Summary: Bone marrow stromal antigen 2
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 "Tetherin". 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 email@example.com 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.
Tetherin Edit Wikipedia article
|, CD317, TETHERIN, Tetherin, bone marrow stromal cell antigen 2|
Tetherin, also known as bone marrow stromal antigen 2, is a lipid raft associated protein that in humans is encoded by the BST2 gene. In addition, tetherin has been designated as CD317 (cluster of differentiation 317). This protein is constitutively expressed in mature B cells, plasma cells and plasmacytoid dendritic cells, and in many other cells, it is only expressed as a response to stimuli from IFN pathway.
Tetherin is part of IFN-dependent antiviral response pathway. When the presence of virus and viral components is detected by recognition molecules such as (RIG-I), a cascades of interactions happen between signaling molecules, eventually the signal reaches the nucleus to upregulate the expression of interferon-stimulated genes (ISGs), this in turn activates IFN-a pathway to send the signal to neighboring cells, which causes upregulation in the expression of other ISGs and many viral restriction factors, such as tetherin.
Tetherin is a human cellular protein which inhibits retrovirus infection by preventing the diffusion of virus particles after budding from infected cells. Initially discovered as an inhibitor to HIV-1 infection in the absence of Vpu, tetherin has also been shown to inhibit the release of other RNA viruses such as the Lassa and Marburg virions suggesting a common mechanism that inhibits enveloped virus release without interaction with viral proteins. In addition, tetherin also restricts neuroinvasion of the DNA virus HSV-1.
Tetherin is a type 2 integral membrane protein, with the N-terminus in the cytoplasm, one membrane spanning domain, and a C-terminus modified by the addition of a glycosyl-phosphatidylinositol (gpi) anchor. The transmembrane of tetherin is predicted to be a single alpha helix. The ectodomain consists of alpha helical coiled-coil region where the coils are slightly spread apart. Although Tetherin is localized to the lipid rafts on the surface of the cells, they are endocytosed to be sorted through TGN by clathrin-dependent pathway. This is mediated by AP2 binding to the dual-tyrosine motif located in the cytosolic domain of tetherin. When the virion buds from the surface of the cell, one of the tetherin membrane domains is in the new viral membrane, the other remains in the plasma membrane, tethering the virion to the cell. It is antagonized by the viral protein Vpu which is thought to work by targeting tetherin for degradation via the β-TrCP2 dependent pathway.
Tetherin exists as a dimer on the surface of cells, and prevention of dimerisation by mutating the cystine residues, prevents tetherin from inhibiting virus release, although it is still detectable in the cell. The stabilization of the protein through disulfide bond within the coiled coil region seems to be important in its function
Interaction with different viruses
Tetherin is known to block many different types of enveloped viruses by tethering the budding virus like particles (VLPs) and inhibiting them from leaving the cell surface. Studies have shown that it is not the amino acid sequence, but the topology of tetherin is required for the tethering of virions on the cell surface. Their unique topology allows them to be in the cell through their N-terminus while using the GPI anchor to attach to budding virions. HIV-1 overcomes this restriction through vpu. Vpu interacts with tethrin by interacting with the protein at its transmembrane domain and recruiting β-TrCP2, which causes ubiquitination and degradation of tetherin. It has been recently shown that tetherin gene variants are associated with HIV disease progression underscoring the role of BST-2 in HIV type 1 infection. Another primate lentivirus, SIV, also, counteracts tetherin by their removal from the plasma membrane. KSHV protein K5 also targets tetherin for degradation through ubiquitination. Ebola counteracts tethrin through two mechanism. VP35 of Ebola, inhibits multiple steps of IFN-signaling pathway, which blocks the induction of tetherin as a downstream effect. Also, it has been noted that the full-length Ebola GP may either translocate tetherin or disrupt the structure of tetherin. Sendai virus proteins HN and F direct tethrin to endosomes or proteasome for degradation. CHIKV protein nsP1 interacts with tetherin by disrupting the tetherin-virion complex formation.
Cell-to-cell transmission through virological synapse in human retroviruses is also inhibited by tetherin. Tetherin aggregates virions and downmodulates the infectivity of the virions. It has also been suggested that tetherin may be involved in the structural integrity of the virological synapse.
Tetherin has also been predicted to be involved in cell adhesion and cell migration. Recently it has, also, been identified as the protein that help stabilize lipid rafts by joining nearby lipid rafts to form a cluster. For some viruses, such as Dengue virus, tetherin inhibits the budding of virions as well as cell-to-cell transmission of the virus. For human cytomegalovirus (HCMV), tetherin promotes entry of the virus, especially during cell differentiation. It has also been shown that tetherin is incorporated into newly formed virions.
- GRCh38: Ensembl release 89: ENSG00000130303 - Ensembl, May 2017
- "Human PubMed Reference:".
- Ishikawa J, Kaisho T, Tomizawa H, Lee BO, Kobune Y, Inazawa J, Oritani K, Itoh M, Ochi T, Ishihara K (Aug 1995). "Molecular cloning and chromosomal mapping of a bone marrow stromal cell surface gene, BST2, that may be involved in pre-B-cell growth". Genomics. 26 (3): 527–34. doi:10.1016/0888-7543(95)80171-H. PMID 7607676.
- "Entrez Gene: BST2 bone marrow stromal cell antigen 2".
- Rollason R, Korolchuk V, Hamilton C, Schu P, Banting G (November 2007). "Clathrin-mediated endocytosis of a lipid-raft-associated protein is mediated through a dual tyrosine motif". Journal of Cell Science. 120 (Pt 21): 3850–8. doi:10.1242/jcs.003343. PMID 17940069.
- Le Tortorec A, Willey S, Neil SJ (May 2011). "Antiviral inhibition of enveloped virus release by tetherin/BST-2: action and counteraction". Viruses. 3 (5): 520–40. doi:10.3390/v3050520. PMC . PMID 21994744.
- Kühl A, Pöhlmann S (September 2012). "How ebola virus counters the interferon system". Zoonoses Public Health. 59 Suppl 2: 116–31. doi:10.1111/j.1863-2378.2012.01454.x. PMID 22958256.
- Douglas JL, Gustin JK, Viswanathan K, Mansouri M, Moses AV, Früh K (May 2010). "The great escape: viral strategies to counter BST-2/tetherin". PLoS Pathogenesis. 6 (5): e1000913. doi:10.1371/journal.ppat.1000913. PMC . PMID 20485522.
- Sakuma T, Noda T, Urata S, Kawaoka Y, Yasuda J (March 2009). "Inhibition of Lassa and Marburg virus production by tetherin". Journal of Virology. 83 (5): 2382–5. doi:10.1128/JVI.01607-08. PMC . PMID 19091864.
- Thaczuk D (2008-02-11). "Tetherin: a newly discovered host cell protein that inhibits HIV replication". NAM AIDS Map.
- Royer D, Carr J (December 2015). "A STING-dependent innate-sensing pathway mediates resistance to corneal HSV-1 infection via upregulation of the antiviral effector tetherin". Mucosal Immunology. 9: 1065–75. doi:10.1038/mi.2015.124. PMID 26627457.
- Andrew AJ, Miyagi E, Kao S, Strebel K (2009). "The formation of cysteine-linked dimers of BST-2/tetherin is important for inhibition of HIV-1 virus release but not for sensitivity to Vpu". Retrovirology. 6: 80. doi:10.1186/1742-4690-6-80. PMC . PMID 19737401.
- Evans DT, Serra-Moreno R, Singh RK, Guatelli JC (September 2010). "BST-2/tetherin: a new component of the innate immune response to enveloped viruses". Trends in Microbiology. 18 (9): 388–96. doi:10.1016/j.tim.2010.06.010. PMC . PMID 20688520.
- Neil SJ, Zang T, Bieniasz PD (January 2008). "Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu". Nature. 451 (7177): 425–30. doi:10.1038/nature06553. PMID 18200009.
- Mangeat B, Gers-Huber G, Lehmann M, Zufferey M, Luban J, Piguet V (September 2009). "HIV-1 Vpu neutralizes the antiviral factor Tetherin/BST-2 by binding it and directing its beta-TrCP2-dependent degradation". PLoS Pathog. 5 (9): e1000574. doi:10.1371/journal.ppat.1000574. PMC . PMID 19730691.
- Iwabu Y, Fujita H, Kinomoto M, Kaneko K, Ishizaka Y, Tanaka Y, Sata T, Tokunaga K (December 2009). "HIV-1 accessory protein Vpu internalizes cell-surface BST-2/tetherin through transmembrane interactions leading to lysosomes". Journal of Biological Chemistry. 284 (50): 35060–72. doi:10.1074/jbc.M109.058305. PMC . PMID 19837671.
- Laplana M, Caruz A, Pineda JA, Puig T, Fibla J (February 2013). "Association of BST-2 gene variants with HIV disease progression underscores the role of BST-2 in HIV type 1 infection". Journal of Infectious Diseases. 207 (3): 411–419. doi:10.1093/infdis/jis685. PMID 23148293.
- Jia B, Serra-Moreno R, Neidermyer W, Rahmberg A, Mackey J, Fofana IB, Johnson WE, Westmoreland S, Evans DT (May 2009). "Species-specific activity of SIV Nef and HIV-1 Vpu in overcoming restriction by tetherin/BST2". PLoS Pathog. 5 (5): e1000429. doi:10.1371/journal.ppat.1000429. PMC . PMID 19436700.
- Harris RS, Hultquist JF, Evans DT (November 2012). "The restriction factors of human immunodeficiency virus". Journal of Biological Chemistry. 287 (49): 40875–83. doi:10.1074/jbc.R112.416925. PMC . PMID 23043100.
- Mansouri M, Viswanathan K, Douglas JL, Hines J, Gustin J, Moses AV, Früh K (October 2009). "Molecular mechanism of BST2/tetherin downregulation by K5/MIR2 of Kaposi's sarcoma-associated herpesvirus". Journal of Virology. 83 (19): 9672–81. doi:10.1128/JVI.00597-09. PMC . PMID 19605472.
- Bampi C, Rasga L, Roux L (March 2013). "Antagonism to human BST-2 / tetherin by Sendai virus glycoproteins". Journal of General Virology. 94 (Pt 6): 1211–9. doi:10.1099/vir.0.051771-0. PMC . PMID 23468424.
- Jones PH, Maric M, Madison MN, Maury W, Roller RJ, Okeoma CM (March 2013). "BST-2/tetherin-mediated restriction of chikungunya (CHIKV) VLP budding is counteracted by CHIKV non-structural protein 1 (nsP1)". Virology. 438 (1): 37–49. doi:10.1016/j.virol.2013.01.010. PMC . PMID 23411007.
- Billcliff PG, Rollason R, Prior I, Owen DM, Gaus K, Banting G (February 2013). "CD317/Tetherin is an organiser of membrane microdomains". Journal of Cell Science. 126 (Pt 7): 1553–64. doi:10.1242/jcs.112953. PMC . PMID 23378022.
- Pan XB, Han JC, Cong X, Wei L (2012). "BST2/tetherin inhibits dengue virus release from human hepatoma cells". PLoS ONE. 7 (12): e51033. doi:10.1371/journal.pone.0051033. PMC . PMID 23236425.
- Viswanathan K, Smith MS, Malouli D, Mansouri M, Nelson JA, Früh K (November 2011). "BST2/Tetherin enhances entry of human cytomegalovirus". PLoS Pathogenesis. 7 (11): e1002332. doi:10.1371/journal.ppat.1002332. PMC . PMID 22072961.
- Maruyama K, Sugano S (1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene. 138 (1–2): 171–4. doi:10.1016/0378-1119(94)90802-8. PMID 8125298.
- Furuya Y, Takasawa S, Yonekura H, Tanaka T, Takahara J, Okamoto H (1996). "Cloning of a cDNA encoding rat bone marrow stromal cell antigen 1 (BST-1) from the islets of Langerhans". Gene. 165 (2): 329–30. doi:10.1016/0378-1119(95)00540-M. PMID 8522202.
- Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S (1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene. 200 (1–2): 149–56. doi:10.1016/S0378-1119(97)00411-3. PMID 9373149.
- Ohtomo T, Sugamata Y, Ozaki Y, Ono K, Yoshimura Y, Kawai S, Koishihara Y, Ozaki S, Kosaka M, Hirano T, Tsuchiya M (1999). "Molecular cloning and characterization of a surface antigen preferentially overexpressed on multiple myeloma cells". Biochemical and Biophysical Research Communications. 258 (3): 583–91. doi:10.1006/bbrc.1999.0683. PMID 10329429.
- Vidal-Laliena M, Romero X, March S, Requena V, Petriz J, Engel P (2006). "Characterization of antibodies submitted to the B cell section of the 8th Human Leukocyte Differentiation Antigens Workshop by flow cytometry and immunohistochemistry". Cellular Immunology. 236 (1–2): 6–16. doi:10.1016/j.cellimm.2005.08.002. PMID 16157322.
- Elortza F, Mohammed S, Bunkenborg J, Foster LJ, Nühse TS, Brodbeck U, Peck SC, Jensen ON (2006). "Modification-specific proteomics of plasma membrane proteins: identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment". Journal of Proteome Research. 5 (4): 935–43. doi:10.1021/pr050419u. PMID 16602701.
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.
Bone marrow stromal antigen 2 Provide feedback
No Pfam abstract.
Yang H, Wang J, Jia X, McNatt MW, Zang T, Pan B, Meng W, Wang HW, Bieniasz PD, Xiong Y;, Proc Natl Acad Sci U S A. 2010;107:18428-18432.: Structural insight into the mechanisms of enveloped virus tethering by tetherin. PUBMED:20940320 EPMC:20940320
This tab holds annotation information from the InterPro database.
InterPro entry IPR024886Bone marrow stromal antigen 2, also known as tetherin, is an antiretroviral defence protein, that blocks release of enveloped virus from the cell surface [PUBMED:18200009, PUBMED:20686043, PUBMED:20940320]. Bst2/tetherin contains two membrane anchors which are employed to retain some enveloped viruses, including HIV-1, tethered to the plasma membrane in the absence of virus encoded antagonists [PUBMED:20399176]. Its expression is induced by interferon-alpha [PUBMED:19032371] and was originally linked to B cell development [PUBMED:7607676].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||defense response to virus (GO:0051607)|
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...
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.
|Number in seed:||17|
|Number in full:||53|
|Average length of the domain:||82.90 aa|
|Average identity of full alignment:||47 %|
|Average coverage of the sequence by the domain:||45.58 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
|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.
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 BST2 domain has been found. There are 47 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 sequence.
Loading structure mapping...