Summary: Gap junction alpha-8 protein (Cx50)

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Wikipedia: GJA8
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GJA8 Edit Wikipedia article

Gap junction protein, alpha 8, 50kDa

Identifiers

Symbols

GJA8; CAE; CAE1; CX50; CZP1; MP70

External IDs

OMIM: 600897 MGI: 99953 HomoloGene: 3857 IUPHAR: Cx50 GeneCards: GJA8 Gene

Gene Ontology
Molecular function	channel activity
Cellular component	integral to plasma membrane connexon complex
Biological process	lens development in camera-type eye transport cell communication visual perception
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 1:
147.37 147.38 Mb

Chr 3:
96.92 96.93 Mb

PubMed search

[1]

[2]

Connexin50

Identifiers

Symbol

Connexin50

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Gap junction alpha-8 protein is a protein that in humans is encoded by the GJA8 gene.^[1]^[2]^[3] It is also known as connexin 50.

[edit] Related gene problems

1q21.1 deletion syndrome^[4]
1q21.1 duplication syndrome^[4]
microphthalmia^[5] and other vision pathologies

[edit] Interactions

GJA8 has been shown to interact with Tight junction protein 1.^[6]

[edit] References

^ Shiels A, Mackay D, Ionides A, Berry V, Moore A, Bhattacharya S (Apr 1998). "A missense mutation in the human connexin50 gene (GJA8) underlies autosomal dominant "zonular pulverulent" cataract, on chromosome 1q". Am J Hum Genet 62 (3): 52632. doi:10.1086/301762. PMC 1376956. PMID 9497259. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1376956.
^ Church RL, Wang JH, Steele E (Aug 1995). "The human lens intrinsic membrane protein MP70 (Cx50) gene: clonal analysis and chromosome mapping". Curr Eye Res 14 (3): 21521. doi:10.3109/02713689509033517. PMID 7796604.
^ "Entrez Gene: GJA8 gap junction protein, alpha 8, 50kDa". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2703.
^ ^a ^b Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, Buysse K, Huang S, Maloney VK, Crolla JA, Baralle D, et al. (October 2008). "Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes". N. Engl. J. Med. 359 (16): 168599. doi:10.1056/NEJMoa0805384. PMC 2703742. PMID 18784092. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2703742.
^ Rong P, Wang X, Niesman I, Wu Y, Benedetti LE, Dunia I, Levy E, Gong X (January 2002). "Disruption of Gja8 (alpha8 connexin) in mice leads to microphthalmia associated with retardation of lens growth and lens fiber maturation". Development 129 (1): 16774. PMID 11782410. http://dev.biologists.org/content/129/1/167.long.
^ Nielsen PA, Baruch A, Shestopalov VI, Giepmans BN, Dunia I, Benedetti EL, Kumar NM (June 2003). "Lens connexins alpha3Cx46 and alpha8Cx50 interact with zonula occludens protein-1 (ZO-1)". Mol. Biol. Cell 14 (6): 247081. doi:10.1091/mbc.E02-10-0637. PMC 194895. PMID 12808044. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=194895.

[edit] Further reading

Andrew L Harris and Darren Locke (2009). Connexins, A Guide. New York: Springer. pp. 574. ISBN 978-1-934115-46-6. http://www.springer.com/978-1-934115-46-6.
Cook PJ, Hamerton JL (1980). "Report of the committee on the genetic constitution of chromosome 1.". Cytogenet. Cell Genet. 25 (1-4): 920. doi:10.1159/000131394. PMID 396131.
Jarvis LJ, Louis CF (1993). "The permeability of reconstituted liposomes containing the purified lens fiber cell integral membrane proteins MP20, MP26 and MP70.". J. Membr. Biol. 130 (3): 25163. PMID 1491428.
Church RL, Wang JH, Steele E (1996). "The human lens intrinsic membrane protein MP70 (Cx50) gene: clonal analysis and chromosome mapping.". Curr. Eye Res. 14 (10): 97981. doi:10.3109/02713689508995138. PMID 8549164.
Geyer DD, Church RL, Steele EC, et al. (1998). "Regional mapping of the human MP70 (Cx50; connexin 50) gene by fluorescence in situ hybridization to 1q21.1.". Mol. Vis. 3: 13. PMID 9479004.
Dunia I, Recouvreur M, Nicolas P, et al. (1998). "Assembly of connexins and MP26 in lens fiber plasma membranes studied by SDS-fracture immunolabeling.". J. Cell. Sci. 111 (15): 210920. PMID 9664032.
Hopperstad MG, Srinivas M, Spray DC (2000). "Properties of gap junction channels formed by Cx46 alone and in combination with Cx50.". Biophys. J. 79 (4): 195466. doi:10.1016/S0006-3495(00)76444-7. PMC 1301086. PMID 11023900. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1301086.
Xu X, Berthoud VM, Beyer EC, Ebihara L (2002). "Functional role of the carboxyl terminal domain of human connexin 50 in gap junctional channels.". J. Membr. Biol. 186 (2): 10112. doi:10.1007/s00232-001-0139-5. PMC 2744361. PMID 11944087. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2744361.
Nielsen PA, Baruch A, Shestopalov VI, et al. (2004). "Lens connexins alpha3Cx46 and alpha8Cx50 interact with zonula occludens protein-1 (ZO-1).". Mol. Biol. Cell 14 (6): 247081. doi:10.1091/mbc.E02-10-0637. PMC 194895. PMID 12808044. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=194895.
Arora A, Minogue PJ, Liu X, et al. (2006). "A novel GJA8 mutation is associated with autosomal dominant lamellar pulverulent cataract: further evidence for gap junction dysfunction in human cataract.". J. Med. Genet. 43 (1): e2. doi:10.1136/jmg.2005.034108. PMC 2564510. PMID 16397066. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2564510.
Devi RR, Vijayalakshmi P (2006). "Novel mutations in GJA8 associated with autosomal dominant congenital cataract and microcornea.". Mol. Vis. 12: 1905. PMID 16604058.
Zhang X, Zou T, Liu Y, Qi Y (2006). "The gating effect of calmodulin and calcium on the connexin50 hemichannel.". Biol. Chem. 387 (5): 595601. doi:10.1515/BC.2006.076. PMID 16740131.
Ni X, Valente J, Azevedo MH, et al. (2007). "Connexin 50 gene on human chromosome 1q21 is associated with schizophrenia in matched case control and family-based studies.". J. Med. Genet. 44 (8): 5326. doi:10.1136/jmg.2006.047944. PMC 2597930. PMID 17412882. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2597930.
Kotsias BA, Salim M, Peracchia LL, Peracchia C (2007). "Interplay between cystic fibrosis transmembrane regulator and gap junction channels made of connexins 45, 40, 32 and 50 expressed in oocytes.". J. Membr. Biol. 214 (1): 18. doi:10.1007/s00232-006-0064-8. PMID 17546509.
Hansen L, Yao W, Eiberg H, et al. (2007). "Genetic heterogeneity in microcornea-cataract: five novel mutations in CRYAA, CRYGD, and GJA8.". Invest. Ophthalmol. Vis. Sci. 48 (9): 393744. doi:10.1167/iovs.07-0013. PMID 17724170.

This article on a gene on chromosome 1 is a stub. You can help Wikipedia by expanding it.

Membrane transport protein: ion channels (TC 1A)

Ca²⁺: Calcium channel

Voltage-gated	L-type/Ca_v? (1.1, 1.2, 1.3, 1.4) · N-type/Ca_v?2.2 · P-type/Ca_v?(2.1) · Q-type/Ca_v?2.1 · R-type/Ca_v?2.3 · T-type/Ca_v?(3.1, 3.2, 3.3) ?₂?-subunits (1, 2) · ?-subunits (?1, ?2, ?3, ?4) · ?-subunits (?1, ?2, ?3, ?4) Cation channels of sperm (1, 2, 3, 4) · Two-pore channel (1, 2)

Ligand-gated	Inositol trisphosphate receptor (1, 2, 3) · Ryanodine receptor (1, 2, 3)

Na⁺: Sodium channel

Constitutively active	Epithelial sodium channel (?, ?, ?, ?)

Proton gated	Amiloride-sensitive cation channel (1, 2, 3, 4)

Voltage-gated	Na_v? (1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 7A) · Na_v? (1, 2, 3, 4)

K⁺: Potassium channel

Voltage-gated	K_v?1-6 (1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8) · (2.1, 2.2) · (3.1, 3.2, 3.3, 3.4) · (4.1, 4.2, 4.3) · (5.1) · (6.1, 6.2, 6.3, 6.4) K_v?7-12 (7.1, 7.2, 7.3, 7.4, 7.5) · (8.1, 8.2) · (9.1, 9.2, 9.3) · (10.1, 10.2) · (11.1/hERG, 11.2, 11.3) · (12.1, 12.2, 12.3) K_v? (1, 2, 3) · KCNIP (1, 2, 3, 4) · minK/ISK · minK/ISK-like · MiRP (1, 2, 3) · Shaker gene

Calcium-activated	BK channel (?1, ?1, ?2, ?3, ?4) · SK channel (SK1, SK2, SK3) · IK channel (IK1) · K_Ca (1.1, 2.1, 2.2, 2.3, 3.1, 4.1, 4.2, 5.1)

Inward-rectifier	K_ATP · K_ir (1.1, 2.1, 2.2, 2.3, 2.4, 2.6) · GIRK/K_ir (3.1, 3.2, 3.3, 3.4) · K_ir (4.1, 4.2, 5.1, 6.1, 6.2, 7.1)

Tandem pore domain	K2P (1, 2, 3, 4, 5, 6, 7, 9, 10, 12, 13, 15, 16, 17, 18)

Other

Cl^-: Chloride channel	ANO1 · Bestrophin (1, 2) · CFTR · CLCA (1, 2, 3, 4) · CLCN (1, 2, 3, 4, 5, 6, 7, KA, KB) · CLIC (1, 2, 3, 4, 5, 6, L1) · CLNS (1A, 1B)

H⁺: Voltage-gated	HVCN1

M⁺: TRP cation channel	TRPA (1) · TRPC (1, 2, 3, 4, 4AP, 5, 6, 7) · TRPM (1, 2, 3, 4, 5, 6, 7, 8) · TRPML (1, 2, 3) · TRPN · TRPP (1, 2) · TRPV (1, 2, 3, 4, 5, 6)

Cyclic nucleotide-gated (FC)	? (1, 2, 3, 4) · ? (1, 2, 3) · HCN (1, 2, 3, 4)

Porin	Aquaporin (0, 1, 2, 3, 4, 5, 6, 7, 8, 9) · Voltage-dependent anion channel (1, 2, 3) · General bacterial porin family

Gap junction	Connexin: A (GJA1, GJA3, GJA4, GJA5, GJA8, GJA9, GJA10) · B (GJB1, GJB2, GJB3, GJB4, GJB5, GJB6, GJB7) · C (GJC1, GJC2, GJC3) · D (GJD2, GJD3, GJD4)) Innexin

General	Ligand-gated ion channel · Voltage-gated ion channel · Stretch-activated ion channel

see also disorders
B memb: cead, trns (1A, 1C, 1F, 2A, 3A1, 3A2-3, 3D), othr

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Gap junction alpha-8 protein (Cx50) Provide feedback

No Pfam abstract.

External database links

PANDIT:	PF03509
Pseudofam:	PF03509
SYSTERS:	Connexin50

This tab holds annotation information from the InterPro database.

InterPro entry IPR002266

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.

Gap junction alpha-8 protein (also called connexin50, Cx50, or lens fibre protein MP70) is a connexin of ~431 amino acid residues. The chicken isoform is shorter (399 residues) and is hence known as Cx45.6. Cx50 and Cx46 are the two gap junction proteins normally found in lens fibre cells of the eye. Evidence from both genetically-engineered mice, and from the identification of mutations in the human Cx50-encoding gene, highlight the importance of this connexin in maintaining lens transparency. Deletion of mice Cx50 produces a viable phenotype, but these animals start to develop cataracts (of the zonular pulverant type) at about one week old. They also have abnormally small eyes and lenses. Similarly, mutations in the human gene encoding Cx50 have been associated with the occurrence of congenital cataracts. Affected individuals develop cataracts (with zonular pulverent opacities), and analysis shows they have a single point mutation in the Cx50 coding region, resulting in a non-conservative substitution in the second putative TM domain of a serine residue for a proline.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	connexon complex (GO:0005922)
Biological process	cell communication (GO:0007154)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: 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
PP/Heatmap: 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

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Stockholm
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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.

Downloading

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.

View options

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.

	Seed (4)	Full (47)	Representative proteomes				NCBI (40)	Meta (0)
	Seed (4)	Full (47)	RP15 (1)	RP35 (4)	RP55 (10)	RP75 (25)	NCBI (40)	Meta (0)
Jalview	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (4)	Full (47)	Representative proteomes				NCBI (40)	Meta (0)
	Seed (4)	Full (47)	RP15 (1)	RP35 (4)	RP55 (10)	RP75 (25)	NCBI (40)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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.

	Seed (4)	Full (47)	Representative proteomes				NCBI (40)	Meta (0)
	Seed (4)	Full (47)	RP15 (1)	RP35 (4)	RP55 (10)	RP75 (25)	NCBI (40)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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 logo

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...

Trees

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.

Curation

Seed source:

PRINTS

Previous IDs:

none

Type:

Family

Author:

Griffiths-Jones SR

Number in seed:

4

Number in full:

47

Average length of the domain:

66.60 aa

Average identity of full alignment:

70 %

Average coverage of the sequence by the domain:

15.69 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	25.0	25.0
Trusted cut-off	48.6	46.6
Noise cut-off	17.3	16.2

Model length:

66

Family (HMM) version:

9

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. 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:

superkingdom
kingdom
phylum
class
order
family
genus
species

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".

Sub-species

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.

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The tree shows the occurrence of this domain across different species. More...

Species trees

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.

Interactive tree

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

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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.

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Connexin50 (PF03509)

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