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 "Connexin". 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.
Connexin Edit Wikipedia article
An open gap junction, composed of six identical connexin proteins. Each of these six units is a single polypeptide which passes the membrane four times (referred to as four-pass transmembrane proteins).
Connexins, or gap junction proteins, are a family of structurally related transmembrane proteins that assemble to form vertebrate gap junctions (an entirely different family of proteins, the innexins, form gap junctions in invertebrates). Each gap junction is composed of two hemichannels, or connexons, which are themselves each constructed out of six connexin molecules. Gap junctions are essential for many physiological processes, such as the coordinated depolarization of cardiac muscle, proper embryonic development, and the conducted response in microvasculature. For this reason, mutations in connexin-encoding genes can lead to functional and developmental abnormalities.
Connexins are four-pass transmembrane proteins with both C and N cytoplasmic termini, a cytoplasmic loop (CL) and two extra-cellular loops, (EL-1) and (EL-2). Connexins are assembled in groups of six to form hemichannels, or connexons, and two hemichannels then combine to form a gap junction. The connexin gene family is diverse, with twenty-one identified members in the sequenced human genome, and twenty in the mouse (nineteen of which are orthologous pairs). They usually weigh between 26 and 60 kDa, and have an average length of 380 amino acids. The various connexins have been observed to combine into both homomeric and heteromeric gap junctions, each of which may exhibit different functional properties including pore conductance, size selectivity, charge selectivity, voltage gating, and chemical gating.
In recent literature, connexins are most commonly named according to their molecular weights, e.g. Cx26 is the connexin protein of 26 kDa. However, this can lead to confusion when connexin genes from different species are compared, e.g. human Cx36 is homologous to zebrafish Cx35. A competing nomenclature is the Gja/Gjb system, where connexins are sorted by their α and β forms, then assigned an identifying number, e.g. Gja1 corresponds to Cx43. The nomenclature of the connexin genes and proteins is currently under review by the HUGO Gene Nomenclature Committee. The term Connexin is abbreviated as Cx or CX.
Biosynthesis and Internalization
A remarkable aspect of connexins is that they have a relatively short half life of only a few hours. The result is the presence of a dynamic cycle by which connexins are synthesized and replaced. It has been suggested that this short life span allows for more finely regulated physiological processes to take place, such as in the myometrium.
From the Nucleus to the Membrane
As they are being translated by ribosomes, connexins are inserted into the membrane of the endoplasmic reticulum (ER) (Bennett and Zukin, 2004). It is in the ER that connexins are properly folded, yielding two extracellular loops, EL-1 and EL-2. It is also in the ER that the oligomerization of connexin molecules into hemichannels begins, a process which may continue in the UR-Golgi intermediate compartment as well. The arrangements of these hemichannels can be homotypic, heterotypic, and combined heterotypic/heteromeric.
After exiting the ER and passing through the ERGIC, the folded connexins will usually enter the cis-Golgi network. However, some connexins, such as Cx26 may be transported independent of the Golgi.
Gap Junction Assembly
After being inserted into the plasma membrane of the cell, the hemichannels freely diffuse within the lipid bilayer. Through the aid of specific proteins, mainly cadherins, the hemichannels are able to dock with hemichannels of adjacent cells forming gap junctions. Recent studies have shown the existence of communication between adherens junctions and gap junctions, suggesting a higher level of coordination than previously thought.
Connexin gap junctions are found only in vertebrates, while a functionally analogous (but genetically unrelated) group of proteins, the innexins, are responsible for gap junctions in invertebrate species. Innexin orthologs have also been identified in Chordates, but they are no longer capable of forming gap junctions. Instead, the channels formed by these proteins (called pannexins) act as very large transmembrane pores that connect the intra- and extracellular compartments.
Within the CNS, gap junctions provide electrical coupling between progenitor cells, neurons, and glial cells. By using specific connexin KO mice, studies revealed that cell coupling is essential for visual signaling. In the retina, ambient light levels influence cell coupling provided by gap junction channels, adapting the visual function for various lighting conditions. Cell coupling is governed by several mechanisms, including connexin expression.
List of human connexins
|Connexin||Gene||Location and Function|
|Cx43||GJA1||Expressed at the surface of vasculature with atherosclerotic plaque, and up-regulated during atherosclerosis in mice. May have pathological effects. Also expressed between granulosa cells, which is required for proliferation. Normally expressed in astrocytes, also detected in most of the human astrocytomas and in the astroglial component of glioneuronal tumors.  It is also the main cardiac connexin, found mainly in ventricular myocardium.  Associated with oculodentodigital dysplasia.|
|Cx37||GJA4||Induced in vascular smooth muscle during coronary arteriogenesis. Cx37 mutations are not lethal. Forms gap junctions between oocytes and granulosa cells, and are required for oocyte survival.|
|Cx40||GJA5||Expressed selectively in atrial myocytes. Responsible for mediating the coordinated electrical activation of atria.|
|Pseudogene in humans|
|Cx50||GJA8||Gap Junctions between A-typ Horizontal cells in Mouse and Rabbit Retina|
|Cx62||GJA10||Human Cx62 complies Cx57 (Mouse). Location in axon-bearing B-typ Horizontal Cell in Rabbit Retina|
|Cx32||GJB1||Major component of the peripheral myelin. Mutations in the human gene cause X-linked Charcot-Marie-Tooth disease, a hereditary neuropathy. In human normal brain CX32 expressed in neurons and oligodendrocytes.|
|Cx26||GJB2||Mutated in Vohwinkel syndrome as well as Keratitis-Icthyosis-Deafness (KID) Syndrome.|
|Cx31||GJB3||Can be associated with Erythrokeratodermia variabilis.|
|Cx30.3||GJB4||Fonseca et al. confirmed Cx30.3 expression in thymocytes. Can be associated with Erythrokeratodermia variabilis.|
|Cx30||GJB6||Mutated in Clouston syndrome (hidrotic ectodermal dysplasia)|
|Cx45||GJC1/GJA7||Human pancreatic ductal epithelial cells. Atrio-ventricular node.|
|Cx47||GJC2/GJA12||Expressed in oligodentrocyte gap junctions|
|Cx30.2||GJC3||Expressed in structures of the inner ear. Thought to have a role in ion transport for signal transduction in hair cells.|
|Cx36||GJD2/GJA9||Pancreatic beta cell function, mediating the release of insulin. Neurones throughout the Central Nervous System where they allow synchronisation of action potential firing between networks of neurones.|
|Cx29||GJE1||Not known to form gap junctions; present in innermost layer of myelin in Schwann cells|
- Lodish, Harvey F.; Arnold Berk, Paul Matsudaira, Chris A. Kaiser, Monty Krieger, Mathew P. Scott, S. Lawrence Zipursky, James Darnell (2004). Molecular Cell Biology (5th ed.). New York: W.H. Freeman and Company. pp. 230–1. ISBN 0-7167-4366-3.
- Laird DW (March 2006). "Life cycle of connexins in health and disease". The Biochemical Journal 394 (3): 527–43. doi:10.1042/BJ20051922. PMC 1383703. PMID 16492141.
- Musil, LS; Goodenough DA (1993). "Multisubunit assembly of an integral plasma membrane channel protein, gap junction connexin43, occurs after exit from the ER". Cell 74 (6): 1065–77. doi:10.1016/0092-8674(93)90728-9. PMID 7691412.
- Evans, W. H.; Ahmad, S., Diez, J., George, C. H., Kendall, J. M. and Martin, P. E. (1999). "Trafficking pathways leading to the formation of gap junctions". Novartis Found. Symp. Novartis Foundation Symposia 219: 44–54. doi:10.1002/9780470515587.ch4. ISBN 978-0-470-51558-7. PMID 10207897.
- George, C. H., Kendall, J. M. and Evans, W. H. (1999). "Intracellular trafficking pathways in the assembly of connexins into gap junctions". J. Biol. Chem. 274 (13): 8678–85. doi:10.1074/jbc.274.13.8678. PMID 10085106.
- George, C. H., Kendall, J. M., Campbell, A. K. and Evans, W. H. (1998). "Connexin–aequorin chimerae report cytoplasmic calcium environments along trafficking pathways leading to gap junction biogenesis in living COS-7 cells". J. Biol. Chem. 274 (45): 29822–9. doi:10.1074/jbc.273.45.29822. PMID 9792698.
- Martin, P. E., George, C. H., Castro, C., Kendall, J. M., Capel, J., Campbell, A. K., Revilla, A., Barrio, L. C. and Evans, W. H. (1998). "Assembly of chimeric connexin–aequorin proteins into functional gap junction channels. Reporting intracellular and plasma membrane calcium environments". J. Biol. Chem. 273 (3): 1719–26. doi:10.1074/jbc.273.3.1719. PMID 9430718.
- Martin, P. E., Errington, R. J. and Evans, W. H. (2001). "Gap junction assembly: multiple connexin fluorophores identify complex trafficking pathways". Cell Commun. Adhes. 8 (4–6): 243–8. doi:10.3109/15419060109080731. PMID 12064596.
- Thomas, T., Jordan, K., Simek, J., Shao, Q., Jedeszko, C., Walton, P. and Laird, D. W. (2005). "Mechanisms of Cx43 and Cx26 transport to the plasma membrane and gap junction regeneration". J. Cell Sci 118 (Pt 19): 4451–62. doi:10.1242/jcs.02569. PMID 16159960.
- Jongen, W. M., Fitzgerald, D. J., Asamoto, M., Piccoli, C., Slaga, T. J., Gros, D., Takeichi, M. and Yamasaki, H. (1991). "Regulation of connexin 43-mediated gap junctional intercellular communication by Ca2+ in mouse epidermal cells is controlled by E- cadherin". J. Cell Biol. 114 (3): 545–555. doi:10.1083/jcb.114.3.545. PMC 2289094. PMID 1650371.
- Wei, C. J., Francis, R., Xu, X. and Lo, C. W. (2005). "Connexin43 associated with an N-cadherin-containing multiprotein complex is required for gap junction formation in NIH3T3 cells". J. Biol. Chem. 280 (20): 19925–36. doi:10.1074/jbc.M412921200. PMID 15741167.
- Dbouk HA, Mroue RM, El-Sabban ME, Talhouk RS (2009). "Connexins: a myriad of functions extending beyond assembly of gap junction channels". Cell Commun. Signal 7: 4. doi:10.1186/1478-811X-7-4. PMC 2660342. PMID 19284610.
- Kihara AH, de Castro LM, Moriscot AS, Hamassaki DE. (May 2006). "Prolonged dark adaptation changes connexin expression in the mouse retina". J Neurosci Res 83 (7): 1331–41. doi:10.1002/jnr.20815. PMID 16496335.
- Aronica E, Gorter J, Jansen G et al. (2001). "Expression of connexin 43 and connexin 32 gap-junction proteins in epilepsy-associated brain tumors and in the perilesional epileptic cortex". Acta Neuropathol. 101 (5): 449–59. PMID 11484816.
- Verheule S, van Kempen MJ, te Welscher PH, Kwak BR, Jongsma HJ (May 1997). "Characterization of gap junction channels in adult rabbit atrial and ventricular myocardium". Circ. Res. 80 (5): 673–81. PMID 9130448.
- Gollob MH et al. (June 22 2006). "Somatic mutations in the connexin 40 gene (GJA5) in atrial fibrillation". N Engl J Med 354 (25): 2677–88. doi:10.1056/NEJMoa052800. PMID 16790700.
- Massey, Stephen (January, 16. 2009). Connexins: A Guide (1st ed.). Springer-Verlag Gmbh. pp. 3–?. ISBN 1-934115-46-0.
- Beyer, Eric C.; Berthound, Viviana M. (January, 16. 2009). Connexins: A Guide (1st ed.). Springer-Verlag Gmbh. pp. 387–417. ISBN 1-934115-46-0.
- Fonseca PC, Nihei OK, Urban-Maldonado M, Abreu S, de Carvalho AC, Spray DC, Savino W, Alves LA (June 2004). "Characterization of connexin 30.3 and 43 in thymocytes". Immuno lett. 94 (1–2): 65–75. doi:10.1016/j.imlet.2004.03.019. PMID 15234537.
- Tai M-H; Olson, LK; Madhukar, BV; Linning, KD; Van Camp, L; Tsao, MS; Trosko, JE (2003). "Characterization of Gap Junctional Intercellular Communication in Immortalized Human Pancreatic Ductal Epithelial Cells With Stem Cell Characteristics". Pancreas 26 (1): e18–e26. doi:10.1097/00006676-200301000-00025. PMID 12499933. Unknown parameter
- Kamasawa N, Sik A, Morita M, et al. (2005). "Connexin-47 and connexin-32 in gap junctions of oligodendrocyte somata, myelin sheaths, paranodal loops and Schmidt-Lanterman incisures: implications for ionic homeostasis and potassium siphoning". Neuroscience 136 (1): 65–86. doi:10.1016/j.neuroscience.2005.08.027. PMC 1550704. PMID 16203097.
- del Castillo I et al. (January 24 2002). "A deletion involving the connexin 30 gene in nonsyndromic hearing impairment". N Engl J Med 346 (4): 343–9. doi:10.1056/NEJMoa012052. PMID 11807148.
- Connors BW, Long MA (2004). "Electrical synapses in the mammalian brain". Annu Rev Neurosci 27: 393–418. doi:10.1146/annurev.neuro.26.041002.131128. PMID 15217338.
- Li X, Lynn BD, Olson C, et al. (September 2002). "Connexin29 expression, immunocytochemistry and freeze-fracture replica immunogold labelling (FRIL) in sciatic nerve". Eur. J. Neurosci. 16 (5): 795–806. PMC 1803218. PMID 12372015.
- Media related to connexins at Wikimedia Commons
- Connexins at the US National Library of Medicine Medical Subject Headings (MeSH)
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.
Connexin Provide feedback
No Pfam abstract.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013092
The connexins are a family of integral membrane proteins that oligomerise to form intercellular channels that are clustered at gap junctions. These channels are specialised sites of cell-cell contact that allow the passage of ions, intracellular metabolites and messenger molecules (with molecular weight less than 1-2kDa) from the cytoplasm of one cell to its opposing neighbours. They are found in almost all vertebrate cell types, and somewhat similar proteins have been cloned from plant species. Invertebrates utilise a different family of molecules, innexins, that share a similar predicted secondary structure to the vertebrate connexins, but have no sequence identity to them [PUBMED:9769729].
Vertebrate gap junction channels are thought to participate in diverse biological functions. For instance, in the heart they permit the rapid cell-cell transfer of action potentials, ensuring coordinated contraction of the cardiomyocytes. They are also responsible for neurotransmission at specialised 'electrical' synapses. In non-excitable tissues, such as the liver, they may allow metabolic cooperation between cells. In the brain, glial cells are extensively-coupled by gap junctions; this allows waves of intracellular Ca2+ to propagate through nervous tissue, and may contribute to their ability to spatially-buffer local changes in extracellular K+ concentration [PUBMED:7685944].
The connexin protein family is encoded by at least 13 genes in rodents, with many homologues cloned from other species. They show overlapping tissue expression patterns, most tissues expressing more than one connexin type. Their conductances, permeability to different molecules, phosphorylation and voltage-dependence of their gating, have been found to vary. Possible communication diversity is increased further by the fact that gap junctions may be formed by the association of different connexin isoforms from apposing cells. However, in vitro studies have shown that not all possible combinations of connexins produce active channels [PUBMED:8811187, PUBMED:8608591].
Hydropathy analysis predicts that all cloned connexins share a common transmembrane (TM) topology. Each connexin is thought to contain 4 TM domains, with two extracellular and three cytoplasmic regions. This model has been validated for several of the family members by in vitro biochemical analysis. Both N- and C-termini are thought to face the cytoplasm, and the third TM domain has an amphipathic character, suggesting that it contributes to the lining of the formed-channel. Amino acid sequence identity between the isoforms is ~50-80%, with the TM domains being well conserved. Both extracellular loops contain characteristically conserved cysteine residues, which likely form intramolecular disulphide bonds. By contrast, the single putative intracellular loop (between TM domains 2 and 3) and the cytoplasmic C terminus are highly variable among the family members. Six connexins are thought to associate to form a hemi-channel, or connexon. Two connexons then interact (likely via the extracellular loops of their connexins) to form the complete gap junction channel.
NH2-*** *** *************-COOH ** ** ** ** ** ** ** ** Cytoplasmic ---**----**-----**----**---------------- ** ** ** ** Membrane ** ** ** ** ---**----**-----**----**---------------- ** ** ** ** Extracellular ** ** ** ** ** **
Two sets of nomenclature have been used to identify the connexins. The first, and most commonly used, classifies the connexin molecules according to molecular weight, such as connexin43 (abbreviated to Cx43), indicating a connexin of molecular weight close to 43kDa. However, studies have revealed cases where clear functional homologues exist across species that have quite different molecular masses; therefore, an alternative nomenclature was proposed based on evolutionary considerations, which divides the family into two major subclasses, alpha and beta, each with a number of members [PUBMED:1320430]. Due to their ubiquity and overlapping tissue distributions, it has proved difficult to elucidate the functions of individual connexin isoforms. To circumvent this problem, particular connexin-encoding genes have been subjected to targeted-disruption in mice, and the phenotype of the resulting animals investigated. Around half the connexin isoforms have been investigated in this manner [PUBMED:9861669]. Further insight into the functional roles of connexins has come from the discovery that a number of human diseases are caused by mutations in connexin genes. For instance, mutations in Cx32 give rise to a form of inherited peripheral neuropathy called X-linked dominant Charcot-Marie-Tooth disease [PUBMED:7570999]. Similarly, mutations in Cx26 are responsible for both autosomal recessive and dominant forms of nonsyndromic deafness, a disorder characterised by hearing loss, with no apparent effects on other organ systems.
This domain is found in the N-terminal region of these 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.
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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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 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.
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
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.
MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
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:||65|
|Number in full:||1256|
|Average length of the domain:||102.60 aa|
|Average identity of full alignment:||49 %|
|Average coverage of the sequence by the domain:||33.51 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|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 Connexin 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...