Summary: Cytolethal distending toxin A/C domain
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "Cytolethal distending toxin". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at firstname.lastname@example.org and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Cytolethal distending toxin Edit Wikipedia article
|Cytolethal distending toxin|
Crystal structure of the fully assembled Haemophilus ducreyi cytolethal distending toxin
Cytolethal distending toxins (abbreviated CDTs) are a class of heterotrimeric toxins produced by certain gram-negative bacteria that display DNase activity. These toxins trigger G2/M cell cycle arrest in specific mammalian cell lines, leading to the enlarged or distended cells for which these toxins are named. Affected cells die by apoptosis.
Each toxin consists of three distinct subunits named alphabetically in the order that their coding genes appear in the cdt operon. Cytolethal distending toxins are classified as AB toxins, with an active ("A") subunit that directly damages DNA and a binding ("B") subunit that helps the toxin attach to the target cells. CdtB is the active subunit and a homolog to mammalian DNase I, whereas CdtA and CdtC make up the binding subunit.
Cytolethal distending toxins are produced by gram-negative pathogenic bacteria from the phylum Proteobacteria. Many of these bacteria, including Shigella dysenteriae, Haemophilus ducreyi, and Escherichia coli, infect humans. Bacteria that produce CDTs often persistently colonize their host.
The first recorded observation of a cytolethal-distending toxin was in 1987 in a pathogenic strain in E. coli isolated from a young patient. Later that year, scientists W.M. Johnson and H. Lior published the journal article “Production of Shiga toxin and a cytolethal distending toxin (CLDT) by serogroups of Shigella spp.” In Microbiology Letters. The discovery of other bacteria producing CDT toxins continues to this day.
In 1994 two scientists, Scott and Kaper, successfully cloned and sequenced a cdt operon from another E. coli strain, publishing their accomplishment in Infection and Immunity. The three genes discovered were denoted cdtA, cdtB, and cdtC.
In 1997, the first paper of many to show G2/M cell cycle arrest caused by a cytolethal distending toxin was published in Molecular Microbiology. The study focused on another E. coli strain. This paper was followed by a 1999 publication in Infectious Immunity, which demonstrated that H. ducreyi CDT causes cell death via apoptosis. This finding was also confirmed for other cytolethal distending toxins in subsequent studies.
The discovery of the homology of cdtB to mammalian DNase I and the current AB model for the toxin were published in early 2000.  Further research and the publication of crystal structures for the CDT toxins from two different species continues to support this model.
All known cytolethal distending toxins are produced by gram-negative bacteria in the gamma and epsilon classes of the Proteobacteria phylum. In several cases, the bacteria producing CDT are human pathogens. Medically important CDT producers include:
- Haemophilus ducreyi (chancroids)
- Aggregatibacter actinomycetemcomitans (periodontitis)
- Escherichia coli (various diseases)
- Shigella dysenteriae (dysentery)
- Salmonella enterica serotype Typhi (typhoid fever)
- Campylobacter upsaliensis (enterocolitis)
- Campylobacter jejuni (enterocolitis)
CDT-producing bacteria are often associated with mucosal linings, such as those in the stomach and intestines, and with persistent infections. The toxins are either secreted freely or associated with the membrane of the producing bacteria.
Individual cytolethal distending toxins are named for the bacterial species that they are isolated from. As of 2011, most scientists have adopted the practice of placing the first letter of both the genus and species in front of the toxin name to reflect its source (i.e., the CDT from Haemaphilus ducreyi is referred to as HdCDT). If several subspecies produce different toxins, as in the case of E. coli, Roman numerals may be added after the second letter. Both complete toxins and individual subunits are labeled using this convention.
In response to the continued discovery of additional cytolethal distending toxins, a 2011 review has proposed that the toxin names be expanded to include the first three letters of the species (i.e., HducCDT for Haemaphilus ducreyi CDT).
CDT toxins are genotoxins capable of directly damaging DNA in target cells. They are the only AB-type toxins discovered that display DNase activity, allowing them to introduce breaks into the target cell's DNA.
In many cell lines including human fibroblasts, epithelial cells, endothelial cells, and keratinocytes, CDTs cause G2/M cell cycle arrest, cytoplasmic distension, and eventual cell death via apoptosis. Most publications attribute the G2/M cycle arrest to the buildup of irreversible DNA damage from the toxin’s DNase activity as the trigger for the G2/M cell cycle arrest, but other research suggests that this model is incomplete. The cytoplasmic distension is a direct result of the G2/M cell cycle arrest. The cell enlarges in preparation for mitosis, but cannot divide to restore its normal size. Aside from classical apoptosis, signs of cellular senescence has also been observed in normal and cancer cell lines (fibroblasts, HeLa and U2-OS) after CDT intoxication
In lymphocytes, cell death occurs quickly and is not preceded by significant cytoplasmic distension. The ability of theses toxins to effect lymphocytes differently may be advantageous to the bacteria that utilize these toxins, but the mechanism behind this phenomenon is not yet well understood.
The active, assembled toxin is a tripartite structure with three distinct subunits- CdtA, CdtB, and CdtC. In terms of function, it is an AB toxin. In this context, the CdtB subunit is actually the catalytically active "A" subunit, and the CdtA and CdtC together form the binding "B" subunit, which helps the toxin bind and enter target cells. Some literature refers to the toxin structure as AB2 to reflect the presence of both CdtA and CdtC.
Different from all other CDTs, Salmonella enterica serovar Typhi CDT (SeCDT) has no CdtA and CdtC homologues. However, encoded closely to the active subunit cdtb, the Pertussis-like toxin A and B (pltA/pltB) have been shown to be essential for cellular intoxication. PltA and PltB have a different structure from CdtA and CdtC, thus promoting CdtB activity in a different way. Both PltA and PltB have been found to bind directly to CdtB in vitro. In addition, different from all other CDTs, Salmonella genotoxin is produced only upon bacterial internalization in infected cells, thus the SeCDT traffic may differ remarkably from the canonical ones.
CdtB is considered the active subunit of the CDT holotoxin. Microinjection of CdtB into susceptible cells without CdtA or CdtC results in the G2/M cell cycle arrest and cytoplasmic distension characteristic of CDT toxins. The structure of CdtB is well-conserved between different bacteria. The CdtB subunit is the most sequentially conserved between species. The molecular weight of CdtB ranges from 28 kDa to 29 kDa, depending on the species.
As the active subunit, CdtB is termed the "A" subunit according to the AB toxin model. This confusing nomenclature is due to the naming of the toxin’s subunits before their individual functions were understood.
CdtB exhibits at least two enzymatic activities- DNase activity capable of introducing double-strand breaks in DNA, and a phosphatase activity that resembles phosphatidylinositol 3,4,5-triphosphatase. Both activities can be demonstrated in vitro in the absence of the other two subunits. The relative importance of each activity in vivo is unclear. Mutations that reduce either activity also reduce the toxin’s ability to induce G2/M phase arrest in at least some of the susceptible cell lines.
Similarities to mammalian DNase I
CdtB is functionally homologous to mammalian DNase I and contains a conserved pentapeptide sequence found in all DNase I enzymes to date. In addition, several residues critical to DNase I’s ability to break the phosphodiester bonds in the DNA backbone are found in the CdtB structure. A 2002 paper studying the effect of point mutations on five of these residues found that four of the five mutations tested abolished both CdtB’s ability to degrade DNA in cell-free extracts and to cause G2/M arrest upon microinjection. The fifth mutation moderately reduced CdtB’s activity.
CdtA and CdtC
CdtA and CdtC make up the B subunit of the CDT holotoxin responsible for targeting the CdtB against susceptible cells. Neither subunit appears highly conserved, with sequence identities between different species often lower than 30%. The molecular weight of CdtA ranges from 23 kDa to 30 kDa, whereas CdtC ranges from 19 kDa to 21 kDa depending on the species.
CdtA and CdtC are both believed to bind to the surface of target cells. The exact mechanism of this binding is unclear, and may not be conserved between CDT toxins from different species. Proposed targets of CdtA and CdtC binding have included cholesterol, N-linked glycans, and glycosphingolipids. Current research has produced conflicting results on the actual importance of these proposed targets. Both CdtA and CdtC contain lectin domains, suggesting that the toxin may bind via carbohydrates on the target cell’s surface, whereas other research has suggested that the targets are surface proteins.
- Rasika N.Jindasa, Stephen E. Bloom, Robert S. Weiss,Gerald E. Duhamel. (2011). "Cytolethal distending toxin: a conserved bacterial genotoxin that blocks cell cycle progression, leading to apoptosis of a broad range of mammalian cell lineages.". Microbiology 157 (7): 1851–1875. doi:10.1099/mic.0.049536-0.
- Cherilyn A. Elwell, Lawrence A. Dreyfus (2000). "DNase I homologous residues in CdtB are critical for cytolethal distending toxin-mediated cell cycle arrest.". Molecular Microbiology 37 (4): 952–963. doi:10.1046/j.1365-2958.2000.02070.x.
- Dreyfus, Lawrence, A. (2003), "Cyotlethal Distending Toxin", in D. Burns; et al., Bacterial Protein Toxins, Washington, DC: ASM Press, pp. 257–270
- Lina Guerra, Ximena Cortes-Bratti, Riccardo Guidi, Teresa Frisan (2011). "The Biology of Cytolethal Distending Toxins". Toxins 3 (3): 172–190. doi:10.3390/toxins3030172.
- D A Scott and J B Kaper (1994). "Cloning and sequencing of the Escherichia coli cytolethal distending toxin.". Infection and Immunity 62 (1): 244–251.
- Maria Lara-Tejero, Jorge E. Galan. (2001). "CdtA, CdtB, and CdtC Form a Tripartite Complex That Is Required for Cytolethal Distending Toxin Activity". Infectious Immunity 69 (7): 4358–4365. doi:10.1128/IAI.69.7.4358-4365.2001. PMC 98507. PMID 11401974.
- Cortes-Bratti, Teresa Frisan, Monica Thelestam. (2001). "The Cytolethal Distending Toxins Induce DNA Damage and Cell Cycle Arrest.". Toxicon 39 (11): 1729–1736. doi:10.1016/S0041-0101(01)00159-3.
- Bruce J. Shenker, Mensur Dlakic, Lisa P. Walker, Dave Besack, Eileen Jaffe, Ed LaBelle, Kathleen Boesze-Battaglia. (2007). "A Novel Mode of Action for a Microbial-Derived Immunotoxin: The Cytolethal Distending Toxin Subunit B Exhibits Phosphatidylinositol 3,4,5-Triphosphate Phosphatase Activity". The Journal of Immunology 178 (8): 5099–5108. doi:10.4049/jimmunol.178.8.5099.
- Blazkova, Hana; Krejcikova, Katerina; Moudry, Pavel; Frisan, Teresa; Hodny, Zdenek; Bartek, Jiri (1 January 2010). "Bacterial intoxication evokes cellular senescence with persistent DNA damage and cytokine signalling". Journal of Cellular and Molecular Medicine 14 (1-2): 357–367. doi:10.1111/j.1582-4934.2009.00862.x.
- Spanò, Stefania; Ugalde, Juan E.; Galán, Jorge E. (31 December 2007). "Delivery of a Salmonella Typhi Exotoxin from a Host Intracellular Compartment". Cell Host & Microbe 3 (1): 30–38. doi:10.1016/j.chom.2007.11.001.
- Aria Eshraghi, Francisco J. Maldonado-Arocho, Amandeep Gargi, Marissa M. Cardwell, Michael G. Prouty, Steven R. Blanke, and Kenneth A. Bradley. (2010). "Cytolethal Distending Toxin Family Members are Differentially Affected by Alterations in Host Glycans and Membrane Cholesterol". The Journal of Biological Chemistry 285 (24): 18199–18207. doi:10.1074/jbc.m110.112912.
- Dragana Nesic, Yun Hsu, C. Erec Stebbins. (2004). "Assembly and Function of A Bacterial Genotoxin.". Nature 429 (6990): 429–433. doi:10.1038/nature02532. PMID 15164065.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Cytolethal distending toxin A/C domain Provide feedback
No Pfam abstract.
Internal database links
|SCOOP:||Hira Nup160 RicinB_lectin_2 PALB2_WD40|
|Similarity to PfamA using HHSearch:||RicinB_lectin_2|
This tab holds annotation information from the InterPro database.
InterPro entry IPR003558Escherichia coli, Haemophilus spp and Campylobacter spp. all produce a toxin that is seen to cause distension in certain cell lines [PUBMED:8112838, PUBMED:10203548], which eventually disintegrate and die. This novel toxin, termed cytolethal distending toxin (cdt), has three subunits: A, B and C. Their sizes are approx. 27.7, 29.5 and 19.9kDa respectively [PUBMED:8112838], and they appear to be entirely novel [PUBMED:10203548].
Further research on the complete toxin has revealed that it blocks the cell cycle at stage G2, through inactivation of the cyclin-dependent kinase Cdk1, and without induction of DNA breaks. This leads to multipolar abortive mitosis and micronucleation, associated with centrosomal amplification [PUBMED:10777111]. The roles of each subunit are unclear, but it is believed that they have separate roles in pathogenicity.
This entry represents the A and C subunits.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||pathogenesis (GO:0009405)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
This family corresponds to a large set of related beta-trefoil proteins . The beta-trefoil is formed by six two-stranded hairpins . Three of these form a barrel structure and the other three are in a triangular array that caps the barrel. The arrangement of the secondary structures gives the molecules a pseudo 3-fold axis.
The clan contains the following 16 members:AbfB Agglutinin Botulinum_HA-17 CDtoxinA DUF569 Fascin FGF FRG1 IL1 Inhibitor_I66 Ins145_P3_rec Kunitz_legume MIR Ricin_B_lectin RicinB_lectin_2 Toxin_R_bind_C
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Author:||Griffiths-Jones SR, Bateman A|
|Number in seed:||10|
|Number in full:||25|
|Average length of the domain:||141.80 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||68.86 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CDtoxinA domain has been found. There are 6 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
Loading structure mapping...