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Cadherin Edit Wikipedia article
Cadherins (named for "calcium-dependent adhesion") are a type of cell adhesion molecule (CAM) that is important in the formation of adherens junctions to bind cells with each other. Cadherins are a class of type-1 transmembrane proteins. They are dependent on calcium (Ca2+) ions to function, hence their name. Cell-cell adhesion is mediated by extracellular cadherin domains, whereas the intracellular cytoplasmic tail associates with a large number of adaptor and signaling proteins, collectively referred to as the cadherin adhesome.
The cadherin superfamily includes cadherins, protocadherins, desmogleins, and desmocollins, and more. In structure, they share cadherin repeats, which are the extracellular Ca2+-binding domains. There are multiple classes of cadherin molecule, each designated with a prefix (in general, noting the type of tissue with which it is associated). It has been observed that cells containing a specific cadherin subtype tend to cluster together to the exclusion of other types, both in cell culture and during development. For example, cells containing N-cadherin tend to cluster with other N-cadherin-expressing cells. However, it has been noted that the mixing speed in the cell culture experiments can have an effect on the extent of homotypic specificity. In addition, several groups have observed heterotypic binding affinity (i.e., binding of different types of cadherin together) in various assays. One current model proposes that cells distinguish cadherin subtypes based on kinetic specificity rather than thermodynamic specificity, as different types of cadherin homotypic bonds have different lifetimes.
Structure and function
Cadherins are synthesized as polypeptides and undergo many post-translational modifications to become the proteins which mediate cell-cell adhesion and recognition. These polypeptides are approximately 720–750 amino acids long. Each cadherin has a small cytoplasmic component, a transmembrane component, and the remaining bulk of the protein is extra-cellular (outside the cell). The transmembrane component consists of single chain glycoprotein repeats. Because cadherins are Ca2+ dependent, they have five tandem extracellular domain repeats that act as the binding site for Ca2+ ions. Their extracellular domain interacts in two separate trans dimer conformations: strand-swap dimers (S-dimers) and X-dimers. To date, over 100 types of cadherins in humans have been identified and sequenced.
The functionality of cadherins relies upon the formation of two identical subunits, known as homodimers. The homodimeric cadherins create cell-cell adhesion with cadherins present in the membranes of other cells through changing conformation from cis-dimers to trans-dimers. Once the cell-cell adhesion between cadherins present in the cell membranes of two different cells has formed, adherens junctions can then be made when protein complexes, usually composed of α-, β-, and γ-catenins, bind to the actin cytoskeleton portion of the cadherin.
Cadherins behave as both receptors and ligands for other molecules. During development, their behavior assists in properly positioning cells: they are responsible for the separation of the different tissue layers, and for cellular migration. In the very early stages of development, E-cadherin (epithelial cadherin) is most greatly expressed. Many cadherins are specified for specific functions in the cell, and they are differentially expressed in a developing embryo. For example, during neurulation, when the neural plate is forming in the embryo, the tissues residing near the cranial neural folds have decreased N-cadherin expression. Conversely, the expression of the N-cadherins remains unchanged in the other regions of the neural tube that is located on the anterior-posterior axis of the vertebrate. The expression of the different types of cadherins in the cell are varying dependent upon the specific differentiation and specification of the organism during development.
Cadherins play a vital role in the migration of cells through the epithelial-mesenchymal transition (EMT), which requires cadherins to forms adherents junctions with neighboring cells. In neural crest cells, which are transient cells that arise in the developing organism during gastrulation and function in the patterning of the vertebrate body plan, the cadherins are necessary to allow migration of cells to form tissues or organs. In addition, cadherins responsible in the EMT event in early development have also been shown to be critical in the reprogramming of specified adult cells into a pluripotent state, forming induced pluripotent stem cells (iPSCs).
After development, cadherins play a role in maintaining cell and tissue structure, and in cellular movement. Regulation of cadherin expression can occur through promoter methylation among other epigenetic mechanisms.
The E-cadherin–catenin complex plays a key role in cellular adhesion; loss of this function has been associated with greater tumour metastasis.
There are said to be over 100 different types of cadherins found in vertebrates, which can be classified into four groups: classical, desmosomal, protocadherins, and unconventional. This large amount of diversity is accomplished by having multiple cadherin encoding genes combined with alternative RNA splicing mechanisms. Invertebrates contain fewer than 20 types of cadherins.
Different members of the cadherin family are found in different locations.
- CDH1 – E-cadherin (epithelial): E-cadherins are found in epithelial tissue
- CDH2 – N-cadherin (neural): N-cadherins are found in neurons
- CDH12 – cadherin 12, type 2 (N-cadherin 2)
- CDH3 – P-cadherin (placental): P-cadherins are found in the placenta.
PCDH15; PCDH17; PCDH18; PCDH19; PCDH20; PCDH7; PCDH8; PCDH9; PCDHA1; PCDHA10; PCDHA11; PCDHA12; PCDHA13; PCDHA2; PCDHA3; PCDHA4; PCDHA5; PCDHA6; PCDHA7; PCDHA8; PCDHA9; PCDHAC1; PCDHAC2; PCDHB1; PCDHB10; PCDHB11; PCDHB12; PCDHB13; PCDHB14; PCDHB15; PCDHB16; PCDHB17; PCDHB18; PCDHB2; PCDHB3; PCDHB4; PCDHB5; PCDHB6; PCDHB7; PCDHB8; PCDHB9; PCDHGA1; PCDHGA10; PCDHGA11; PCDHGA12; PCDHGA2; PCDHGA3; PCDHGA4; PCDHGA5; PCDHGA6; PCDHGA7; PCDHGA8; PCDHGA9; PCDHGB1; PCDHGB2; PCDHGB3; PCDHGB4; PCDHGB5; PCDHGB6; PCDHGB7; PCDHGC3; PCDHGC4; PCDHGC5
- CDH9 – cadherin 9, type 2 (T1-cadherin)
- CDH10 – cadherin 10, type 2 (T2-cadherin)
- CDH4 – R-cadherin (retinal)
- CDH5 – VE-cadherin (vascular endothelial)
- CDH6 – K-cadherin (kidney)
- CDH7 – cadherin 7, type 2
- CDH8 – cadherin 8, type 2
- CDH11 – OB-cadherin (osteoblast)
- CDH13 – T-cadherin – H-cadherin (heart)
- CDH15 – M-cadherin (myotubule)
- CDH16 – KSP-cadherin
- CDH17 – LI cadherin (liver-intestine)
- CDH18 – cadherin 18, type 2
- CDH19 – cadherin 19, type 2
- CDH20 – cadherin 20, type 2
- CDH23 – cadherin 23 (neurosensory epithelium)
- CDH10; CDH11; CDH13; CDH15; CDH16; CDH17;
- Alimperti, Stella; Andreadis, Stelios T. "CDH2 and CDH11 act as regulators of stem cell fate decisions". Stem Cell Research. 14 (3): 270–282. doi:10.1016/j.scr.2015.02.002.
- Hulpiau P, van Roy F (February 2009). "Molecular evolution of the cadherin superfamily". Int. J. Biochem. Cell Biol. 41 (2): 349–69. doi:10.1016/j.biocel.2008.09.027. PMID 18848899.
- Angst B, Marcozzi C, Magee A (February 2001). "The cadherin superfamily: diversity in form and function". J Cell Sci. 114 (Pt 4): 629–41. PMID 11171368.
- Bello, S.M.; Millo, H.; Rajebhosale, M.; Price, S.R. (2012). "Catenin-dependent cadherin function drives divisional segregation of spinal chord motor neurons". Journal of Neuroscience. 32 (2): 490–505. doi:10.1523/jneurosci.4382-11.2012.
- Duguay, D.; A. Foty R., RA; S. Steinberg M., MS (2003). "Cadherin-mediated cell adhesion and tissue segregation: qualitative and quantitative determinants". Dev. Biol. 253 (2): 309–323. doi:10.1016/S0012-1606(02)00016-7. PMID 12645933.
- Niessen, Carien M.; Gumbiner, Barry M. (2002). "Cadherin-mediated cell sorting not determined by binding or adhesion specificity". The Journal of Cell Biology. 156 (2): 389–399. doi:10.1083/jcb.200108040. PMC . PMID 11790800.
- Volk, T.; Cohen, O.; Geiger, B. (1987). "Formation of heterotypic adherens-type junctions between L-CAM containing liver cells and A-CAM containing lens cells". Cell. 50 (6): 987–994. doi:10.1016/0092-8674(87)90525-3. PMID 3621349.
- Bayas, Marco V.; Leung, Andrew; Evans, Evan; Leckband, Deborah (2005). "Lifetime Measurements Reveal Kinetic Differences between Homophilic Cadherin Bonds". Biophysical Journal. 90 (4): 1385–95. doi:10.1529/biophysj.105.069583. PMC . PMID 16326909.
- Harris, T. J.; Tepass, U (2010). "Adherens junctions: From molecules to morphogenesis". Nature Reviews Molecular Cell Biology. 11 (7): 502–14. doi:10.1038/nrm2927. PMID 20571587.
- Marie, Pierre J.; Haÿ, Eric; Modrowski, Dominique; Revollo, Leila; Mbalaviele, Gabriel; Civitelli, Roberto (2014-01-01). "Cadherin-Mediated Cell–Cell Adhesion and Signaling in the Skeleton". Calcified Tissue International. 94 (1): 46–54. doi:10.1007/s00223-013-9733-7. ISSN 0171-967X. PMC .
- Priest, Andrew Vae; Shafraz, Omer; Sivasankar, Sanjeevi. "Biophysical basis of cadherin mediated cell-cell adhesion". Experimental Cell Research. 358 (1): 10–13. doi:10.1016/j.yexcr.2017.03.015.
- Tepass, U; Truong, K; Godt, D; Ikura, M; Peifer, M (2000). "Cadherins in embryonic and neural morphogenesis". Nature Reviews Molecular Cell Biology. 1 (2): 91–100. doi:10.1038/35040042. PMID 11253370.
- Gumbiner, B. M. (2005). "Regulation of cadherin-mediated adhesion in morphogenesis". Nature Reviews Molecular Cell Biology. 6 (8): 622–34. doi:10.1038/nrm1699. PMID 16025097.
- Taneyhill, Lisa A.; Schiffmacher, Andrew T. (2017-06-01). "Should I stay or should I go? Cadherin function and regulation in the neural crest". genesis. 55 (6): n/a–n/a. doi:10.1002/dvg.23028. ISSN 1526-968X.
- Reinhold, WC; Reimers, MA; Maunakea, AK; Kim, S; Lababidi, S; Scherf, U; Shankavaram, UT; Ziegler, MS; Stewart, C; Kouros-Mehr, Hosein; Cui, H; Dolginow, D; Scudiero, DA; Pommier, YG; Munroe, DJ; Feinberg, AP; Weinstein, JN (Feb 2007). "Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells". Molecular cancer therapeutics. 6 (2): 391–403. doi:10.1158/1535-7163.MCT-06-0609. PMID 17272646.
- Beavon, IR (August 2000). "The E-cadherin-catenin complex in tumour metastasis: structure, function and regulation". European Journal of Cancer. 36 (13 Spec No): 1607–20. doi:10.1016/S0959-8049(00)00158-1. PMID 10959047.
- "The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins". Structure. 19 (2): 244–56. doi:10.1016/j.str.2010.11.016. PMC . PMID 21300292.; rendered with PyMOL; Harrison, O.J.; Jin, X.; Hong, S.; Bahna, F.; Ahlsen, G.; Brasch, J.; Wu, Y.; Vendome, J.; Felsovalyi, K.; Hampton, C.M.; Troyanovsky, R.B.; Ben-Shaul, A.; Frank, J.; Troyanovsky, S.M.; Shapiro, L.; Honig, B. (2011).
- Stefan Offermanns; Walter Rosenthal (2008). Encyclopedia of Molecular Pharmacology. Springer. pp. 306–. ISBN 978-3-540-38916-3. Retrieved 14 December 2010.
- Lodish, Harvey; Berk, Arnold; Kaiser, Chris; Krieger, Monte; Bretscher, Anthony; Ploegh, Hidde; Amon, Angelika (2013). Molecular Cell Biology (Seventh ed.). New York: Worth Publ. p. 934. ISBN 978-1-4292-3413-9.
- Beavon IR (2000). "The E-cadherin-catenin complex in tumour metastasis: structure, function and regulation". Eur. J. Cancer. 36 (13 Spec No): 1607–20. doi:10.1016/S0959-8049(00)00158-1. PMID 10959047.
- Berx G, Becker KF, Höfler H, van Roy F (1998). "Mutations of the human E-cadherin (CDH1) gene". Hum. Mutat. 12 (4): 226–37. doi:10.1002/(SICI)1098-1004(1998)12:4<226::AID-HUMU2>3.0.CO;2-D. PMID 9744472.
- Bryant DM, Stow JL (2005). "The ins and outs of E-cadherin trafficking". Trends Cell Biol. 14 (8): 427–34. doi:10.1016/j.tcb.2004.07.007. PMID 15308209.
- Chun YS, Lindor NM, Smyrk TC, et al. (2001). "Germline E-cadherin gene mutations: is prophylactic total gastrectomy indicated?". Cancer. 92 (1): 181–7. doi:10.1002/1097-0142(20010701)92:1<181::AID-CNCR1307>3.0.CO;2-J. PMID 11443625.
- Georgolios A, Batistatou A, Manolopoulos L, Charalabopoulos K (2006). "Role and expression patterns of E-cadherin in head and neck squamous cell carcinoma (HNSCC)". J. Exp. Clin. Cancer Res. 25 (1): 5–14. PMID 16761612.
- Hazan RB, Qiao R, Keren R, et al. (2004). "Cadherin switch in tumor progression". Ann. N. Y. Acad. Sci. 1014 (1): 155–63. doi:10.1196/annals.1294.016. PMID 15153430.
- Moran CJ, Joyce M, McAnena OJ (2005). "CDH1 associated gastric cancer: a report of a family and review of the literature". Eur J Surg Oncol. 31 (3): 259–64. doi:10.1016/j.ejso.2004.12.010. PMID 15780560.
- Reynolds AB, Carnahan RH (2005). "Regulation of cadherin stability and turnover by p120ctn: implications in disease and cancer". Semin. Cell Dev. Biol. 15 (6): 657–63. doi:10.1016/j.semcdb.2004.09.003. PMID 15561585.
- Wang HD, Ren J, Zhang L (2004). "CDH1 germline mutation in hereditary gastric carcinoma". World J. Gastroenterol. 10 (21): 3088–93. PMID 15457549.
- Wijnhoven BP, Dinjens WN, Pignatelli M (2000). "E-cadherin-catenin cell-cell adhesion complex and human cancer". The British journal of surgery. 87 (8): 992–1005. doi:10.1046/j.1365-2168.2000.01513.x. PMID 10931041.
- Wilson PD (2001). "Polycystin: new aspects of structure, function, and regulation". J. Am. Soc. Nephrol. 12 (4): 834–45. PMID 11274246.
- Renaud-Young M, Gallin WJ (2002). "In the first extracellular domain of E-cadherin, heterophilic interactions, but not the conserved His-Ala-Val motif, are required for adhesion". Journal of Biological Chemistry. 277 (42): 39609–39616. doi:10.1074/jbc.M201256200. PMID 12154084.
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.
Cadherin-like Provide feedback
This cadherin domain is usually the most N-terminal copy of the domain.
Elledge HM, Kazmierczak P, Clark P, Joseph JS, Kolatkar A, Kuhn P, Muller U;, Proc Natl Acad Sci U S A. 2010;107:10708-10712.: Structure of the N terminus of cadherin 23 reveals a new adhesion mechanism for a subset of cadherin superfamily members. PUBMED:20498078 EPMC:20498078
Trivedi M, Laurence JS, Williams TD, Middaugh CR, Siahaan TJ;, Int J Pharm. 2012;431:16-25.: Improving the stability of the EC1 domain of E-cadherin by thiol alkylation of the cysteine residue. PUBMED:22531851 EPMC:22531851
Internal database links
|Similarity to PfamA using HHSearch:||Cadherin|
This tab holds annotation information from the InterPro database.
InterPro entry IPR013164
Cadherins are a family of adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in all solid tissues of the organism which modulate a wide variety of processes including cell polarisation and migration [PUBMED:2197976, PUBMED:14570569]. Cadherin-mediated cell-cell junctions are formed as a result of interaction between extracellular domains of identical cadherins, which are located on the membranes of the neighbouring cells. The stability of these adhesive junctions is ensured by binding of the intracellular cadherin domain with the actin cytoskeleton. There are a number of different isoforms distributed in a tissue-specific manner in a wide variety of organisms. Cells containing different cadherins tend to segregate in vitro, while those that contain the same cadherins tend to preferentially aggregate together. This observation is linked to the finding that cadherin expression causes morphological changes involving the positional segregation of cells into layers, suggesting they may play an important role in the sorting of different cell types during morphogenesis, histogenesis and regeneration. They may also be involved in the regulation of tight and gap junctions, and in the control of intercellular spacing. Cadherins are evolutionary related to the desmogleins which are component of intercellular desmosome junctions involved in the interaction of plaque proteins.
Structurally, cadherins comprise a number of domains: classically, these include a signal sequence; a propeptide of around 130 residues; a single transmembrane domain and five tandemly repeated extracellular cadherin domains, 4 of which are cadherin repeats, and the fifth contains 4 conserved cysteines and a N-terminal cytoplasmic domain [PUBMED:11736639]. However, proteins are designated as members of the broadly defined cadherin family if they have one or more cadherin repeats. A cadherin repeat is an independently folding sequence of approximately 110 amino acids that contains motifs with the conserved sequences DRE, DXNDNAPXF, and DXD. Crystal structures have revealed that multiple cadherin domains form Ca2+-dependent rod-like structures with a conserved Ca2+-binding pocket at the domain-domain interface. Cadherins depend on calcium for their function: calcium ions bind to specific residues in each cadherin repeat to ensure its proper folding, to confer rigidity upon the extracellular domain and is essential for cadherin adhesive function and for protection against protease digestion.
This entry represents a cadherin domain that is usually found at the N terminus of cadherin proteins.
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.
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This clan includes a diverse range of domains that have an Ig-like fold and appear to be distantly related to each other. The clan includes: PKD domains, cadherins and several families of bacterial Ig-like domains as well as viral tail fibre proteins. it also includes several Fibronectin type III domain-containing families.
The clan contains the following 93 members:A2M A2M_N A2M_N_2 AlcCBM31 Alpha-amylase_N Alpha_adaptinC2 Arch_flagellin Arylsulfotran_N Big_1 Big_2 Big_3 Big_3_2 Big_3_3 Big_3_5 Big_4 Big_5 BiPBP_C BsuPI Cadherin Cadherin-like Cadherin_2 Cadherin_3 Cadherin_pro Calx-beta CARDB CBM39 CBM_X2 CelD_N CHB_HEX_C CHB_HEX_C_1 ChitinaseA_N CHU_C Coatamer_beta_C COP-gamma_platf CopC DUF11 DUF1410 DUF2271 DUF3244 DUF4165 DUF4625 DUF5011 DUF916 EpoR_lig-bind Filamin FixG_C FlgD_ig fn3 Fn3-like fn3_2 fn3_4 fn3_5 Fn3_assoc GBS_Bsp-like Glyco_hydro_61 He_PIG HYR IFNGR1 IL12p40_C IL17R_fnIII_D2 IL4Ra_N IL6Ra-bind Integrin_alpha2 Interfer-bind Invasin_D3 LEA_2 Lep_receptor_Ig LPMO_10 LRR_adjacent MG1 Mo-co_dimer Neurexophilin NPCBM_assoc PhoD_N PKD PKD_2 PKD_3 Pur_ac_phosph_N Qn_am_d_aIII REJ RHD_dimer Rib SoxZ SprB SVA SWM_repeat T2SS-T3SS_pil_N TcfC TIG Tissue_fac Transglut_C TRAP_beta Y_Y_Y
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.
|Seed source:||Pfam-B_179 (release 17.0)|
|Number in seed:||49|
|Number in full:||3091|
|Average length of the domain:||82.10 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||9.33 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -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
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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 Cadherin_2 domain has been found. There are 44 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...