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 > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < 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 σ-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