Summary: Chaperonin 10 Kd subunit

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

Wikipedia: GroES
Pfam
InterPro

This is the Wikipedia entry entitled "GroES". 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 pfam-help@sanger.ac.uk and we will try to help.

Contact us

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.

GroES Edit Wikipedia article

Heat shock 10kDa protein 1 (chaperonin 10)

Identifiers

Symbols

HSPE1; CPN10; EPF; GROES; HSP10

External IDs

OMIM: 600141 MGI: 104680 HomoloGene: 20500 GeneCards: HSPE1 Gene

Gene Ontology
Molecular function	• protein binding • ATP binding • unfolded protein binding • chaperone binding
Cellular component	• mitochondrion • mitochondrial matrix
Biological process	• protein folding • activation of cysteine-type endopeptidase activity involved in apoptotic process • response to unfolded protein
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 2:
198.36 – 198.37 Mb

Chr 1:
55.09 – 55.09 Mb

PubMed search

[1]

[2]

Cpn10

gp31 co-chaperonin from bacteriophage t4

Identifiers

Symbol

Cpn10

Pfam clan

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

Heat shock 10 kDa protein 1 (Hsp10) also known as chaperonin 10 (cpn10) or early-pregnancy factor (EPF) is a protein that in humans is encoded by the HSPE1 gene. The homolog in E. coli is GroES that is a chaperonin which usually works in conjunction with GroEL.^[1]

GroES exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits.^[2] These ring structures assemble by self-stimulation in the presence of Mg²⁺-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides an isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg²⁺-ATP dependent manner.^[3] The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60.

Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL.^[4] Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.

[edit] Interactions

GroES has been shown to interact with GroEL.^[5]^[6]

[edit] References

^ "Entrez Gene: HSPE1 heat shock 10kDa protein 1 (chaperonin 10)".
^ Hemmingsen SM, Woolford C, van der Vies SM, Tilly K, Dennis DT, Georgopoulos CP, Hendrix RW, Ellis RJ (May 1988). "Homologous plant and bacterial proteins chaperone oligomeric protein assembly". Nature 333 (6171): 330–4. doi:10.1038/333330a0. PMID 2897629.
^ Schmidt A, Schiesswohl M, Volker U, Hecker M, Schumann W (June 1992). "Cloning, sequencing, mapping, and transcriptional analysis of the groESL operon from Bacillus subtilis". J. Bacteriol. 174 (12): 3993–9. PMC 206108. PMID 1350777.
^ Martin J, Geromanos S, Tempst P, Hartl FU (November 1993). "Identification of nucleotide-binding regions in the chaperonin proteins GroEL and GroES". Nature 366 (6452): 279–82. doi:10.1038/366279a0. PMID 7901771.
^ Samali A, Cai J, Zhivotovsky B, Jones DP, Orrenius S (April 1999). "Presence of a pre-apoptotic complex of pro-caspase-3, Hsp60 and Hsp10 in the mitochondrial fraction of jurkat cells". EMBO J. 18 (8): 2040–8. doi:10.1093/emboj/18.8.2040. PMC 1171288. PMID 10205158.
^ Lee KH, Kim HS, Jeong HS, Lee YS (October 2002). "Chaperonin GroESL mediates the protein folding of human liver mitochondrial aldehyde dehydrogenase in Escherichia coli". Biochem. Biophys. Res. Commun. 298 (2): 216–24. doi:10.1016/S0006-291X(02)02423-3. PMID 12387818.

[edit] Further reading

Czarnecka AM, Campanella C, Zummo G, Cappello F (2007). "Heat shock protein 10 and signal transduction: a "capsula eburnea" of carcinogenesis?". Cell Stress Chaperones 11 (4): 287–94. doi:10.1379/CSC-200.1. PMC 1713189. PMID 17278877.
Legname G, Fossati G, Gromo G, et al. (1995). "Expression in Escherichia coli, purification and functional activity of recombinant human chaperonin 10". FEBS Lett. 361 (2-3): 211–4. doi:10.1016/0014-5793(95)00184-B. PMID 7698325.
Cavanagh AC, Morton H (1994). "The purification of early-pregnancy factor to homogeneity from human platelets and identification as chaperonin 10". Eur. J. Biochem. 222 (2): 551–60. doi:10.1111/j.1432-1033.1994.tb18897.x. PMID 7912672.
Monzini N, Legname G, Marcucci F, et al. (1994). "Identification and cloning of human chaperonin 10 homologue". Biochim. Biophys. Acta 1218 (3): 478–80. PMID 7914093.
Chen JJ, McNealy DJ, Dalal S, Androphy EJ (1994). "Isolation, sequence analysis and characterization of a cDNA encoding human chaperonin 10". Biochim. Biophys. Acta 1219 (1): 189–90. PMID 7916212.
Samali A, Cai J, Zhivotovsky B, et al. (1999). "Presence of a pre-apoptotic complex of pro-caspase-3, Hsp60 and Hsp10 in the mitochondrial fraction of jurkat cells". EMBO J. 18 (8): 2040–8. doi:10.1093/emboj/18.8.2040. PMC 1171288. PMID 10205158.
Summers KM, Fletcher BH, Macaranas DD, et al. (2000). "Mapping and characterization of the eukaryotic early pregnancy factor/chaperonin 10 gene family". Somat. Cell Mol. Genet. 24 (6): 315–26. doi:10.1023/A:1024488422990. PMID 10763410.
Richardson A, Schwager F, Landry SJ, Georgopoulos C (2001). "The importance of a mobile loop in regulating chaperonin/ co-chaperonin interaction: humans versus Escherichia coli". J. Biol. Chem. 276 (7): 4981–7. doi:10.1074/jbc.M008628200. PMID 11050098.
Fletcher BH, Cassady AI, Summers KM, Cavanagh AC (2001). "The murine chaperonin 10 gene family contains an intronless, putative gene for early pregnancy factor, Cpn10-rs1". Mamm. Genome 12 (2): 133–40. doi:10.1007/s003350010250. PMID 11210183.
Parissi V, Calmels C, De Soultrait VR, et al. (2001). "Functional interactions of human immunodeficiency virus type 1 integrase with human and yeast HSP60". J. Virol. 75 (23): 11344–53. doi:10.1128/JVI.75.23.11344-11353.2001. PMC 114720. PMID 11689615.
Hansen JJ, Dürr A, Cournu-Rebeix I, et al. (2002). "Hereditary spastic paraplegia SPG13 is associated with a mutation in the gene encoding the mitochondrial chaperonin Hsp60". Am. J. Hum. Genet. 70 (5): 1328–32. doi:10.1086/339935. PMC 447607. PMID 11898127.
Guidry JJ, Wittung-Stafshede P (2002). "Low stability for monomeric human chaperonin protein 10: interprotein interactions contribute majority of oligomer stability". Arch. Biochem. Biophys. 405 (2): 280–2. doi:10.1016/S0003-9861(02)00406-X. PMID 12220543.
Lee KH, Kim HS, Jeong HS, Lee YS (2002). "Chaperonin GroESL mediates the protein folding of human liver mitochondrial aldehyde dehydrogenase in Escherichia coli". Biochem. Biophys. Res. Commun. 298 (2): 216–24. doi:10.1016/S0006-291X(02)02423-3. PMID 12387818.
Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
Hansen JJ, Bross P, Westergaard M, et al. (2003). "Genomic structure of the human mitochondrial chaperonin genes: HSP60 and HSP10 are localised head to head on chromosome 2 separated by a bidirectional promoter". Hum. Genet. 112 (1): 71–7. doi:10.1007/s00439-002-0837-9. PMID 12483302.
Mansell JP, Yarram SJ, Brown NL, Sandy JR (2004). "Type I collagen synthesis by human osteoblasts in response to placental lactogen and chaperonin 10, a homolog of early-pregnancy factor". In Vitro Cell. Dev. Biol. Anim. 38 (9): 518–22. doi:10.1290/1071-2690(2002)038<0518:TICSBH>2.0.CO;2. PMID 12703979.
Cappello F, Bellafiore M, David S, et al. (2003). "Ten kilodalton heat shock protein (HSP10) is overexpressed during carcinogenesis of large bowel and uterine exocervix". Cancer Lett. 196 (1): 35–41. doi:10.1016/S0304-3835(03)00212-X. PMID 12860287.
Shan YX, Liu TJ, Su HF, et al. (2004). "Hsp10 and Hsp60 modulate Bcl-2 family and mitochondria apoptosis signaling induced by doxorubicin in cardiac muscle cells". J. Mol. Cell. Cardiol. 35 (9): 1135–43. doi:10.1016/S0022-2828(03)00229-3. PMID 12967636.
Shan YX, Yang TL, Mestril R, Wang PH (2003). "Hsp10 and Hsp60 suppress ubiquitination of insulin-like growth factor-1 receptor and augment insulin-like growth factor-1 receptor signaling in cardiac muscle: implications on decreased myocardial protection in diabetic cardiomyopathy". J. Biol. Chem. 278 (46): 45492–8. doi:10.1074/jbc.M304498200. PMID 12970367.
Guidry JJ, Shewmaker F, Maskos K, et al. (2004). "Probing the interface in a human co-chaperonin heptamer: residues disrupting oligomeric unfolded state identified". BMC Biochem. 4: 14. doi:10.1186/1471-2091-4-14. PMC 270013. PMID 14525625.

[edit] External links

GroES Protein at the US National Library of Medicine Medical Subject Headings (MeSH)
3D macromolecular structures of GroES in EMDB

This article on a gene on chromosome 2 is a stub. You can help Wikipedia by expanding it.

Posttranslational modification

Chaperones/
protein folding

Heat shock proteins/ Chaperonins	Hsp10/GroES Early pregnancy factor Hsp27 Hsp47 HSP60/GroEL Hsp40/DnaJ A1 A2 A3 B1 B2 B11 B4 B6 B9 C1 C3 C5 C6 C7 C10 C11 C13 C14 C19 Hsp70 1A 1B 1L 2 4 4L 5 6 7 8 9 12A 14 Hsp90 α₁ α₂ β ER TRAP1

Other	Alpha crystallin Clusterin Survival of motor neuron SMN1 SMN2

Protein targeting

Signal peptide Mitochondrial targeting signal

Ubiquitin

E1 Ubiquitin-activating enzyme
- UBA1
- UBA2
- UBA3
- UBA5
- UBA6
- UBA7
- ATG7
- NAE1
- SAE1

E2 Ubiquitin-conjugating enzyme
- A
- B
- C
- D1
- D2
- D3
- E1
- E2
- E3
- G1
- G2
- H
- I
- J1
- J2
- K
- L1
- L2
- L3
- L4
- L6
- M
- N
- O
- Q1
- Q2
- R1 (CDC34)
- R2
- S
- V1
- V2
- Z

E3 Ubiquitin ligase
- VHL
- Cullin
- CBL
- MDM2
- FANCL
- UBR1

Other

Ubiquitin-like modifiers
- SUMO protein
- ISG15
- URM1
- NEDD8
- FAT10
- ATG8
- ATG12
- FUB1
- MUB
- UFM1
- UBL5

See also: posttranslational modification disorders
B bsyn: dna (repl, cycl, reco, repr) · tscr (fact, tcrg, nucl, rnat, rept, ptts) · tltn (risu, pttl, nexn) · dnab, rnab/runp · stru (domn, 1°, 2°, 3°, 4°)

This article incorporates text from the public domain Pfam and InterPro IPR020818

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.

Chaperonin 10 Kd subunit Provide feedback

This family contains GroES and Gp31-like chaperonins. Gp31 is a functional co-chaperonin that is required for the folding and assembly of Gp23, a major capsid protein, during phage morphogenesis [1].

Literature references

Hunt JF, van der Vies SM, Henry L, Deisenhofer J; , Cell 1997;90:361-371.: Structural adaptations in the specialized bacteriophage T4 co-chaperonin Gp31 expand the size of the Anfinsen cage. PUBMED:9244309 EPMC:9244309

External database links

HOMSTRAD:	cpn10
PANDIT:	PF00166
PRINTS:	PR00297
PROSITE:	PDOC00576
Pseudofam:	PF00166
SCOP:	1lep
SYSTERS:	Cpn10

This tab holds annotation information from the InterPro database.

InterPro entry IPR020818

The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins [PUBMED:1349837]. These are required for normal cell growth [PUBMED:2897629], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) [PUBMED:12354603].

The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits [PUBMED:2897629]. These ring structures assemble by self-stimulation in the presence of Mg²⁺-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg²⁺-ATP dependent manner [PUBMED:1350777]. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60.

Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL [PUBMED:7901771]. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.

Gene Ontology

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

Cellular component	cytoplasm (GO:0005737)
Biological process	protein folding (GO:0006457)

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan GroES (CL0296), which contains the following 2 members:

ADH_N Cpn10

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:

Selex
Stockholm
FASTA
MSF

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 (48)	Full (6057)	Representative proteomes				NCBI (3685)	Meta (2838)
	Seed (48)	Full (6057)	RP15 (540)	RP35 (1020)	RP55 (1322)	RP75 (1577)	NCBI (3685)	Meta (2838)
Jalview	View	View	View	View	View	View	View	View
HTML	View		View	View	View	View
PP/heatmap	₁		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 (48)	Full (6057)	Representative proteomes				NCBI (3685)	Meta (2838)
	Seed (48)	Full (6057)	RP15 (540)	RP35 (1020)	RP55 (1322)	RP75 (1577)	NCBI (3685)	Meta (2838)
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 (48)	Full (6057)	Representative proteomes				NCBI (3685)	Meta (2838)
	Seed (48)	Full (6057)	RP15 (540)	RP35 (1020)	RP55 (1322)	RP75 (1577)	NCBI (3685)	Meta (2838)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	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:

Prosite

Previous IDs:

cpn10;

Type:

Domain

Author:

Sonnhammer ELL, Finn RD

Number in seed:

48

Number in full:

6057

Average length of the domain:

90.70 aa

Average identity of full alignment:

44 %

Average coverage of the sequence by the domain:

92.00 %

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	21.1	21.1
Trusted cut-off	21.1	21.2
Noise cut-off	21.0	21.0

Model length:

93

Family (HMM) version:

16

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.

Loading sunburst data...

Tree controls

Hide

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

Loading...

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.

Interactions

There are 2 interactions for this family. More...

Cpn10 Cpn60_TCP1

Structures

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 Cpn10 domain has been found. There are 114 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...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Cpn10 (PF00166)

Jump to...