2.1 01-14-2021 A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning. Meng LIU ICEO: Ontology of Integrative and Conjugative Elements The ICEO Ontology is licensed under CC BY 4.0. Meng LIU A biological ontology in the domain of Integrative and Conjugative Elements. Yongqun He http://creativecommons.org/licenses/by/4.0/ This is an ICE ontology 2.1, representing the information of 271 experimentally verified ICEs from 235 bacterial strains and 311 putative ICEs from 272 Klebsiella pneumoniae. Hong-Yu Ou Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition definition textual definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition definition textual definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor term editor Mia alternative term alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source curator note curator note imported from imported from expand expression to expand expression to OBO foundry unique label OBO foundry unique label elucidation elucidation has associated axiom(nl) has associated axiom(nl) has associated axiom(fol) has associated axiom(fol) An annotation property that represents the ID of oriT sequence in the oriT database oriTDB. Meng LIU (Mia), Oliver He has oriTDB accession An annotation property that represents the ID of a ICE/IME/CIME in the ICE database ICEberg. Meng LIU (Mia), Oliver He has ICEberg accession An annotation property that represents the ID of a T4SS sequence in the T4SS database SecReT4. Meng LIU (Mia), Oliver He has SecReT4 accession has SecReT4 accession An annotation property that represents the hyperlink of a oriT sequence in the oriT database oriTDB. Meng LIU (Mia), Oliver He has oriTDB hyperlink An annotation property that represents the hyperlink of a ICE/IME/CIME in the ICE database ICEberg. Meng LIU (Mia), Oliver He has ICEberg hyperlink has ICEberg hyperlink isolation source of the organism Meng LIU (Mia), Oliver He raw isolation Sequencing Technology of the organism Meng LIU (Mia), Oliver He raw sequencing location source of the organism, inculding continent and country. Meng LIU (Mia), Oliver He raw location Mutilocus sequence typing and serotype of the organism Meng LIU (Mia), Oliver He typing of organism Reannotated signature proteins by ICEberg. protein reannotated role protein reannotated role GI number is a series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record. Meng LIU (Mia), Oliver He has NCBI GI number has NCBI GI number An annotation property that represents the length of a sequence or how big something is Meng LIU (Mia), Oliver He has_size has_size An annotation property that represents which species that a ICE or a moblie genetic element can transfer to. Meng LIU (Mia), Oliver He species can be transferred to an annotation property that represents the completeness of the sequence. Meng LIU (Mia), Oliver He sequence status sequence status An annotation property that represents the ID of a ICE sequence or the host genome in the NCBI GeneBank database. Meng LIU (Mia), Oliver He has NCBI GeneBank accession has NCBI GeneBank accession GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases on a DNA or RNA molecule that are either guanine or cytosine (from a possibility of four different ones, also including adenine and thymine in DNA and adenine and uracil in RNA). Meng LIU (Mia), Oliver He the number outside the square brackets are the GC content of the ICE while the number inside the square brackets are the GC content of the host genome GC content[Genome] GC content[Genome] the coordinates of genetic elements or genes in the chromosome Meng LIU (Mia), Oliver He genome coordinates genome coordinates confirmation status inculdes: experimental verified; predicted in silico; not sure Meng LIU (Mia), Oliver He confirmation status An annotation property that represents a ICE or a mobile genetic element has transfer interaction with IME. Meng LIU (Mia), Oliver He has interaction with IME Meng LIU (Mia), Oliver He An annotation property that represents a ICE or a mobile genetic element has transfer interaction with CIME. has interaction with CIME An annotation property that represents the Meng LIU (Mia), Oliver He insertion site insertion site A GeneID in the NCBI Gene database Oliver He, Yue Liu NCBI GeneID NCBI GeneID the NCBI LocusTag name of a gene Oliver He, Yue Liu NCBI LocusTag NCBI LocusTag a date of content modification Oliver He, Yue Liu modification date modification date The NCBITaxon ontology ID of an organism. Oliver He, Yue Liu organism NCBITaxon ID organism NCBITaxon ID A chromosome ID where a gene is located. Oliver He chromosome ID of gene chromosome ID of gene an annotation property that specifies the type of a gene Oliver He type of gene type of gene an annotation property that specifies a nomenclature status Oliver He nomenclature status nomenclature status An annotation property that represents a gene's association with PubMed publication(s). Yongqun He YH: use the format: PMID: pmid1, pmid2, ... where pmid1 and pmid2 are specfic PubMed IDs (PMIDs). has PubMed association has PubMed association An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property logical macro assertion on an object property Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" cjm 2018-03-13T23:59:29Z is directional form of cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored has_rank has_rank Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Title description Mark Miller 2018-05-11T13:47:29Z has_alternative_id has_alternative_id has_broad_synonym database_cross_reference database_cross_reference has_exact_synonym has_exact_synonym has_narrow_synonym has_narrow_synonym has_obo_namespace has_obo_namespace has_related_synonym has_related_synonym in_subset in_subset label label part of part of has part has part inheres in at all times realizes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes occupies spatial region at some time Meng LIU (Mia), Oliver He exists at a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'. (iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001] has disposition at all times specifically depends on at some time has continuant part at some time has continuant part at all times that part exists Meng LIU (Mia), Oliver He has predicted part a relation between a protein and the organism where this protein belongs to the organism. Meng LIU (Mia), Oliver He is protein of organism The organism where the ICE is first identifed from. Meng LIU (Mia), Oliver He is ICE of organism Meng LIU (Mia), Oliver He a relation between a sequence and the organism where this sequence belongs to the organism. is sequence of organism a in silico relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence Meng LIU (Mia), Oliver He has susceptibility role has gene participant has protein participant has sequence participant a relation between a gene and the ICE where this gene belongs to the ICE in nature. It does not include a foreign gene that is transferred to an ICE by a genetic engineering method. Oliver He, Yue Liu is gene of ICE has susceptibility gene participant Meng LIU (Mia), Oliver He transferred as the inverse property of encodes Meng LIU (Mia), Oliver He encoded_by to specify the genetic code for Meng LIU (Mia), Oliver He encodes a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method. Oliver He, Yue Liu is gene of organism is gene of organism inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role happens during A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) positively regulates A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall adjacent to Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Meng LIU (Mia), Oliver He ends with cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to regulated by negatively regulated by positively regulated by This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within causally downstream of or within p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes directly regulates cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect Clusters of antibiotic resistance genes. May be regulated by a shared promoter or repressor. antibiotic_resistance ARO:0000010 antibiotic resistance gene cluster, cassette, or operon entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity continuant Continuant BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant occurrent Occurrent BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant spatial region temporal region process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocitosis and exocitosis the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89 BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role three-dimensional spatial region site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site bfo BFO:0000030 object gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] bfo BFO:0000040 material entity material entity immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. chebi_ontology CHEBI:23367 molecular entity A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chebi_ontology CHEBI:24431 chemical entity A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. chebi_ontology CHEBI:50047 organic amino compound The removal of the oligonucleotide that contains the DNA damage. The oligonucleotide is formed by dual incisions that flank the site of DNA damage. biological_process GO:0000718 nucleotide-excision repair, DNA damage removal The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms. Wikipedia:Conjugation biological_process GO:0000746 conjugation The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. GO:0055133 MIPS_funcat:10.01.03 Wikipedia:DNA_replication biological_process GO:0006260 DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. DNA replication A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. biological_process Catalysis of the integration of one segment of DNA into another. Reactome:R-HSA-164523 molecular_function GO:0008907 integrase activity Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a phosphotyrosyl intermediate in which the target sequence is first cleaved by the nucleophilic attack by a tyrosine in the active site. tyrosine recombinase site-specific tyrosine recombinase activity molecular_function GO:0009037 tyrosine-based site-specific recombinase activity The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome. MIPS_funcat:10.01.05.03.05 biological_process GO:0015074 DNA integration The removal of a section of DNA from a larger DNA molecule by the making of dual incisions that flank the section to be excised. janelomax 2011-08-03T10:56:37Z biological_process GO:0044349 DNA excision Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation A DNA-dependent DNA replication process in which a single-stranded DNA molecule is synthesized from a circular duplex template. Replication typically does not cease when one circumference has been replicated, but continues around the circumference several more times, producing a long single strand comprising multimers of the replicon. midori 2009-04-22T02:53:52Z rolling circle replication biological_process GO:0070581 rolling circle DNA replication A bacterial protein complex that neutralises its own toxin by complexing the toxin with the antitoxin. The antitoxin can be either a protein or an RNA. The neutralising toxin-antitoxin complex also acts as a transcriptional repressor of the toxin-antitoxin operon. toxin-antitoxin system kmv IntAct:EBI-10919614 IntAct:EBI-13949147 IntAct:EBI-13949218 IntAct:EBI-13949593 IntAct:EBI-13949715 IntAct:EBI-13949851 cellular_component GO:0110001 An example is YoeB (P69348) in Escherichia coli in PMID:16109374 (inferred by direct evidence). toxin-antitoxin complex highly modular mobile genetic element, which has both plasmid-and bacteriophage-like features, encodes gene and proteins for its excision, its transfer by conjugation and its integration. Meng LIU (Mia), Oliver He ICE http://db-mml.sjtu.edu.cn/ICEberg/ integrative and conjugative element Meng LIU (Mia), Oliver He - Pseudomonas aeruginosa PSE9 Meng LIU (Mia), Oliver He - Pseudomonas syringae pv. phaseolicola 1302A Meng LIU (Mia), Oliver He 40 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=40 80.6 kb AM942759 46.73[38.9] 2649499..2730130 ICE with experimental support prfC (PMI2422) ICEPmiUSA1 the integration and excision module of ICE ICEPmiUSA1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiUSA1 IEM the conjugation module of ICE ICEPmiUSA1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiUSA1 CM the regulation module of ICE ICEPmiUSA1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiUSA1 RM the accessory module of ICE ICEPmiUSA1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiUSA1 AM Meng LIU (Mia), Oliver He 39 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=39 111.2 kb Shewanella putrefaciens CP000503 48.28[44.63] 1224492..1335682 ICE with experimental support prfC (Sputw3181_1184) ICESpuPO1 the integration and excision module of ICE ICESpuPO1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpuPO1 IEM the conjugation module of ICE ICESpuPO1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpuPO1 CM the regulation module of ICE ICESpuPO1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpuPO1 RM the accessory module of ICE ICESpuPO1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpuPO1 AM Meng LIU (Mia), Oliver He 16 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=16 107.7 kb CP001485 36.4 2958347..3066049 ICE with experimental support prfC (VCD_003660) ICEVchBan9 the integration and excision module of ICE ICEVchBan9. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchBan9 IEM the conjugation module of ICE ICEVchBan9. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchBan9 CM the regulation module of ICE ICEVchBan9. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchBan9 RM the accessory module of ICE ICEVchBan9. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchBan9 AM Meng LIU (Mia), Oliver He 12 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=12 102.1 kb Bacteroides spp. GQ463140 47.28 1..102122 ICE with experimental support prfC ICEVchBan5 the integration and excision module of ICE ICEVchBan5. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchBan5 IEM the conjugation module of ICE ICEVchBan5. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchBan5 CM the regulation module of ICE ICEVchBan5. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchBan5 RM the accessory module of ICE ICEVchBan5. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchBan5 AM Meng LIU (Mia), Oliver He 22 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=22 98 kb GQ463142 46.73 1..97952 ICE with experimental support prfC ICEVchInd5 [ICEVchHai1] the integration and excision module of ICE ICEVchInd5 [ICEVchHai1]. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchInd5 [ICEVchHai1] IEM the conjugation module of ICE ICEVchInd5 [ICEVchHai1]. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchInd5 [ICEVchHai1] CM the regulation module of ICE ICEVchInd5 [ICEVchHai1]. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchInd5 [ICEVchHai1] RM the accessory module of ICE ICEVchInd5 [ICEVchHai1]. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchInd5 [ICEVchHai1] AM Meng LIU (Mia), Oliver He 23 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=23 83.2 kb GQ463143 46.73 1..83194 ICE with experimental support prfC ICEVchMex1 the integration and excision module of ICE ICEVchMex1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchMex1 IEM the conjugation module of ICE ICEVchMex1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchMex1 CM the regulation module of ICE ICEVchMex1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchMex1 RM the accessory module of ICE ICEVchMex1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchMex1 AM Meng LIU (Mia), Oliver He 21 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=21 95.3 kb GQ463141 46.87 1..95326 ICE with experimental support prfC ICEVchInd4 the integration and excision module of ICE ICEVchInd4. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchInd4 IEM the conjugation module of ICE ICEVchInd4. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchInd4 CM the regulation module of ICE ICEVchInd4. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchInd4 RM the accessory module of ICE ICEVchInd4. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchInd4 AM Meng LIU (Mia), Oliver He 36 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=36 114.2 kb GQ463144 47.59 1..114195 ICE with experimental support MGIVglInd1 MGIVglInd1 can be mobilized in trans by ICEVflInd1 from Vibrio fluvialis/ E. coli CAG18439 to Escherichia coli. (PMID: 20807202; 23204461) prfC ICEVflInd1 the integration and excision module of ICE ICEVflInd1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVflInd1 IEM the conjugation module of ICE ICEVflInd1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVflInd1 CM the regulation module of ICE ICEVflInd1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVflInd1 RM the accessory module of ICE ICEVflInd1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVflInd1 AM Meng LIU (Mia), Oliver He 37 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=37 96.7 kb GQ463139 47.09 1..96676 ICE with experimental support prfC ICEPalBan1 the integration and excision module of ICE ICEPalBan1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPalBan1 IEM the conjugation module of ICE ICEPalBan1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPalBan1 CM the regulation module of ICE ICEPalBan1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPalBan1 RM the accessory module of ICE ICEPalBan1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPalBan1 AM Meng LIU (Mia), Oliver He 38 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=38 103 kb Escherichia coli AJ870986 46.34 1..102985 ICE with experimental support prfC ICEPdaSpa1 the integration and excision module of ICE ICEPdaSpa1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPdaSpa1 IEM the conjugation module of ICE ICEPdaSpa1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPdaSpa1 CM the regulation module of ICE ICEPdaSpa1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPdaSpa1 RM the accessory module of ICE ICEPdaSpa1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPdaSpa1 AM Meng LIU (Mia), Oliver He 43 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=43 88.5 kb Escherichia coli; Bacteroides spp. AY090559 46.48 1..88532 ICE with experimental support prfC R391 the integration and excision module of ICE R391. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ R391 IEM the conjugation module of ICE R391. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ R391 CM the regulation module of ICE R391. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ R391 RM the accessory module of ICE R391. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ R391 AM Meng LIU (Mia), Oliver He 44 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=44 99.5 kb Vibrio cholerae; Escherichia coli; Salmonella enterica serovar Typhimurium AY055428 47.05 1..99483 ICE with experimental support MGIVchUSA1 MGIVchUSA1 can be mobilized in trans by SXT(MO10) from E. coli CAG18420 to E. coli VB112. (PMID: 20807202) MGIVflInd1 MGIVflInd1 can be mobilized in trans by SXT(MO10) from E. coli AD64 to E. coli CAG18439. (PMID: 20807202) MGIVvuTai1 MGIVvuTai1 can be mobilized in trans by SXT(MO10) from E. coli CAG18420 to E. coli VB112. (PMID: 20807202) prfC Resistance to the antibiotics sulfamethoxazole, trimethoprim, chloramphenicol, and streptomycin; Toxin-Antitoxin System SXT(MO10) the integration and excision module of ICE SXT(MO10). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ SXT(MO10) IEM the conjugation module of ICE SXT(MO10). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ SXT(MO10) CM the regulation module of ICE SXT(MO10). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ SXT(MO10) RM the accessory module of ICE SXT(MO10). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ SXT(MO10) AM Meng LIU (Mia), Oliver He 1016 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1016 92.8 kb Escherichia coli 48.01 ICE with experimental support prfC ICEPmiChn1 the integration and excision module of ICE ICEPmiChn1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn1 IEM the conjugation module of ICE ICEPmiChn1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn1 CM the regulation module of ICE ICEPmiChn1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn1 RM the accessory module of ICE ICEPmiChn1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn1 AM Meng LIU (Mia), Oliver He - Escherichia coli ECOR31 Meng LIU (Mia), Oliver He 200013 http://202.120.12.135/oriTDB/browse_oriT_result.php?acc=200013 250 nt intact experimental 17981959 oriT_ ICEKp1 Meng LIU (Mia), Oliver He - Pseudomonas aeruginosa FFUP_PS_690 gene that encodes a protein which nicks the dsDNA and remains covalently bound to the resulting ssDNA Meng LIU (Mia), Oliver He https://en.wikipedia.org/wiki/Relaxase relaxase gene Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/nuccore/AM180355 604427..606028 272563 - protein-coding PMID: 16804543 Recombinase site-specific resolvase family Tn5397, CTn3-Orf3 CD630_05110(tndx) A role played by gene that encodes a protein which has the ability to neutralize a specific toxin. Meng LIU (Mia), Oliver He antitoxin gene role A role played by a material entity that has the ability to neutralize a specific toxin. Meng LIU (Mia), Oliver He https://en.wikipedia.org/wiki/Antitoxin antitoxin role Meng LIU (Mia), Oliver He T4SS gene component type IV secretion system gene component A relaxase is a single-strand DNA transesterase enzyme produced by some prokaryotes and viruses, which nicks the dsDNA and remains covalently bound to the resulting ssDNA. Relaxases are responsible for site- and strand-specific nicks in double-stranded DNA. Meng LIU (Mia), Oliver He MOB https://en.wikipedia.org/wiki/Relaxase relaxase A role played by gene that encodes a protein which is poisonous. Meng LIU (Mia), Oliver He toxin gene role Meng LIU (Mia), Oliver He recombinase gene gene encoding products that mediate an exchange reaction between two DNA templates, resulting in integration of DNA from one of the templates into the other. integrase gene a protein component of T4SS Meng LIU (Mia), Oliver He T4SS protein component https://academic.oup.com/nar/article/47/D1/D660/5165266 type IV secretion system protein component A role played by a protein which is part of T4SS (a cell envelope-spanning complexes that form a channel through which DNA and proteins can travel from the cytoplasm of the donor cell to the cytoplasm of the recipient cell. ) Meng LIU (Mia), Oliver He T4SS protein component role type IV secretion system protein component role A role played by a gene that encodes products to mediate an exchange reaction between two DNA templates and result in integration of DNA from one of the templates into the other. Meng LIU (Mia), Oliver He integrase gene role gene that encodes a transposase enzyme with the DDE motif. Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991504/ DDE transposase gene gene encoding one family of recombinases that use serine to attack and covalently link the DNA during strand exchange. Meng LIU (Mia), Oliver He https://en.wikipedia.org/wiki/Site-specific_recombination serine recombinase gene gene encoding one family of recombinases that use tyrosine to attack and covalently link the DNA during strand exchange. Meng LIU (Mia), Oliver He https://en.wikipedia.org/wiki/Site-specific_recombination tyrosine recombinase gene ICE from Klebsiella pneumoniae Meng LIU (Mia), Oliver He ICEberg database http://db-mml.sjtu.edu.cn/ICEberg/ ICEKp ICE The integration and excision module refers to those genes and sequence within the ICE responsible for the integration and excision of the element from the host chromosome, including genes encoding the integrase and or recombination directionality factor (also known as excisionase, which influences the direction of recombination mediated by the integrase to favor excision). Meng LIU (Mia), Oliver He recombination module component https://academic.oup.com/nar/article/47/D1/D660/5165266 ICE IEM for integration A role played by a gene that encodes a protein for nicking the dsDNA. Meng LIU (Mia), Oliver He relaxase gene role A role played by a gene that encodes products for controlling the directionality of integrase-mediated site-specific recombination reactions. Meng LIU (Mia), Oliver He RDF gene role recombination directionality factor gene role Gene encoding products that involved in controlling the directionality of integrase-mediated site-specific recombination reactions. Meng LIU (Mia), Oliver He RDF gene https://www.ncbi.nlm.nih.gov/pmc/articles/PMC55702/ recombination directionality factor gene gene encoding products that link translocating substrates to the transenvelope secretion conduit. Meng LIU (Mia), Oliver He gene of T4CP https://www.nature.com/articles/nmicrobiol2017114 gene of type IV coupling protein Meng LIU (Mia), Oliver He gene of T4CP role a role played by a gene that encodes a protein which links translocating substrates to the transenvelope secretion conduit. gene of type IV coupling protein role a role played by a gene that encodes a protein for energizing the T4SS system from the cytoplasm and driving the complex assembly and substrate translocation through the channel. Meng LIU (Mia), Oliver He T4SS ATPase gene role Meng LIU (Mia), Oliver He gene of T4SS ATPase A role played by a material entity that contributes to the integration and excision of the element from the host chromosome. Meng LIU (Mia), Oliver He integration and excision module component role The integration and excision module refers to those genes and sequence within the ICE responsible for the integration and excision of the element from the host chromosome, including genes encoding the integrase and or recombination directionality factor (also known as excisionase, which influences the direction of recombination mediated by the integrase to favor excision). Meng LIU (Mia), Oliver He recombination module component https://academic.oup.com/nar/article/47/D1/D660/5165266 ICE IEM for excision Meng LIU (Mia), Oliver He strain An enzyme that mediates an exchange reaction between two DNA templates, resulting in integration of DNA from one of the templates into the other. Meng LIU (Mia), Oliver He Int recombinase https://jb.asm.org/content/185/17/5045 integrase Meng LIU (Mia), Oliver He 46 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=46 54.7 kb Cupriavidus metallidurans AJ536756 63.49 1..54657 ICE with experimental support TTTTTCAT Tn4371 the integration and excision module of ICE Tn4371. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn4371 IEM the conjugation module of ICE Tn4371. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn4371 CM the regulation module of ICE Tn4371. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn4371 RM the accessory module of ICE Tn4371. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn4371 AM Accessory module component refers to genes such as virulence factor (VF) genes and acquired antibiotic resistance genes (ARG) that often exist inside ICEs as the cargo genes and can confer the hosts with selective advantages, which make ICEs a vital role in the process of bacterial adaptation and evolution. Meng LIU (Mia), Oliver He https://academic.oup.com/nar/article/47/D1/D660/5165266 ICE accessory module Meng LIU (Mia), Oliver He 166 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=166 61.8 kb AB546270 63.97 1..61807 ICE with experimental support ICE-KKS the integration and excision module of ICE ICE-KKS. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-KKS IEM the conjugation module of ICE ICE-KKS. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-KKS CM the regulation module of ICE ICE-KKS. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-KKS RM the accessory module of ICE ICE-KKS. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-KKS AM Meng LIU (Mia), Oliver He 2 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=2 52 kb Bacteroides spp. AY515263 49.49 1..51993 ICE with experimental support Tn4555 Tn4555 can be mobilized in trans by CTn341 from Bacteroides vulgatus to Escherichia coli. (PMID: 14702313) CTn341 the integration and excision module of ICE CTn341. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn341 IEM the conjugation module of ICE CTn341. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn341 CM the regulation module of ICE CTn341. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn341 RM the accessory module of ICE CTn341. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn341 AM Meng LIU (Mia), Oliver He 219 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=219 255.5 kb AM902716 61.73[65.48] 1083989..1339502 ICE with experimental support tRNA-Gly (tRNA-10) ICE-GI1 the integration and excision module of ICE ICE-GI1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI1 IEM the conjugation module of ICE ICE-GI1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI1 CM the regulation module of ICE ICE-GI1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI1 RM the accessory module of ICE ICE-GI1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI1 AM gene encoding products that can confer the the ability of bacteria and other microorganisms to resist the effects of an antibiotic to which they were once sensitive. Meng LIU (Mia), Oliver He https://www.medicinenet.com/script/main/art.asp?articlekey=2276 Antibiotic resistance is a major concern of overuse of antibiotics. antibiotic resistance gene Meng LIU (Mia), Oliver He 220 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=220 143.4 kb AM902716 60.59[65.48] 1350129..1493558 ICE with experimental support ICE-GI2 the integration and excision module of ICE ICE-GI2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI2 IEM the conjugation module of ICE ICE-GI2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI2 CM the regulation module of ICE ICE-GI2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI2 RM the accessory module of ICE ICE-GI2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI2 AM Meng LIU (Mia), Oliver He 221 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=221 102.1 kb AM902716 63.02[65.48] 1493541..1595651 ICE with experimental support tRNA-Gly (tRNA-11) ICE-GI3 the integration and excision module of ICE ICE-GI3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI3 IEM the conjugation module of ICE ICE-GI3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI3 CM the regulation module of ICE ICE-GI3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI3 RM the accessory module of ICE ICE-GI3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI3 AM Meng LIU (Mia), Oliver He 222 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=222 159.1 kb AM902716 61.15[65.48] 4417743..4576839 ICE with experimental support tRNA-Gly (tRNA-44) ICE-GI6 the integration and excision module of ICE ICE-GI6. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI6 IEM the conjugation module of ICE ICE-GI6. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI6 CM the regulation module of ICE ICE-GI6. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI6 RM the accessory module of ICE ICE-GI6. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE-GI6 AM Meng LIU (Mia), Oliver He gene encoding products that assist the bacterium colonize the host at the cellular level and are either secretory, membrane associated or cytosolic in nature. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5243249/ virulence factor gene The conjugation module denotes those genes and sequences involved in the conjugal process, such as genes encoding relaxase and the type IV secretion system (T4SS). Meng LIU (Mia), Oliver He https://academic.oup.com/nar/article/47/D1/D660/5165266 ICE conjugation module Meng LIU (Mia), Oliver He 56 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=56 102.8 kb Pseudomonas putida; Pseudomonas aeruginosa; Cupriavidus necator AJ617740 62.51 60..102843 ICE with experimental support tRNA-Gly ICEclc(B13) the integration and excision module of ICE ICEclc(B13). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEclc(B13) IEM the conjugation module of ICE ICEclc(B13). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEclc(B13) CM the regulation module of ICE ICEclc(B13). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEclc(B13) RM the accessory module of ICE ICEclc(B13). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEclc(B13) AM Meng LIU (Mia), Oliver He 174 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=174 105 kb AF440523 64.71 27286..132240 ICE with experimental support tRNA-Gly PAGI-2 the integration and excision module of ICE PAGI-2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAGI-2 IEM the conjugation module of ICE PAGI-2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAGI-2 CM the regulation module of ICE PAGI-2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAGI-2 RM the accessory module of ICE PAGI-2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAGI-2 AM Meng LIU (Mia), Oliver He 1077 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1077 173.8 kb Azoarcus sp. CIBTRif CP011072 4894159..5067957 ICE with experimental support tRNAGly(TTCGATTCCCATCGCCCGCTCCA) ICEXTD the integration and excision module of ICE ICEXTD. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEXTD IEM the conjugation module of ICE ICEXTD. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEXTD CM the regulation module of ICE ICEXTD. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEXTD RM the accessory module of ICE ICEXTD. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEXTD AM Meng LIU (Mia), Oliver He 1010 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1010 86.2 kb Pseudomonas aeruginosa KY852375 63.05 315..86517 ICE with experimental support tRNAGly ICEPae690 the integration and excision module of ICE ICEPae690. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPae690 IEM the conjugation module of ICE ICEPae690. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPae690 CM the regulation module of ICE ICEPae690. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPae690 RM the accessory module of ICE ICEPae690. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPae690 AM Meng LIU (Mia), Oliver He 59 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=59 20.5 kb Bacillus and Listeria species AL009126 35.7[43.51] 529423..549932 ICE with experimental support tRNA-Leu(BSU_tRNA_51) ICEBs1 the integration and excision module of ICE ICEBs1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEBs1 IEM the conjugation module of ICE ICEBs1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEBs1 CM the regulation module of ICE ICEBs1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEBs1 RM the accessory module of ICE ICEBs1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEBs1 AM Meng LIU (Mia), Oliver He 60 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=60 59.4 kb Haemophilus influenzae; Haemophilus parainfluenzae AJ627386 39.1 1..59393 ICE with experimental support tRNA-Leu ICEHin1056 the integration and excision module of ICE ICEHin1056. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEHin1056 IEM the conjugation module of ICE ICEHin1056. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEHin1056 CM the regulation module of ICE ICEHin1056. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEHin1056 RM the accessory module of ICE ICEHin1056. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEHin1056 AM Meng LIU (Mia), Oliver He 960 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=960 56.1 kb Actinobacillus pleuropneumoniae KU551309 27..56176 ICE with experimental support tRNA-Leu (TAA) ICEApl1 the integration and excision module of ICE ICEApl1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEApl1 IEM the conjugation module of ICE ICEApl1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEApl1 CM the regulation module of ICE ICEApl1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEApl1 RM the accessory module of ICE ICEApl1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEApl1 AM Meng LIU (Mia), Oliver He 175 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=175 108 kb CP000438 59.74[66.29] 5251440..5359392 ICE with experimental support tRNA-Lys (Lys47) PAPI-1 the integration and excision module of ICE PAPI-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAPI-1 IEM the conjugation module of ICE PAPI-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAPI-1 CM the regulation module of ICE PAPI-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAPI-1 RM the accessory module of ICE PAPI-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAPI-1 AM Meng LIU (Mia), Oliver He 173 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=173 103.5 kb AY257538 60.93 1..103532 ICE with experimental support tRNA-Lys pKLC102 the integration and excision module of ICE pKLC102. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ pKLC102 IEM the conjugation module of ICE pKLC102. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ pKLC102 CM the regulation module of ICE pKLC102. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ pKLC102 RM the accessory module of ICE pKLC102. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ pKLC102 AM Meng LIU (Mia), Oliver He 176 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=176 99.3 kb EF611301 59.62 1..99276 ICE with experimental support tRNA-Lys (Lys47) PAGI-5 the integration and excision module of ICE PAGI-5. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAGI-5 IEM the conjugation module of ICE PAGI-5. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAGI-5 CM the regulation module of ICE PAGI-5. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAGI-5 RM the accessory module of ICE PAGI-5. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PAGI-5 AM Meng LIU (Mia), Oliver He 78 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=78 35.9 kb AJ278471 34.99 1290..36049 ICE with experimental support fda ICESt1 the integration and excision module of ICE ICESt1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESt1 IEM the conjugation module of ICE ICESt1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESt1 CM the regulation module of ICE ICESt1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESt1 RM the accessory module of ICE ICESt1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESt1 AM Meng LIU (Mia), Oliver He 79 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=79 28.1 kb Streptococcus pyogenes; Enterococcus faecalis AJ586568 36.9 204..28293 ICE with experimental support IME_GB00957_oriT IME_GB00957_oriT is predicted to be mobilized in trans by ICESt3 (PMID: 25832353; 28373865) CIME19258 CIME19258 is predicted to be mobilized in cis by ICESt3 (PMID: 21722203) CIME9 CIME9 is predicted to be mobilized in cic by ICESt3 (PMID: 21722203) CIMEL3catR3 CIMEL3catR3 can be mobilized in cis by ICESt3 from Streptococcus thermophilus to Streptococcus thermophilus (PMID: 21722203) fda ICESt3 the integration and excision module of ICE ICESt3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESt3 IEM the conjugation module of ICE ICESt3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESt3 CM the regulation module of ICE ICESt3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESt3 RM the accessory module of ICE ICESt3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESt3 AM Meng LIU (Mia), Oliver He 288 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=288 133.5 kb AL513382 49.68[52.09] 4409574..4543073 ICE with experimental support tRNA-PheU SPI-7 the integration and excision module of ICE SPI-7. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ SPI-7 IEM the conjugation module of ICE SPI-7. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ SPI-7 CM the regulation module of ICE SPI-7. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ SPI-7 RM the accessory module of ICE SPI-7. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ SPI-7 AM Meng LIU (Mia), Oliver He 113 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=113 109.4 kb FN298494 51.02 1785..111202 ICE with experimental support tRNA-Phe ICESb1 the integration and excision module of ICE ICESb1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESb1 IEM the conjugation module of ICE ICESb1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESb1 CM the regulation module of ICE ICESb1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESb1 RM the accessory module of ICE ICESb1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESb1 AM Meng LIU (Mia), Oliver He 358 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=358 13.3 kb AB435014 30.14 928..14266 ICE with experimental support Tn6012 the integration and excision module of ICE Tn6012. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6012 IEM the conjugation module of ICE Tn6012. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6012 CM the regulation module of ICE Tn6012. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6012 RM the accessory module of ICE Tn6012. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6012 AM Meng LIU (Mia), Oliver He 68 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=68 19.9 kb Staphylococcus aureus FJ231270 29.62 1..19905 ICE with experimental support ICE6013 the integration and excision module of ICE ICE6013. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE6013 IEM the conjugation module of ICE ICE6013. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE6013 CM the regulation module of ICE ICE6013. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE6013 RM the accessory module of ICE ICE6013. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE6013 AM Meng LIU (Mia), Oliver He 160 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=160 47.1 kb NC_004368 37.66[35.63] 385757..432824 ICE with experimental support TnGBS1 the integration and excision module of ICE TnGBS1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ TnGBS1 IEM the conjugation module of ICE TnGBS1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ TnGBS1 CM the regulation module of ICE TnGBS1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ TnGBS1 RM the accessory module of ICE TnGBS1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ TnGBS1 AM Meng LIU (Mia), Oliver He 165 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=165 61 kb FR670347 33.18 1..61030 ICE with experimental support ICE6094 the integration and excision module of ICE ICE6094. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE6094 IEM the conjugation module of ICE ICE6094. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE6094 CM the regulation module of ICE ICE6094. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE6094 RM the accessory module of ICE ICE6094. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE6094 AM Meng LIU (Mia), Oliver He 377 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=377 54.3 kb AE009948 38.35[35.65] 1256680..1311028 ICE with experimental support ICESa2603 the integration and excision module of ICE ICESa2603. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESa2603 IEM the conjugation module of ICE ICESa2603. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESa2603 CM the regulation module of ICE ICESa2603. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESa2603 RM the accessory module of ICE ICESa2603. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESa2603 AM Meng LIU (Mia), Oliver He 311 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=311 88.9 kb CP000407 38.79[41.11] 872967..961817 ICE with experimental support TTATTTAAGAGTAAC ICESsu05ZYH33-1 the integration and excision module of ICE ICESsu05ZYH33-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu05ZYH33-1 IEM the conjugation module of ICE ICESsu05ZYH33-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu05ZYH33-1 CM the regulation module of ICE ICESsu05ZYH33-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu05ZYH33-1 RM the accessory module of ICE ICESsu05ZYH33-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu05ZYH33-1 AM Meng LIU (Mia), Oliver He 76 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=76 63.7 kb Hemolytic Streptococci EU142041 38.14 1..63668 ICE with experimental support ICESde3396 the integration and excision module of ICE ICESde3396. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESde3396 IEM the conjugation module of ICE ICESde3396. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESde3396 CM the regulation module of ICE ICESde3396. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESde3396 RM the accessory module of ICE ICESde3396. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESde3396 AM Meng LIU (Mia), Oliver He 445 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=445 54.9 kb Streptococcus suis v36RF; Streptococcus pyogenes 12RF; Streptococcus pneumoniae R6RF; Streptococcus agalactiae 1357RF FR823304 38.89 1..54879 ICE with experimental support TTATTTAAGAGTAAC ICESsu32457 the integration and excision module of ICE ICESsu32457. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu32457 IEM the conjugation module of ICE ICESsu32457. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu32457 CM the regulation module of ICE ICESsu32457. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu32457 RM the accessory module of ICE ICESsu32457. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu32457 AM Meng LIU (Mia), Oliver He 791 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=791 73.4 kb Streptococcus agalactiae Streptococcus pneumoniae; Streptococcus gordonii; Streptococcus pyogenes; Streptococcus agalactiae;Enterococcus faecalis; Bacillus subtilis CP019978 37.73 629058..702486 ICE with experimental support rumA ICESag37 the integration and excision module of ICE ICESag37. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESag37 IEM the conjugation module of ICE ICESag37. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESag37 CM the regulation module of ICE ICESag37. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESag37 RM the accessory module of ICE ICESag37. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESag37 AM Meng LIU (Mia), Oliver He protein of Bacteria a typical class of ICEs which transfer as single stranded DNA molecules and require T4SS and can both found in Gram-positive bacteria and Gram-negative bacteria Meng LIU (Mia), Oliver He T4SS-type ICE http://db-mml.sjtu.edu.cn/ICEberg/ T4SS-type integrative and conjugative element a T4SS-type ICE of Gram-positive bacteria Meng LIU (Mia), Oliver He T4SS-type ICE in Gram-positive bacteria http://db-mml.sjtu.edu.cn/ICEberg/ T4SS-type integrative and conjugative element in Gram-positive bacteria a T4SS-type ICE of Gram-negative bacteria Meng LIU (Mia), Oliver He T4SS-type ICE in Gram-negative bacteria http://db-mml.sjtu.edu.cn/ICEberg/ T4SS-type integrative and conjugative element in Gram-negative bacteria Meng LIU (Mia), Oliver He 70 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=70 38.9 kb Escherichia coli AY233333 47.73 1..38927 ICE with experimental support tRNA-Asn ICEEc1 the integration and excision module of ICE ICEEc1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEc1 IEM the conjugation module of ICE ICEEc1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEc1 CM the regulation module of ICE ICEEc1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEc1 RM the accessory module of ICE ICEEc1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEc1 AM 126 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=126 75935 bp Klebsiella pneumoniae;Escherichia coli 3: complete in a genome file AP006725 52.18[57.68] 3395836..3471770 1: experimental GIE492 GIE492 is predicted to be mobilized in trans by ICEKp1 (PMID: 27375573; 29165361) tRNA-asn(KP1_6086) 19447910; 17981959 ICEKp1 the integration and excision module of ICE ICEKp1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEKp1 IEM The set of gene and non-gene sequence responsible for the DNA integration process in the integration and excision module of ICE ICEKp1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEKp1 IEM for integration Meng LIU (Mia), Oliver He The set of gene and non-gene sequence responsible for the DNA excision process in the integration and excision module of ICE ICEKp1. http://db-mml.sjtu.edu.cn/ICEberg/ ICEKp1 IEM for excision the conjugation module of ICE ICEKp1 Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEKp1 CM the regulation module of ICE ICEKp1 Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEKp1 RM the accessory module of ICE ICEKp1 Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEKp1 AM Meng LIU (Mia), Oliver He 961 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=961 92.7 kb Actinobacillus pleuropneumoniae MF187965 46.94 1..92660 ICE with experimental support prfC ICEApl2 the integration and excision module of ICE ICEApl2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEApl2 IEM the conjugation module of ICE ICEApl2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEApl2 CM the regulation module of ICE ICEApl2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEApl2 RM the accessory module of ICE ICEApl2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEApl2 AM Meng LIU (Mia), Oliver He 1017 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1017 99.4 kb KX243404 46.98 1..99355 ICE with experimental support ICEPmiCHN1586 the integration and excision module of ICE ICEPmiCHN1586. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN1586 IEM the conjugation module of ICE ICEPmiCHN1586. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN1586 CM the regulation module of ICE ICEPmiCHN1586. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN1586 RM the accessory module of ICE ICEPmiCHN1586. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN1586 AM Meng LIU (Mia), Oliver He 1020 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1020 97.1 kb KX243405 47.03 1..97078 ICE with experimental support ICEPmiCHN2407 the integration and excision module of ICE ICEPmiCHN2407. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN2407 IEM the conjugation module of ICE ICEPmiCHN2407. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN2407 CM the regulation module of ICE ICEPmiCHN2407. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN2407 RM the accessory module of ICE ICEPmiCHN2407. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN2407 AM Meng LIU (Mia), Oliver He 1028 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1028 90.6 kb Escherichia coli J53 KY437728 47.54 1..90566 ICE with experimental support ICEPmiChn4 the integration and excision module of ICE ICEPmiChn4. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn4 IEM the conjugation module of ICE ICEPmiChn4. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn4 CM the regulation module of ICE ICEPmiChn4. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn4 RM the accessory module of ICE ICEPmiChn4. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn4 AM Meng LIU (Mia), Oliver He 1019 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1019 104.4 kb Escherichia coli J53 KY437726 47.34 1..104371 ICE with experimental support ICEPmiChn2 the integration and excision module of ICE ICEPmiChn2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn2 IEM the conjugation module of ICE ICEPmiChn2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn2 CM the regulation module of ICE ICEPmiChn2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn2 RM the accessory module of ICE ICEPmiChn2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiChn2 AM Meng LIU (Mia), Oliver He 1018 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1018 76.2 kb KX243413 47.11 1..76218 ICE with experimental support ICEPmiCHN1809 the integration and excision module of ICE ICEPmiCHN1809. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN1809 IEM the conjugation module of ICE ICEPmiCHN1809. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN1809 CM the regulation module of ICE ICEPmiCHN1809. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN1809 RM the accessory module of ICE ICEPmiCHN1809. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN1809 AM Meng LIU (Mia), Oliver He 1027 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1027 90 kb KX243416 47.77 1..89996 ICE with experimental support ICEPmiCHN3335 the integration and excision module of ICE ICEPmiCHN3335. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN3335 IEM the conjugation module of ICE ICEPmiCHN3335. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN3335 CM the regulation module of ICE ICEPmiCHN3335. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN3335 RM the accessory module of ICE ICEPmiCHN3335. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmiCHN3335 AM a special class of ICEs, which have the ability to replicate autonomously like a plasmid, transfer as double stranded circular DNA molecules and do not require a genuine T4SS and are only found in Actinobacteria. Meng LIU (Mia), Oliver He AICE http://db-mml.sjtu.edu.cn/ICEberg/ actinomycete integrative and conjugative element Meng LIU (Mia), Oliver He protein of Klebsiella Meng LIU (Mia), Oliver He protein of Klebsiella pneumoniae NTUH-K2044 Meng LIU (Mia), Oliver He 827 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=827 55.3 kb Streptococcus pyogenes; Streptococcus pneumoniae KU056701 39.56 1..55259 ICE with experimental support ICESpy009 the integration and excision module of ICE ICESpy009. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpy009 IEM the conjugation module of ICE ICESpy009. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpy009 CM the regulation module of ICE ICESpy009. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpy009 RM the accessory module of ICE ICESpy009. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpy009 AM Meng LIU (Mia), Oliver He 406 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=406 98.1 kb AJ627388 47.78 1402..99513 ICE with experimental support tRNA-Phe YAPI the integration and excision module of ICE YAPI. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ YAPI IEM the conjugation module of ICE YAPI. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ YAPI CM the regulation module of ICE YAPI. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ YAPI RM the accessory module of ICE YAPI. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ YAPI AM Meng LIU (Mia), Oliver He 172 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=172 52.5 kb Mycoplasma agalactiae AY657002 39.15 1..52491 ICE with experimental support Tn1207.3 the integration and excision module of ICE Tn1207.3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn1207.3 IEM the conjugation module of ICE Tn1207.3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn1207.3 CM the regulation module of ICE Tn1207.3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn1207.3 RM the accessory module of ICE Tn1207.3. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn1207.3 AM Meng LIU (Mia), Oliver He 409 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=409 45.5 kb FR691054 31.07 1694..47149 ICE with experimental support 3' end of the rum gene ICESp1108 the integration and excision module of ICE ICESp1108. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp1108 IEM the conjugation module of ICE ICESp1108. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp1108 CM the regulation module of ICE ICESp1108. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp1108 RM the accessory module of ICE ICESp1108. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp1108 AM Meng LIU (Mia), Oliver He 69 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=69 27.2 kb Mycoplasma agalactiae FP671138 27.37[29.62] 813253..840487 ICE with experimental support ICEA(5632)-I the integration and excision module of ICE ICEA(5632)-I. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-I IEM the conjugation module of ICE ICEA(5632)-I. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-I CM the regulation module of ICE ICEA(5632)-I. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-I RM the accessory module of ICE ICEA(5632)-I. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-I AM Meng LIU (Mia), Oliver He 225 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=225 27.2 kb FP671138 27.39[29.62] 343591..370761 ICE with experimental support ICEA(5632)-II the integration and excision module of ICE ICEA(5632)-II. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-II IEM the conjugation module of ICE ICEA(5632)-II. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-II CM the regulation module of ICE ICEA(5632)-II. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-II RM the accessory module of ICE ICEA(5632)-II. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-II AM Meng LIU (Mia), Oliver He 226 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=226 27.2 kb FP671138 27.37[29.62] 560640..587874 ICE with experimental support ICEA(5632)-III the integration and excision module of ICE ICEA(5632)-III. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-III IEM the conjugation module of ICE ICEA(5632)-III. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-III CM the regulation module of ICE ICEA(5632)-III. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-III RM the accessory module of ICE ICEA(5632)-III. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEA(5632)-III AM Meng LIU (Mia), Oliver He 72 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=72 23.8 kb AY168953 28.63 2674..26451 ICE with experimental support pdhA, orf251 ICEF-I the integration and excision module of ICE ICEF-I. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEF-I IEM the conjugation module of ICE ICEF-I. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEF-I CM the regulation module of ICE ICEF-I. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEF-I RM the accessory module of ICE ICEF-I. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEF-I AM Meng LIU (Mia), Oliver He 224 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=224 25.6 kb BA000017 35.39[32.88] 436064..461681 ICE with experimental support GMP-synthase gene (SAV0391) Tn5801 the integration and excision module of ICE Tn5801. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5801 IEM the conjugation module of ICE Tn5801. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5801 CM the regulation module of ICE Tn5801. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5801 RM the accessory module of ICE Tn5801. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5801 AM Meng LIU (Mia), Oliver He - Bacteroides uniformis WH207 Meng LIU (Mia), Oliver He 159 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=159 33.4 kb Hemolytic Streptococci NC_004368 38.11[35.63] 1163887..1197331 ICE with experimental support Intergenic regions upstream of &sigma;-A promoters TnGBS2 (genomic island X) the integration and excision module of ICE TnGBS2 (genomic island X). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ TnGBS2 (genomic island X) IEM the conjugation module of ICE TnGBS2 (genomic island X). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ TnGBS2 (genomic island X) CM the regulation module of ICE TnGBS2 (genomic island X). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ TnGBS2 (genomic island X) RM the accessory module of ICE TnGBS2 (genomic island X). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ TnGBS2 (genomic island X) AM Meng LIU (Mia), Oliver He 242 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=242 71 kb AE017125 33.15[35.93] 223218..294244 ICE with experimental support HH0233/HH0302 HHGI1 the integration and excision module of ICE HHGI1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ HHGI1 IEM the conjugation module of ICE HHGI1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ HHGI1 CM the regulation module of ICE HHGI1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ HHGI1 RM the accessory module of ICE HHGI1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ HHGI1 AM Meng LIU (Mia), Oliver He 152 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=152 77.1 kb Bacteroides fragilis CR626927 45.44[43.19] 1727162..1804281 ICE with experimental support CTn9343 the integration and excision module of ICE CTn9343. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn9343 IEM the conjugation module of ICE CTn9343. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn9343 CM the regulation module of ICE CTn9343. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn9343 RM the accessory module of ICE CTn9343. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn9343 AM Meng LIU (Mia), Oliver He 375 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=375 92.5 kb AM942759 44.85[38.9] 2793762..2886224 ICE with experimental support tRNA-Phe (PMIt057) ICEPm1 the integration and excision module of ICE ICEPm1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPm1 IEM the conjugation module of ICE ICEPm1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPm1 CM the regulation module of ICE ICEPm1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPm1 RM the accessory module of ICE ICEPm1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPm1 AM Meng LIU (Mia), Oliver He 394 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=394 51.4 kb CP001834 34.99[34.91] 2295682..2347036 ICE with experimental support TTATACCATAATTAC Tn6098 the integration and excision module of ICE Tn6098. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6098 IEM the conjugation module of ICE Tn6098. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6098 CM the regulation module of ICE Tn6098. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6098 RM the accessory module of ICE Tn6098. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6098 AM Meng LIU (Mia), Oliver He 396 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=396 42.7 kb CP001217 33.95[38.81] 451991..494695 ICE with experimental support type I R-M system R protein (HPP12_0436) ICEHpyP12-1 the integration and excision module of ICE ICEHpyP12-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEHpyP12-1 IEM the conjugation module of ICE ICEHpyP12-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEHpyP12-1 CM the regulation module of ICE ICEHpyP12-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEHpyP12-1 RM the accessory module of ICE ICEHpyP12-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEHpyP12-1 AM Meng LIU (Mia), Oliver He 436 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=436 106 kb AJ870974 54.03 1298..107263 ICE with experimental support tRNA-Lys PPHGI-1 the integration and excision module of ICE PPHGI-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PPHGI-1 IEM the conjugation module of ICE PPHGI-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PPHGI-1 CM the regulation module of ICE PPHGI-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PPHGI-1 RM the accessory module of ICE PPHGI-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ PPHGI-1 AM Meng LIU (Mia), Oliver He 64 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=64 100.9 kb Bacteroides spp.; Escherichia coli AY345595 47.49 1..100903 ICE with experimental support AATCTGNNAAAT CTnBST the integration and excision module of ICE CTnBST. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnBST IEM the conjugation module of ICE CTnBST. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnBST CM the regulation module of ICE CTnBST. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnBST RM the accessory module of ICE CTnBST. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnBST AM Meng LIU (Mia), Oliver He 66 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=66 114.3 kb Escherichia coli FN298496 54.95 11966..126312 ICE with experimental support tRNA-Phe CTnscr94 the integration and excision module of ICE CTnscr94. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnscr94 IEM the conjugation module of ICE CTnscr94. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnscr94 CM the regulation module of ICE CTnscr94. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnscr94 RM the accessory module of ICE CTnscr94. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnscr94 AM Meng LIU (Mia), Oliver He 67 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=67 33.3 kb Enterococcus faecium FN555436 34.69 1..33262 ICE with experimental support ribosomal L31 gene Tn6000 (EfcTn1) the integration and excision module of ICE Tn6000 (EfcTn1). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6000 (EfcTn1) IEM the conjugation module of ICE Tn6000 (EfcTn1). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6000 (EfcTn1) CM the regulation module of ICE Tn6000 (EfcTn1). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6000 (EfcTn1) RM the accessory module of ICE Tn6000 (EfcTn1). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6000 (EfcTn1) AM Meng LIU (Mia), Oliver He 71 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=71 93.9 kb Salmonella enterica serovar Typhimurium and Yersinia pseudotuberculosis GU725392 50.84 77..93971 ICE with experimental support tRNA-Phe ICEEc2 the integration and excision module of ICE ICEEc2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEc2 IEM the conjugation module of ICE ICEEc2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEc2 CM the regulation module of ICE ICEEc2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEc2 RM the accessory module of ICE ICEEc2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEc2 AM Meng LIU (Mia), Oliver He 74 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=74 54.4 kb Enterobacteriaceae AM229678 53.06 292..54752 ICE with experimental support tRNA-Asn ICEEcIHE3034-1 the integration and excision module of ICE ICEEcIHE3034-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEcIHE3034-1 IEM the conjugation module of ICE ICEEcIHE3034-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEcIHE3034-1 CM the regulation module of ICE ICEEcIHE3034-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEcIHE3034-1 RM the accessory module of ICE ICEEcIHE3034-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEEcIHE3034-1 AM Meng LIU (Mia), Oliver He 77 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=77 63.1 kb Streptococcus equi FM204883 30.6[41.28] 1206317..1269371 ICE with experimental support ICESe2 the integration and excision module of ICE ICESe2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESe2 IEM the conjugation module of ICE ICESe2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESe2 CM the regulation module of ICE ICESe2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESe2 RM the accessory module of ICE ICESe2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESe2 AM Meng LIU (Mia), Oliver He 92 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=92 33.8 kb Enterococcus faecalis; Enterococcus faecium; Clostridium symbiosum AF192329 52.83 1..33805 ICE with experimental support Tn1549 the integration and excision module of ICE Tn1549. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn1549 IEM the conjugation module of ICE Tn1549. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn1549 CM the regulation module of ICE Tn1549. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn1549 RM the accessory module of ICE Tn1549. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn1549 AM Meng LIU (Mia), Oliver He 102 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=102 29.2 kb DQ321786 39.98 67..29238 ICE with experimental support Tn5386 the integration and excision module of ICE Tn5386. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5386 IEM the conjugation module of ICE Tn5386. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5386 CM the regulation module of ICE Tn5386. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5386 RM the accessory module of ICE Tn5386. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5386 AM Meng LIU (Mia), Oliver He 438 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=438 240.8 kb NC_015563 66.26[66.72] 1833691..2074538 ICE with experimental support DelCs14_1618 phn Island the integration and excision module of ICE phn Island. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ phn Island IEM the conjugation module of ICE phn Island. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ phn Island CM the regulation module of ICE phn Island. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ phn Island RM the accessory module of ICE phn Island. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ phn Island AM Meng LIU (Mia), Oliver He 439 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=439 65.6 kb Streptococcus pyogenes 24RF FR691055 36.4 1659..67233 ICE with experimental support IMESp2907 IMESp2907 is predicted to be mobilized in cis by ICESp2905 (PMID: 26679245) Tet(O) element Tet(O) element is predicted to be mobilized in trans by ICESp2905 (PMID: 29165361) rum (23S rRNA m(5)U 1939 methyltransferase) ICESp2905 the integration and excision module of ICE ICESp2905. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp2905 IEM the conjugation module of ICE ICESp2905. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp2905 CM the regulation module of ICE ICESp2905. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp2905 RM the accessory module of ICE ICESp2905. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp2905 AM Meng LIU (Mia), Oliver He 440 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=440 82.2 kb Escherichia coli HK22511; Pasteurella multocida E348-08 (capsular type F); Mannheimia haemolytica 39229 CP003022 41.9 273284..355497 ICE with experimental support tRNA-Leu [DRs: GATTTTGAATCAA] ICEPmu1 the integration and excision module of ICE ICEPmu1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmu1 IEM the conjugation module of ICE ICEPmu1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmu1 CM the regulation module of ICE ICEPmu1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmu1 RM the accessory module of ICE ICEPmu1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPmu1 AM Meng LIU (Mia), Oliver He 937 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=937 131.5 kb Bacteroides fragilis 638R KJ816753 46.08 1..131471 ICE with experimental support GAAAGTGAA or TTTGA CTnHyb the integration and excision module of ICE CTnHyb. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnHyb IEM the conjugation module of ICE CTnHyb. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnHyb CM the regulation module of ICE CTnHyb. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnHyb RM the accessory module of ICE CTnHyb. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTnHyb AM Meng LIU (Mia), Oliver He 861 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=861 28 kb Clostridium difficile; Enterococcus faecalis HG475346 39.06 1..28014 ICE with experimental support 7 different instertion sites in Clostridium difficile ;tRNAArg(in Enterococcus faecalis) Tn6194-like the integration and excision module of ICE Tn6194-like. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6194-like IEM the conjugation module of ICE Tn6194-like. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6194-like CM the regulation module of ICE Tn6194-like. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6194-like RM the accessory module of ICE Tn6194-like. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6194-like AM Meng LIU (Mia), Oliver He 1079 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1079 64.4 kb Legionella pneumophila JR32 CP000675 39 2781725..2846914 ICE with experimental support tRNAMet LpcGI-2 the integration and excision module of ICE LpcGI-2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ LpcGI-2 IEM the conjugation module of ICE LpcGI-2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ LpcGI-2 CM the regulation module of ICE LpcGI-2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ LpcGI-2 RM the accessory module of ICE LpcGI-2. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ LpcGI-2 AM Meng LIU (Mia), Oliver He 1091 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1091 42.7 kb Legionella pneumophila JR32 Sm; Legionella micdadei (ATCC 33218) CP000675 39.44 614497..656813 ICE with experimental support tRNAPro (lpc2778) Trb-1 the integration and excision module of ICE Trb-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Trb-1 IEM the conjugation module of ICE Trb-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Trb-1 CM the regulation module of ICE Trb-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Trb-1 RM the accessory module of ICE Trb-1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Trb-1 AM Type IV coupling protein (T4CP) is a hexameric ATPase that links translocating substrates to the transenvelope secretion conduit. Meng LIU (Mia), Oliver He T4CP https://www.nature.com/articles/nmicrobiol2017114 type IV coupling protein Meng LIU (Mia), Oliver He 1096 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1096 445.2 kb NC_014923 5680050..6125270 ICE with experimental support ICEMcSym(1271)-alpha the integration and excision module of ICE ICEMcSym(1271)-alpha. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-alpha IEM the conjugation module of ICE ICEMcSym(1271)-alpha. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-alpha CM the regulation module of ICE ICEMcSym(1271)-alpha. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-alpha RM the accessory module of ICE ICEMcSym(1271)-alpha. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-alpha AM Meng LIU (Mia), Oliver He 1101 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1101 23 kb NC_014923 2669947..2692919 ICE with experimental support ICEMcSym(1271)-beta the integration and excision module of ICE ICEMcSym(1271)-beta. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-beta IEM the conjugation module of ICE ICEMcSym(1271)-beta. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-beta CM the regulation module of ICE ICEMcSym(1271)-beta. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-beta RM the accessory module of ICE ICEMcSym(1271)-beta. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-beta AM The mating pair formation (Mpf) system functions as a secretion machinery for intercellular DNA transfer during bacterial conjugation. Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/pubmed/15907535 mating pair formation MPF(F) is one of four MPF familes that have been described in Proteobacteria based on plasmid F. Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027160/ MPF(F) MPF(T) is one of four MPF familes that have been described in Proteobacteria based on the T-DNA conjugation system of A. tumefaciens plasmid Ti. Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027160/ VirB-like mating pair systems (MPF(T)) are the most numerous among the four MPF classes encompassing the conjugation systems of Proteobacteria and closely related taxa. MPF(T) MPF(I) is one of four MPF familes that have been described in Proteobacteria based on the IncI plasmid R64. Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027160/ MPF(I) MPF(G) is one of four MPF familes that have been described in Proteobacteria based on ICEHIN1056. Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027160/ MPF(G) T4SS ATPase is the enzyme which energizes the T4SS system from the cytoplasm, driving the complex assembly and substrate translocation through the channel. Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070162/ VirB4 and TraU are the major ATPases founded in ICEs. T4SS ATPase Meng LIU (Mia), Oliver He 1106 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1106 7.8 kb NC_014923 2444639..2452398 ICE with experimental support ICEMcSym(1271)-gamma the integration and excision module of ICE ICEMcSym(1271)-gamma. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-gamma IEM the conjugation module of ICE ICEMcSym(1271)-gamma. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-gamma CM the regulation module of ICE ICEMcSym(1271)-gamma. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-gamma RM the accessory module of ICE ICEMcSym(1271)-gamma. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMcSym(1271)-gamma AM Meng LIU (Mia), Oliver He - Streptococcus thermophilus CNRZ368 T4SS are cell envelope-spanning complexes that form a channel through which DNA and proteins can travel from the cytoplasm of the donor cell to the cytoplasm of the recipient cell. T4SS is one of important secretion systems and usually consists of several components: mating-pair formation proteins (MPFs), which serve to establish physical contacts with a recipient bacterium; and, finally, a coupling protein (T4cp), which binds MOB and ssDNA to MPF . Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/SecReT4/ https://en.wikipedia.org/wiki/Secretion type IV secretion system T4SS in Gram negative bacteria Meng LIU (Mia), Oliver He Due to differences in cell membrane structure, Gram-positive and Gram-negative bacteria may have different T4SS organization and features. type IV secretion system in Gram negative bacteria T4SS in Gram positive bacteria Meng LIU (Mia), Oliver He Due to differences in cell membrane structure, Gram-positive and Gram-negative bacteria may have different T4SS organization and features. type IV secretion system in Gram positive bacteria The integration and excision module refers to those genes and sequence within the ICE responsible for the integration and excision of the element from the host chromosome, including genes encoding the integrase and or recombination directionality factor (also known as excisionase, which influences the direction of recombination mediated by the integrase to favor excision). Meng LIU (Mia), Oliver He recombination module component https://academic.oup.com/nar/article/47/D1/D660/5165266 ICE integration and excision module One family of recombinases based on amino acid sequence homology and mechanistic relatedness. Tyrosine is the conserved nucleophilic amino acid residue that tyrosine recombinases use to attack the DNA and which becomes covalently linked to it during strand exchange. Meng LIU (Mia), Oliver He https://en.wikipedia.org/wiki/Site-specific_recombination tyrosine recombinase is the most common integrase seen in T4SS-type ICEs tyrosine recombinase One family of recombinases based on amino acid sequence homology and mechanistic relatedness. Serine is the conserved nucleophilic amino acid residue that serine recombinases use to attack the DNA and which becomes covalently linked to it during strand exchange. Meng LIU (Mia), Oliver He https://en.wikipedia.org/wiki/Site-specific_recombination serine recombinase is the second most common integrase seen in T4SS-type ICEs serine recombinase A transposase enzyme with the DDE motif. Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991504/ DDE transposase is the third most common integrase seen in T4SS-type ICEs DDE transposase The oriT region, which is usually tens to hundreds of base pairs in length, contains a conserved nick region (flanking the nic site) and variable numbers of inverted repeats (IRs) Meng LIU (Mia), Oliver He oriT origin of transfer http://bioinfo-mml.sjtu.edu.cn/oriTDB origin of transfer sequence A short DNA sequence that recombinases recognize, bind to and then cleave the DNA backbone, exchange the two DNA helices involved and rejoin the DNA strands. Meng LIU (Mia), Oliver He https://en.wikipedia.org/wiki/Site-specific_recombination recombination attachment site The integration reaction is catalyzed by the integrase and, as a result of the site-specific recombination, will lead to direct repeats (typically between 10 and 60 bp) forming on either end of the integrated element, that are now named attL (left end) and attR (right end). Meng LIU (Mia), Oliver He https://academic.oup.com/femsre/article/41/4/512/3089980 attL The integration reaction is catalyzed by the integrase and, as a result of the site-specific recombination, will lead to direct repeats (typically between 10 and 60 bp) forming on either end of the integrated element, that are nownamed attL (left end) and attR (right end). Meng LIU (Mia), Oliver He https://academic.oup.com/femsre/article/41/4/512/3089980 attR attB is the attachment site in the host chromosome during the recombination. Meng LIU (Mia), Oliver He https://academic.oup.com/femsre/article/41/4/512/3089980 attB Meng LIU (Mia), Oliver He attP attI (or attP) is the attachment site on the circular ICE during the recombination. attI After transfer, the circular ICE integrates into a replicon, mainly at the 3' end of a tRNA or protein-encoding gene, which is called insertion site Meng LIU (Mia), Oliver He https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566197/ 3 end of a tRNA gene (tRNALeu, tRNAThr, or tRNALys), a gene encoding a ribosomal protein (rpsI, rplL, or rpmG-3), or the guaA gene are the common insertion site of ICE. insertion site Meng LIU (Mia), Oliver He 1098 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1098 528.5 kb CP016079 6351798..6880279 ICE with experimental support ICEMlSym(NZP2037)-alpha the integration and excision module of ICE ICEMlSym(NZP2037)-alpha. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-alpha IEM the conjugation module of ICE ICEMlSym(NZP2037)-alpha. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-alpha CM the regulation module of ICE ICEMlSym(NZP2037)-alpha. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-alpha RM the accessory module of ICE ICEMlSym(NZP2037)-alpha. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-alpha AM Meng LIU (Mia), Oliver He 1103 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1103 27.6 kb CP016079 3031358..3058942 ICE with experimental support ICEMlSym(NZP2037)-beta the integration and excision module of ICE ICEMlSym(NZP2037)-beta. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-beta IEM the conjugation module of ICE ICEMlSym(NZP2037)-beta. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-beta CM the regulation module of ICE ICEMlSym(NZP2037)-beta. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-beta RM the accessory module of ICE ICEMlSym(NZP2037)-beta. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-beta AM Meng LIU (Mia), Oliver He 1108 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1108 6.2 kb CP016079 2577929..2584131 ICE with experimental support ICEMlSym(NZP2037)-gamma the integration and excision module of ICE ICEMlSym(NZP2037)-gamma. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-gamma IEM the conjugation module of ICE ICEMlSym(NZP2037)-gamma. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-gamma CM the regulation module of ICE ICEMlSym(NZP2037)-gamma. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-gamma RM the accessory module of ICE ICEMlSym(NZP2037)-gamma. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEMlSym(NZP2037)-gamma AM Meng LIU (Mia), Oliver He 811 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=811 94.2 kb HE963029 43.96 1..94189 ICE with experimental support tRNA (uracil-5)-methyltransferase rumA; CACGTGGAGTGCGTAGTGTT(attL); TTCTCAAGGACCAGACAACA(attR) ICESluvan the integration and excision module of ICE ICESluvan. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESluvan IEM the conjugation module of ICE ICESluvan. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESluvan CM the regulation module of ICE ICESluvan. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESluvan RM the accessory module of ICE ICESluvan. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESluvan AM Meng LIU (Mia), Oliver He 812 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=812 49.2 kb Streptococcus pyogenes HE802677 35.24 1..49160 ICE with experimental support rpmH ICESp1116 the integration and excision module of ICE ICESp1116. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp1116 IEM the conjugation module of ICE ICESp1116. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp1116 CM the regulation module of ICE ICESp1116. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp1116 RM the accessory module of ICE ICESp1116. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESp1116 AM Meng LIU (Mia), Oliver He 743 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=743 29.7 kb Streptococcus salivarius; Streptococcus thermophilus; Enterococcus faecalis LT622827 35.33 1..29716 ICE with experimental support fda ICE_SsaF1-4_fda the integration and excision module of ICE ICE_SsaF1-4_fda. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE_SsaF1-4_fda IEM the conjugation module of ICE ICE_SsaF1-4_fda. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE_SsaF1-4_fda CM the regulation module of ICE ICE_SsaF1-4_fda. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE_SsaF1-4_fda RM the accessory module of ICE ICE_SsaF1-4_fda. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE_SsaF1-4_fda AM Meng LIU (Mia), Oliver He 745 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=745 30.2 kb Streptococcus salivarius; Streptococcus thermophilus; Enterococcus faecalis LT622829 35.61 1..30222 ICE with experimental support fda ICE_SsaF4-2_fda the integration and excision module of ICE ICE_SsaF4-2_fda. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE_SsaF4-2_fda IEM the conjugation module of ICE ICE_SsaF4-2_fda. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE_SsaF4-2_fda CM the regulation module of ICE ICE_SsaF4-2_fda. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE_SsaF4-2_fda RM the accessory module of ICE ICE_SsaF4-2_fda. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE_SsaF4-2_fda AM Meng LIU (Mia), Oliver He 829 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=829 88.9 kb Streptococcus suis P1/7RF; Streptococcus suis SS-1RF KX077888 36.81 875..89748 ICE with experimental support rplL ICESsu05SC260 the integration and excision module of ICE ICESsu05SC260. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu05SC260 IEM the conjugation module of ICE ICESsu05SC260. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu05SC260 CM the regulation module of ICE ICESsu05SC260. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu05SC260 RM the accessory module of ICE ICESsu05SC260. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsu05SC260 AM Meng LIU (Mia), Oliver He 837 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=837 29.7 kb KU215704 34.14 1..29661 ICE with experimental support ICESsuNC28 the integration and excision module of ICE ICESsuNC28. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsuNC28 IEM the conjugation module of ICE ICESsuNC28. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsuNC28 CM the regulation module of ICE ICESsuNC28. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsuNC28 RM the accessory module of ICE ICESsuNC28. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESsuNC28 AM Meng LIU (Mia), Oliver He - Streptococcus thermophilus CNRZ385 Meng LIU (Mia), Oliver He - Haemophilus influenzae 1056 Meng LIU (Mia), Oliver He - Ralstonia oxalatica A5 Meng LIU (Mia), Oliver He - Streptococcus parauberis NUF1049 Meng LIU (Mia), Oliver He - Streptococcus pneumoniae 05P294 Meng LIU (Mia), Oliver He - Streptococcus pneumoniae DP1322 Recombination directionality factors (RDFs) are a diverse group of proteins involved in controlling the directionality of integrase-mediated site-specific recombination reactions. Meng LIU (Mia), Oliver He RDF Xis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC55702/ Typically, RDFs are small DNA-binding proteins acting as accessory factors to influence the choice of substrates that are recombined by their cognate recombinase recombination directionality factor Meng LIU (Mia), Oliver He - Streptococcus pneumoniae Ar4 Meng LIU (Mia), Oliver He - Streptococcus oralis F.MI.5 The regulation module refers to those genes and sequence contributing to stabilization and maintenance of ICEs. Meng LIU (Mia), Oliver He https://academic.oup.com/nar/article/47/D1/D660/5165266 ICE regulation module toxin–antitoxin system is small genetic element composed of a stable toxin protein and a labile cognate antitoxin encoded by a bicistronic locus. TA system is involved in regulation of bacterial metabolic activity and plays important role in plasmid maintenance and ICE post-segregational killing systems. Meng LIU (Mia), Oliver He http://bioinfo-mml.sjtu.edu.cn/TADB2/ https://academic.oup.com/femspd/article/70/3/240/567411 Toxin-antitoxin (TA) loci play a role in bacterial stress physiology and the stabilisation of horizontally acquired elements. TA loci are found abundantly distributed among free-living Bacteria and Archaea. toxin–antitoxin system true Restriction-modification system is a defense system developed by bacteria to defend themselves from invasions of phage (or viruses ). Restriction-modification system composed of a restriction endonuclease enzyme and a methylase enzyme and each bacterial species and strain has their own combination of restriction and methylating enzymes. Meng LIU (Mia), Oliver He https://www.ndsu.edu/pubweb/~mcclean/plsc731/dna/dna5.htm DNA restriction-modification system true Meng LIU (Mia), Oliver He Listeria monocytogenes TTH-2007 - Listeria monocytogenes strain TTH-2007 Meng LIU (Mia), Oliver He - Staphylococcus rostri RST11 Meng LIU (Mia), Oliver He - Photobacterium damselae subsp. piscicida PC554.2 Meng LIU (Mia), Oliver He - Proteus mirabilis 08MAS1586 Meng LIU (Mia), Oliver He - Proteus mirabilis TJ1809 A role played by a material entity where the circular ICE integrates into a replicon after transfer. Meng LIU (Mia), Oliver He insertion site role Meng LIU (Mia), Oliver He - Proteus mirabilis JN7 Meng LIU (Mia), Oliver He - Proteus mirabilis 09MAS2407 Meng LIU (Mia), Oliver He 1035 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1035 94.3 kb KX243403 46.77 1..94340 ICE with experimental support ICEPvuCHN2213 the integration and excision module of ICE ICEPvuCHN2213. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPvuCHN2213 IEM the conjugation module of ICE ICEPvuCHN2213. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPvuCHN2213 CM the regulation module of ICE ICEPvuCHN2213. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPvuCHN2213 RM the accessory module of ICE ICEPvuCHN2213. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEPvuCHN2213 AM Meng LIU (Mia), Oliver He 1068 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1068 97.4 kb KC886257 46.79 528..97877 ICE with experimental support ICEVchNep1 the integration and excision module of ICE ICEVchNep1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchNep1 IEM the conjugation module of ICE ICEVchNep1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchNep1 CM the regulation module of ICE ICEVchNep1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchNep1 RM the accessory module of ICE ICEVchNep1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchNep1 AM Meng LIU (Mia), Oliver He 1069 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=1069 97 kb KC886258 46.79 528..97570 ICE with experimental support ICEVchNig1 the integration and excision module of ICE ICEVchNig1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchNig1 IEM the conjugation module of ICE ICEVchNig1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchNig1 CM the regulation module of ICE ICEVchNig1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchNig1 RM the accessory module of ICE ICEVchNig1. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICEVchNig1 AM Meng LIU (Mia), Oliver He 103 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=103 20.7 kb Bacillus subtilis; Clostridium difficile AM180355 38.32[29.06] 585384..606040 ICE with experimental support Tn5398 Tn5398 is predicted to be mobilized in cis by Tn5397. AT rich regions Tn5397 the integration and excision module of ICE Tn5397. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5397 IEM the conjugation module of ICE Tn5397. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5397 CM the regulation module of ICE Tn5397. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5397 RM the accessory module of ICE Tn5397. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5397 AM the integration and excision module of ICE Tn916(pAM120). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916(pAM120) IEM the conjugation module of ICE Tn916(pAM120). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916(pAM120) CM the regulation module of ICE Tn916(pAM120). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916(pAM120) RM the accessory module of ICE Tn916(pAM120). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916(pAM120) AM Meng LIU (Mia), Oliver He 306 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=306 18 kb AY855841 38.73[36.1] 40068..58099 ICE with experimental support AT rich regions this ICE was found in Enterococcus faecalis plasmid pCF10 Tn925 the integration and excision module of ICE Tn925. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn925 IEM the conjugation module of ICE Tn925. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn925 CM the regulation module of ICE Tn925. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn925 RM the accessory module of ICE Tn925. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn925 AM Meng LIU (Mia), Oliver He 307 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=307 18 kb FN550102 38.7 1..18032 ICE with experimental support AT rich regions Tn916(RST11) the integration and excision module of ICE Tn916(RST11). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916(RST11) IEM the conjugation module of ICE Tn916(RST11). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916(RST11) CM the regulation module of ICE Tn916(RST11). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916(RST11) RM the accessory module of ICE Tn916(RST11). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916(RST11) AM Meng LIU (Mia), Oliver He 308 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=308 18 kb AB468159 38.71 3016..21046 ICE with experimental support AT rich regions ICESpaNUF1049 the integration and excision module of ICE ICESpaNUF1049. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpaNUF1049 IEM the conjugation module of ICE ICESpaNUF1049. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpaNUF1049 CM the regulation module of ICE ICESpaNUF1049. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpaNUF1049 RM the accessory module of ICE ICESpaNUF1049. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICESpaNUF1049 AM Meng LIU (Mia), Oliver He 318 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=318 20.8 kb 38.46 ICE with experimental support AT rich regions Tn6085b the integration and excision module of ICE Tn6085b. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6085b IEM the conjugation module of ICE Tn6085b. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6085b CM the regulation module of ICE Tn6085b. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6085b RM the accessory module of ICE Tn6085b. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6085b AM Meng LIU (Mia), Oliver He 319 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=319 20.8 kb HM243621 38.46 6653..27441 ICE with experimental support AT rich regions Tn6085a the integration and excision module of ICE Tn6085a. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6085a IEM the conjugation module of ICE Tn6085a. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6085a CM the regulation module of ICE Tn6085a. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6085a RM the accessory module of ICE Tn6085a. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6085a AM Meng LIU (Mia), Oliver He 328 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=328 22.3 kb HM243622 38.42 34197..56508 ICE with experimental support AT rich regions Tn6084 the integration and excision module of ICE Tn6084. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6084 IEM the conjugation module of ICE Tn6084. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6084 CM the regulation module of ICE Tn6084. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6084 RM the accessory module of ICE Tn6084. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6084 AM Meng LIU (Mia), Oliver He 321 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=321 25.1 kb AM410044 37.98 1..25101 ICE with experimental support AT rich regions Tn6003 the integration and excision module of ICE Tn6003. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6003 IEM the conjugation module of ICE Tn6003. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6003 CM the regulation module of ICE Tn6003. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6003 RM the accessory module of ICE Tn6003. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6003 AM Meng LIU (Mia), Oliver He 325 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=325 26.4 kb AB426620 37.89 1..26390 ICE with experimental support AT rich regions Tn2010 the integration and excision module of ICE Tn2010. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn2010 IEM the conjugation module of ICE Tn2010. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn2010 CM the regulation module of ICE Tn2010. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn2010 RM the accessory module of ICE Tn2010. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn2010 AM a role played by a material entity that often involves in the conjugal process. Meng LIU (Mia), Oliver He conjugation module component role a role played by a protein which links translocating substrates to the transenvelope secretion conduit. Meng LIU (Mia), Oliver He T4CP role type IV coupling protein role Meng LIU (Mia), Oliver He - Proteus mirabilis TJ3335 Meng LIU (Mia), Oliver He - Proteus mirabilis JN14 a role played by a protein that energizes the T4SS system from the cytoplasm and drives the complex assembly and substrate translocation through the channel. Meng LIU (Mia), Oliver He T4SS ATPase role Meng LIU (Mia), Oliver He - Amycolatopsis mediterranei LBG A3136 Meng LIU (Mia), Oliver He - Proteus vulgaris 08MAS2213 A role played by a gene that encodes a protein which is part of T4SS (a cell envelope-spanning complexes that form a channel through which DNA and proteins can travel from the cytoplasm of the donor cell to the cytoplasm of the recipient cell. ) Meng LIU (Mia), Oliver He T4SS gene component role type IV secretion system gene component role Meng LIU (Mia), Oliver He - Shewanella putrefaciens W3-18-1 Meng LIU (Mia), Oliver He - Bacteroides fragilis 86-5443-2-2 Meng LIU (Mia), Oliver He Clostridium difficile CII7 - Clostridium difficile strain CII7 A role played by a protein that mediates an exchange reaction between two DNA templates and results in integration of DNA from one of the templates into the other. Meng LIU (Mia), Oliver He integrase role A role played by a material entity that contains a conserved nick region (flanking the nic site) and variable numbers of inverted repeats (IRs) and served as origin site of transfer. Meng LIU (Mia), Oliver He oriT role origin of transfer role A role played by a short DNA sequence that recombinases recognize, bind to and then cleave the DNA backbone, exchange the two DNA helices involved and rejoin the DNA strands. Meng LIU (Mia), Oliver He recombination attachment site role Meng LIU (Mia), Oliver He protein of Escherichia coli ECOR31 Meng LIU (Mia), Oliver He - Enterococcus casseliflavus 664.1H1 Meng LIU (Mia), Oliver He - Enterococcus faecalis BM4382 Meng LIU (Mia), Oliver He - Enterococcus faecium D344R Meng LIU (Mia), Oliver He - Escherichia coli BEN374 Meng LIU (Mia), Oliver He - Salmonella bongori CEIM46082 Meng LIU (Mia), Oliver He Salmonella enterica subsp. enterica serovar Senftenberg, strain 5494-57 - Salmonella enterica subsp. enterica serovar Senftenberg, 5494-57 Meng LIU (Mia), Oliver He - Staphylococcus aureus JCSC6826 Meng LIU (Mia), Oliver He - Staphylococcus aureus HDG2 Meng LIU (Mia), Oliver He - Streptococcus agalactiae Sag37 Meng LIU (Mia), Oliver He - Streptococcus dysgalactiae subsp. equisimilis NS3396 Meng LIU (Mia), Oliver He - Streptococcus lutetiensis 5-F9 Meng LIU (Mia), Oliver He - Streptococcus pneumoniae Pn19 Meng LIU (Mia), Oliver He - Streptococcus pyogenes C1 Meng LIU (Mia), Oliver He - Streptococcus pyogenes iB21 Meng LIU (Mia), Oliver He - Streptococcus pyogenes MB56Spyo009 A role played by a protein that controlls the directionality of integrase-mediated site-specific recombination reactions. Meng LIU (Mia), Oliver He RDF role recombination directionality factor role a role played by a material entity that involves in stabilization and maintenance of ICEs. Meng LIU (Mia), Oliver He regulation module component role a role played by a material entity that often exists inside ICEs as the cargo genes and can confer the hosts with selective advantages. Meng LIU (Mia), Oliver He accessory module component role a role played by a material entity that can confer the the ability of bacteria and other microorganisms to resist the effects of an antibiotic to which they were once sensitive. Meng LIU (Mia), Oliver He antibiotic resistance gene role A role played by a gene that encodes products which assist the bacterium colonize the host at the cellular level and are either secretory, membrane associated or cytosolic in nature. Meng LIU (Mia), Oliver He VF gene role virulence factor gene role Meng LIU (Mia), Oliver He - Streptococcus pyogenes strain A-3 Streptococcus pyogenes 2812A Meng LIU (Mia), Oliver He - Streptococcus salivarius strain F1-4 Meng LIU (Mia), Oliver He - Streptococcus salivarius strain F4-2 gene of Escherichia coli ECOR31 protein-coding gene of Escherichia coli ECOR31 RNA gene of Escherichia coli ECOR31 A role played by a protein that nicks the dsDNA and remains covalently bound to the resulting ssDNA Meng LIU (Mia), Oliver He relaxase role a ICE of Gammaproteobacteria Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ ICE in Gammaproteobacteria Meng LIU (Mia), Oliver He 326 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=326 21.2 kb HQ663849 38.23 1..21169 ICE with experimental support AT rich regions Tn6087 the integration and excision module of ICE Tn6087. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6087 IEM the conjugation module of ICE Tn6087. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6087 CM the regulation module of ICE Tn6087. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6087 RM the accessory module of ICE Tn6087. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6087 AM Meng LIU (Mia), Oliver He 47 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=47 18 kb Streptococcus pneumoniae; Streptococcus gordonii; Streptococcus pyogenes; Streptococcus agalactiae;Enterococcus faecalis; Bacillus subtilis FJ711160 38.85 1..18033 ICE with experimental support AT rich regions Tn5251 (part of Tn5253) the integration and excision module of ICE Tn5251 (part of Tn5253). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5251 (part of Tn5253) IEM the conjugation module of ICE Tn5251 (part of Tn5253). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5251 (part of Tn5253) CM the regulation module of ICE Tn5251 (part of Tn5253). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5251 (part of Tn5253) RM the accessory module of ICE Tn5251 (part of Tn5253). Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn5251 (part of Tn5253) AM Meng LIU (Mia), Oliver He 45 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=45 18 kb Enterococcus faecalis; Butyrivibrio proteoclasticus; Streptococcus spp.; Lactococcus lactis; Lactobacillus paracasei; Neisseria sp.; Escherichia coli; Desulfitobacterium dehalogenans; Bacillus subtilis; Bacillus thuringiensis subsp. Israelensis U09422 38.75 1..18032 ICE with experimental support IME_GB00957_oriT IME_GB00957_oriT is predicted to be mobilized in trans by Tn916 (PMID: 25832353; 26410170) MTnSag1 [tISSag10] MTnSag1 [tISSag10] can be mobilized in trans by Tn916 from Streptococcus agalactiae UCN36 to Streptococcus agalactiae BM134/Streptococcus agalactiae BM132. (PMID: 17416666) tISCpe8 tISCpe8 can be mobilized in trans by Tn916 from Clostridium perfringens JIR4225 to Clostridium perfringens JIR4394. (PMID: 19684139) AT rich regions Tn916 the integration and excision module of ICE Tn916. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916 IEM the conjugation module of ICE Tn916. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916 CM the regulation module of ICE Tn916. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916 RM the accessory module of ICE Tn916. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn916 AM Meng LIU (Mia), Oliver He 62 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=62 20.9 kb Streptococcus cristatus; Streptococcus sanguinis AY898750 38.23 1..20880 ICE with experimental support CTn6002 the integration and excision module of ICE CTn6002. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn6002 IEM the conjugation module of ICE CTn6002. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn6002 CM the regulation module of ICE CTn6002. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn6002 RM the accessory module of ICE CTn6002. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ CTn6002 AM Meng LIU (Mia), Oliver He 862 http://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=862 21.3 kb JX120102 37.93 1..21322 ICE with experimental support Tn6198 the integration and excision module of ICE Tn6198. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6198 IEM the conjugation module of ICE Tn6198. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6198 CM the regulation module of ICE Tn6198. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6198 RM the accessory module of ICE Tn6198. Meng LIU (Mia), Oliver He http://db-mml.sjtu.edu.cn/ICEberg/ Tn6198 AM Meng LIU (Mia), Oliver He - Streptococcus suis 32457 Meng LIU (Mia), Oliver He - Streptococcus suis 05SC260 Meng LIU (Mia), Oliver He - Streptococcus suis strain nc286A7 Meng LIU (Mia), Oliver He - Yersinia pseudotuberculosis 32777 Meng LIU (Mia), Oliver He T4ASS type T4SS gene Meng LIU (Mia), Oliver He type F T4SS gene Meng LIU (Mia), Oliver He type I T4SS gene Meng LIU (Mia), Oliver He type P T4SS gene Meng LIU (Mia), Oliver He T4BSS type T4SS gene Meng LIU (Mia), Oliver He BAH64175.1(Int) BAH64176.1(YbtS) BAH64177.1(YbtX) BAH64178.1(YbtQ) BAH64179.1(YbtP) BAH64180.1(YbtA) BAH64181.1(Irp2) BAH64182.1(Irp1) BAH64183.1(YbtU) BAH64184.1(YbtT) yersiniabactin siderophore biosynthetic protein BAH64185.1(YbtE) BAH64186.1(FyuA) BAH64187.1 BAH64188.1(AlpA2) BAH64189.1 BAH64190.1 BAH64191.1 BAH64192.1 BAH64193.1 BAH64194.1 BAH64195.1 BAH64196.1(VagC) BAH64197.1(VagD) BAH64198.1 BAH64199.1(IroN) BAH64200.1(IroB) BAH64201.1(IroC) BAH64202.1(IroD) BAH64203.1(PagO) BAH64204.1 BAH64205.1 BAH64206.1(RmpA) BAH64207.1 BAH64208.1 BAH64209.1 BAH64210.1 BAH64211.1 BAH64212.1(VirB1) BAH64213.1(VirB2) BAH64214.1(VirB3-4) BAH64215.1(VirB5) BAH64216.1 BAH64217.1(VirB6) BAH64218.1(VirB8) BAH64219.1(VirB9) BAH64220.1(VirB10) BAH64221.1(VirB11) BAH64222.1 BAH64223.1 BAH64224.1 BAH64225.1 BAH64226.1(MobB) BAH64227.1(MobC) BAH64228.1(ArdC) BAH64229.1 BAH64230.1 BAH64231.1 BAH64232.1 BAH64233.1 BAH64234.1 BAH64235.1 BAH64236.1 Meng LIU (Mia), Oliver He - Bacteroides fragilis LV23 Meng LIU (Mia), Oliver He - Bacteroides thetaiotaomicron 7853 Meng LIU (Mia), Oliver He - Butyrivibrio fibrisolvens 1.230 Meng LIU (Mia), Oliver He - Clostridium perfringens CW459 Meng LIU (Mia), Oliver He - Elizabethkingia anophelis CSID_3015183678 Meng LIU (Mia), Oliver He - Enterococcus faecalis JH2-7 Meng LIU (Mia), Oliver He - Enterococcus faecium 9830414-1 Meng LIU (Mia), Oliver He - Klebsiella pneumoniae 41 Meng LIU (Mia), Oliver He - Lactococcus lactis 11454 Meng LIU (Mia), Oliver He - Lactococcus lactis FI5876 Meng LIU (Mia), Oliver He - Lactococcus lactis R5 Meng LIU (Mia), Oliver He - Lactococcus lactis subsp. lactis ML3 Meng LIU (Mia), Oliver He - Micromonospora rosaria SCC2095 Meng LIU (Mia), Oliver He - Pectobacterium carotovorum subsp. brasiliensis ICMP Meng LIU (Mia), Oliver He - Proteus mirabilis TUM4660 Meng LIU (Mia), Oliver He - Pseudomonas putida KF715 Meng LIU (Mia), Oliver He - Saccharopolyspora endophytica YIM 61095 Meng LIU (Mia), Oliver He - Staphylococcus aureus 1591 Meng LIU (Mia), Oliver He - Staphylococcus aureus 21995 Meng LIU (Mia), Oliver He - Staphylococcus aureus 22034 Meng LIU (Mia), Oliver He - Staphylococcus aureus 34801 Meng LIU (Mia), Oliver He - Staphylococcus aureus 35366 Meng LIU (Mia), Oliver He - Staphylococcus aureus 35414 Meng LIU (Mia), Oliver He - Staphylococcus aureus 35679 Meng LIU (Mia), Oliver He - Staphylococcus aureus 4520 Meng LIU (Mia), Oliver He - Staphylococcus aureus 4865 Meng LIU (Mia), Oliver He - Staphylococcus aureus 5331 Meng LIU (Mia), Oliver He - Staphylococcus aureus 5377 Meng LIU (Mia), Oliver He - Staphylococcus aureus 617 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7215190-1 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7215311-1 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7312330-1 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7412791-1 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7413093-4 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7413714-1 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7512166-1 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7512986-1 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7611280-5 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7612628-4 Meng LIU (Mia), Oliver He - Staphylococcus aureus 7711730-1 Meng LIU (Mia), Oliver He - Staphylococcus aureus 8797 Meng LIU (Mia), Oliver He - Staphylococcus aureus 9877324-3_H39 Meng LIU (Mia), Oliver He - Staphylococcus aureus SW356 Meng LIU (Mia), Oliver He - Staphylococcus aureus USA42 Meng LIU (Mia), Oliver He - Streptococcus agalactiae Sag236 Meng LIU (Mia), Oliver He - Streptococcus agalactiae SagTR7 Meng LIU (Mia), Oliver He - Streptococcus dysgalactiae subsp. equisimilis (Sde5580) Meng LIU (Mia), Oliver He - Streptococcus intermedius 15.3T.2 Meng LIU (Mia), Oliver He - Streptococcus pneumoniae BM4200 Meng LIU (Mia), Oliver He - Streptococcus pneumoniae BM6001