of one or more of its host proteins. Phage ontology phi:0000336 plasmid mediated modulation of host functions phi:0000336 Any process by which a plasmid activates or represses the expression or the activity of one or more of its host proteins. PHI:AT Any process that results in preventing or decreasing the SOS response of the bacterial host. Phage ontology phi:0000337 plasmid mediated inhibition of host SOS repsonse phi:0000337 Any process that results in preventing or decreasing the SOS response of the bacterial host. PHI:AT A protein activity necessary for the correct non-covalent folding or unfolding of another protein. http://en.wikipedia.org/wiki/Autoinducer Phage ontology phi:0000338 chaperon activity phi:0000338 A protein activity necessary for the correct non-covalent folding or unfolding of another protein. PHI:AT Cell wall transglycosylase synthesized by a phage during its lytic cycle and responsible for host cell lysis. Phage ontology phi:0000339 cell wall degrading lysozyme activity phi:0000339 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 Cell wall amidase synthesized by a phage during its lytic cycle and responsible for host cell lysis. Phage ontology phi:0000340 cell wall degrading amidase activity phi:0000340 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 Cell wall endopeptidase synthesized by a phage during its lytic cycle and responsible for host cell lysis. Phage ontology phi:0000341 cell wall degrading endopeptidase activity phi:0000341 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 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. PMID:17900620 Phage ontology phi:0000342 spanin phi:0000342 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 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. PMID:17900620 Phage ontology phi:0000343 Rz/Rz1-type spanin phi:0000343 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 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. PMID:17900620 Phage ontology phi:0000344 phage T1-type spanin phi:0000344 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 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. PMID:17900620 Phage ontology phi:0000345 Rz-type spanin component phi:0000345 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 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. PMID:17900620 Phage ontology phi:0000346 Rz1-type spanin component phi:0000346 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 Tail fiber component, which during infection is injected into the host, likely piercing a hole in the host cell envelope. PMID:18059287 Phage ontology phi:0000347 phage tail needle phi:0000347 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 Cell wall transglycosylase synthesized by a phage during its lytic cycle and responsible for host cell lysis. Phage ontology phi:0000348 cell wall degrading transglycosylase activity phi:0000348 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 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). Phage ontology phi:0000349 target site selection protein phi:0000349 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 Any process that controls the process of DNA transposition. Phage ontology phi:0000350 regulation of DNA transposition phi:0000350 Any process that controls the process of DNA transposition. PHI:AT Any process that stimulates the process of DNA transposition. Phage ontology phi:0000351 positive regulation of DNA transposition phi:0000351 Any process that stimulates the process of DNA transposition. PHI:AT Any process that inhibits the process of DNA transposition. Phage ontology phi:0000352 negative regulation of DNA transposition phi:0000352 Any process that inhibits the process of DNA transposition. PHI:AT Any phage activity that provokes the disruption of the host bacterial nuceloid. Phage ontology phi:0000353 host nucleoid disruption activity phi:0000353 Any phage activity that provokes the disruption of the host bacterial nuceloid. PHI:AT The process by which genetic material is organized and physically separated and apportioned to two daughter bacterial cells. Phage ontology chromosome segregation phi:0000354 genome segregation phi:0000354 The process by which genetic material is organized and physically separated and apportioned to two daughter bacterial cells. PHI:AT chromosome segregation GO:0007059 A phage or plasmid-mediated process that prevents entry of an infecting phage into the host cell. Phage ontology abortive infection phi:0000355 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. phage entry exclusion phi:0000355 A phage or plasmid-mediated process that prevents entry of an infecting phage into the host cell. PHI:AT abortive infection phi:0000059 Definition? PMID:17046813 Phage ontology phi:0000356 site-specific endoribonuclease activity phi:0000356 Definition? PHI:AT 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. Phage ontology phi:0000357 Is a synonym of type III secretion complex type III secretion complex injectisome true phi:0000357 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 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. Phage ontology phi:0000358 relaxosome assembly phi:0000358 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 This is a temporary term: parent to all functions related to plasmid processes, components and molecular activities. Phage ontology phi:0000359 plasmid phi:0000359 This is a temporary term: parent to all functions related to plasmid processes, components and molecular activities. PHI:AT Any process that inhibits the process of transcription of plasmid genes. Phage ontology phi:0000360 negative regulation of plasmid gene expression phi:0000360 Any process that inhibits the process of transcription of plasmid genes. PHI:AT Any process that stimulates the process of transcription of plasmid genes. Phage ontology phi:0000361 positive regulation of plasmid gene expression phi:0000361 Any process that stimulates the process of transcription of plasmid genes. PHI:AT true phi:0000362 Any process that influences the level of plasmid gene transcription. Phage ontology phi:0000363 regulation of plasmid gene expression phi:0000363 Any process that influences the level of plasmid gene transcription. PHI:AT Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s). Wiki:http://en.wikipedia.org/wiki/Bacteriocin Phage ontology phi:0000364 bacteriocin phi:0000364 Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s). PH:AT 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. Phage ontology phi:0000365 cobalamin biosynthesis phi:0000365 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 Process by which a phage genome reaches a latent state, becoming a component of its host genome. establishment of viral latency GO:0019043 Phage ontology phi:0000366 establishment as a prophage phi:0000366 Process by which a phage genome reaches a latent state, becoming a component of its host genome. PHI:AT PHI:IM PHI:SC establishment of viral latency GO:0019043 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. negative regulation by host of viral transcription GO:0043922 Phage ontology phi:0000367 negative regulation by host of phage transcription phi:0000367 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 negative regulation by host of viral transcription GO:0043922 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. positive regulation by host of viral transcription GO:0043923 Phage ontology phi:0000368 positive regulation by host of phage transcription phi:0000368 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 The process by which a capsid acquires a membrane envelope. viral capsid envelopment GO:0046744 Phage ontology phi:0000369 phage capsid envelopment phi:0000369 The process by which a capsid acquires a membrane envelope. PHI:AT viral capsid envelopment GO:0046744 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. Ariane 2009-06-02T04:00:05Z Phage ontology phi:0000370 lysis-inhibition phi:0000370 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 A resistance to drug that mitigates the damaging effects of an antibiotic. Ariane 2009-06-02T04:47:24Z IDO:0000581 Phage ontology phi:0000371 is_a response to drug, GO:0042493. antibiotic resistance phi:0000371 A resistance to drug that mitigates the damaging effects of an antibiotic. IDO:0000581 The set of processes by which a bacteriophage produces infectious progeny. Ariane 2010-04-21T05:45:42Z Phage ontology phi:0000372 Formerly Ejection/injection. phage lytic cycle phi:0000372 The set of processes by which a bacteriophage produces infectious progeny. PHI:AT PHI:IM PHI:SC 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. Ariane 2010-04-23T02:50:09Z : effector Phage ontology phi:0000373 endotoxin phi:0000373 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 : http://en.wikipedia.org/wiki/Endotoxin 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. Ariane 2010-04-23T02:52:50Z : IDO:0000550 effector Phage ontology phi:0000374 exotoxin phi:0000374 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 : http://en.wikipedia.org/wiki/Exotoxin No process, component or activity can yet be assigned to this predicted prophage function. ariane 2011-07-12T01:43:27Z Phage ontology phi:0000375 predicted prophage function unknown phi:0000375 No process, component or activity can yet be assigned to this predicted prophage function. PHI:AT OBO-Edit 2.1-beta13 01:11:2011 15:47 Phage ontology 1.2 ariane