Summary: Enolase, C-terminal TIM barrel domain
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 "Enolase". 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.
Enolase Edit Wikipedia article
Yeast enolase dimer.
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
|Enolase, N-terminal domain|
x-ray structure and catalytic mechanism of lobster enolase
Enolase, also known as phosphopyruvate hydratase, is a metalloenzyme responsible for the catalysis of the conversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP), the ninth and penultimate step of glycolysis. The chemical reaction catalyzed by enolase is:
- 2-phospho-D-glycerate phosphoenolpyruvate + H2O
Enolase belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic name of this enzyme is 2-phospho-D-glycerate hydro-lyase (phosphoenolpyruvate-forming).
The reaction is reversible, depending on environmental concentrations of substrates. The optimum pH for the human enzyme is 6.5. Enolase is present in all tissues and organisms capable of glycolysis or fermentation. The enzyme was discovered by Lohmann and Meyerhof in 1934, and has since been isolated from a variety of sources including human muscle and erythrocytes. In humans, deficiency of ENO1 is linked to hereditary haemolytic anemia while ENO3 deficiency is linked to glycogen storage disease XIII.
In humans there are three subunits of enolase, α, β, and γ, each encoded by a separate gene that can combine to form five different isoenzymes: αα, αβ, αγ, ββ, and γγ. Three of these isoenzymes (all homodimers) are more commonly found in adult human cells than the others:
- αα or non-neuronal enolase (NNE), which is found in a variety of tissues, including liver, brain, kidney, spleen, adipose. It is present at some level in all normal human cells. Also known as enolase 1
- ββ or muscle specific enolase (MSE). Also known as enolase 3. This enzyme is largely restricted to muscle where it is present at very high levels in muscle
- γγ or neuron-specific enolase (NSE). Also known as enolase 2. Expressed at very high levels in neurons and neural tissues, where it can account for as much as 3% of total soluble protein. It is expressed at much lower levels in most mammalian cells.
When present in the same cell, different isozymes readily form heterodimers.
Enolase is a member of the large enolase superfamily. It has a molecular weight of 82,000-100,000 Daltons depending on the isoform. In human alpha enolase, the two subunits are antiparallel in orientation so that Glu20 of one subunit forms an ionic bond with Arg414 of the other subunit. Each subunit has two distinct domains. The smaller N-terminal domain consists of three α-helices and four β-sheets. The larger C-terminal domain starts with two β-sheets followed by two α-helices and ends with a barrel composed of alternating β-sheets and α-helices arranged so that the β-beta sheets are surrounded by the α-helices. The enzyme’s compact, globular structure results from significant hydrophobic interactions between these two domains.
Enolase is a highly conserved enzyme with five active-site residues being especially important for activity. When compared to wild-type enolase, a mutant enolase that differs at either the Glu168, Glu211, Lys345, or Lys396 residue has an activity level that is cut by a factor of 105. Also, changes affecting His159 leave the mutant with only 0.01% of its catalytic activity. An integral part of enolase are two Mg2+ cofactors in the active site, which serve to stabilize negative charges in the substrate.
Using isotopic probes, the overall mechanism for converting 2-PG to PEP is proposed to be an E1cb elimination reaction involving a carbanion intermediate. The following detailed mechanism is based on studies of crystal structure and kinetics. When the substrate, 2-phosphoglycerate, binds to α-enolase, its carboxyl group coordinates with two magnesium ion cofactors in the active site. This stabilizes the negative charge on the deprotonated oxygen while increasing the acidity of the alpha hydrogen. Enolase’s Lys345 deprotonates the alpha hydrogen, and the resulting negative charge is stabilized by resonance to the carboxylate oxygen and by the magnesium ion cofactors. Following the creation of the carbanion intermediate, the hydroxide on C3 is eliminated as water with the help of Glu211, and PEP is formed.
Additionally, conformational changes occur within the enzyme that aid catalysis. In human α-enolase, the substrate is rotated into position upon binding to the enzyme due to interactions with the two catalytic magnesium ions, Gln167, and Lys396. Movements of loops Ser36 to His43, Ser158 to Gly162, and Asp255 to Asn256 allow Ser39 to coordinate with Mg2+ and close off the active site. In addition to coordination with the catalytic magnesium ions, the pKa of the substrate’s alpha hydrogen is also lowered due to protonation of the phosphoryl group by His159 and its proximity to Arg374. Arg374 also causes Lys345 in the active site to become deprotonated, which primes Lys345 for its role in the mechanism.
In recent medical experiments, enolase concentrations have been sampled in an attempt to diagnose certain conditions and their severity. For example, higher concentrations of enolase in cerebrospinal fluid more strongly correlated to low-grade astrocytoma than did other enzymes tested (aldolase, pyruvate kinase, creatine kinase, and lactate dehydrogenase). The same study showed that the fastest rate of tumor growth occurred in patients with the highest levels of CSF enolase. Increased levels of enolase have also been identified in patients who have suffered a recent myocardial infarction or cerebrovascular accident. It has been inferred that levels of CSF neuron-specific enolase, serum NSE, and creatine kinase (type BB) are indicative in the prognostic assessment of cardiac arrest victims. Other studies have focused on the prognostic value of NSE values in cerebrovascular accident victims.
Small-molecule inhibitors of enolase have been synthesized as chemical probes (substrate-analogues) of the catalytic mechanism of the enzyme and more recently, have been investigated as potential treatments for cancer and infectious diseases . Most inhibitors have metal chelating properties and bind to enzyme by interactions with the structural Magnesium Atom Mg(A). The most potent of these is phosphonoacetohydroxamate, which in its unprotonated form has pM affinity for the enzyme. It has structural similarity to the presumed catalytic intermediate, between PEP and 2-PG. Attempts have been made to use this inhibitor as an anti-trypanosome drug, and more recently, as an anti-cancer agent, specifically, in glioblastoma that are enolase-deficient due to homozygous deletion of the ENO1 gene as part of the 1p36 tumor suppressor locus (synthetic lethality). A natural product phosphonate antibiotic, SF2312 (CAS 107729-45-3), which is active against gram positive and negative bacteria especially under anaerobic conditions , is a high potency inhibitor of Enolase 4zcw that binds in manner similar to phoshphonoacetohydroxamate 4za0. An allosteric binder, ENOblock  was initially described as an inhibitor of Enolase, but subsequently shown not to actually inhibit the enzyme, but rather, interfere with the Enolase in vitro enzymatic assay .
Fluoride is a known competitor of enolase’s substrate 2-PG. The fluoride is part of a complex with magnesium and phosphate, which binds in the active site instead of 2-PG. As such, drinking fluoridated water provides fluoride at a level that inhibits oral bacteria enolase activity. Disruption of the bacteria’s glycolytic pathway - and, thus, its normal metabolic functioning - prevents dental caries from forming.
- doi:10.1021/bi9712450. PMID 9376357.; Zhang E, Brewer JM, Minor W, Carreira LA, Lebioda L (October 1997). "Mechanism of enolase: the crystal structure of asymmetric dimer enolase-2-phospho-D-glycerate/enolase-phosphoenolpyruvate at 2.0 A resolution". Biochemistry. 36 (41): 12526–34.
- ; Vollmar M, Krysztofinska E, Chaikuad A, Krojer T, Cocking R, Vondelft F, Bountra C, Arrowsmith CH, Weigelt J, Edwards A, Yue WW, Oppermann U (2010). "Crystal structure of human beta enolase ENOB". To be published.
- Pancholi V (June 2001). "Multifunctional alpha-enolase: its role in diseases". Cellular and Molecular Life Sciences. 58 (7): 902–20. doi:10.1007/PL00000910. PMID 11497239.[permanent dead link]
- Hoorn RK, Flickweert JP, Staal GE (1974). "Purification and properties of enolase of human erythroctyes". Int J Biochem. 5 (11–12): 845–52. doi:10.1016/0020-711X(74)90119-0.
- Lohman K & Meyerhof O (1934) Über die enzymatische umwandlung von phosphoglyzerinsäure in brenztraubensäure und phosphorsäure (Enzymatic transformation of phosphoglyceric acid into pyruvic and phosphoric acid). Biochem Z 273, 60–72.
- Peshavaria M, Day IN (April 1991). "Molecular structure of the human muscle-specific enolase gene (ENO3)". The Biochemical Journal. 275 ( Pt 2) (Pt 2): 427–33. doi:10.1042/bj2750427. PMC . PMID 1840492.
- Ehinger S, Schubert WD, Bergmann S, Hammerschmidt S, Heinz DW (October 2004). "Plasmin(ogen)-binding alpha-enolase from Streptococcus pneumoniae: crystal structure and evaluation of plasmin(ogen)-binding sites". Journal of Molecular Biology. 343 (4): 997–1005. doi:10.1016/j.jmb.2004.08.088. PMID 15476816.
- Raghunathan K, Harris PT, Spurbeck RR, Arvidson CG, Arvidson DN (June 2014). "Crystal structure of an efficacious gonococcal adherence inhibitor: an enolase from Lactobacillus gasseri". FEBS Letters. 588 (14): 2212–6. doi:10.1016/j.febslet.2014.05.020. PMID 24859038.
- Dinovo EC, Boyer PD (1971). "Isotopic probes of the enolase reaction mechanism". J Biol Chem. 240: 4586–93.
- Poyner RR, Laughlin LT, Sowa GA, Reed GH (February 1996). "Toward identification of acid/base catalysts in the active site of enolase: comparison of the properties of K345A, E168Q, and E211Q variants". Biochemistry. 35 (5): 1692–9. doi:10.1021/bi952186y. PMID 8634301.
- Reed GH, Poyner RR, Larsen TM, Wedekind JE, Rayment I (December 1996). "Structural and mechanistic studies of enolase". Current Opinion in Structural Biology. 6 (6): 736–43. doi:10.1016/S0959-440X(96)80002-9. PMID 8994873.
- Wedekind JE, Reed GH, Rayment I (April 1995). "Octahedral coordination at the high-affinity metal site in enolase: crystallographic analysis of the MgII--enzyme complex from yeast at 1.9 A resolution". Biochemistry. 34 (13): 4325–30. doi:10.1021/bi00013a022. PMID 7703246.
- Wedekind JE, Poyner RR, Reed GH, Rayment I (August 1994). "Chelation of serine 39 to Mg2+ latches a gate at the active site of enolase: structure of the bis(Mg2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-A resolution". Biochemistry. 33 (31): 9333–42. doi:10.1021/bi00197a038. PMID 8049235.
- Larsen TM, Wedekind JE, Rayment I, Reed GH (April 1996). "A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution". Biochemistry. 35 (14): 4349–58. doi:10.1021/bi952859c. PMID 8605183.
- Duquerroy S, Camus C, Janin J (October 1995). "X-ray structure and catalytic mechanism of lobster enolase". Biochemistry. 34 (39): 12513–23. doi:10.1021/bi00039a005. PMID 7547999.
- Royds JA, Timperley WR, Taylor CB (December 1981). "Levels of enolase and other enzymes in the cerebrospinal fluid as indices of pathological change". Journal of Neurology, Neurosurgery, and Psychiatry. 44 (12): 1129–35. doi:10.1136/jnnp.44.12.1129. PMC . PMID 7334408.
- Roine RO, Somer H, Kaste M, Viinikka L, Karonen SL (July 1989). "Neurological outcome after out-of-hospital cardiac arrest. Prediction by cerebrospinal fluid enzyme analysis". Archives of Neurology. 46 (7): 753–6. doi:10.1001/archneur.1989.00520430047015. PMID 2742544.
- Hay E, Royds JA, Davies-Jones GA, Lewtas NA, Timperley WR, Taylor CB (July 1984). "Cerebrospinal fluid enolase in stroke". Journal of Neurology, Neurosurgery, and Psychiatry. 47 (7): 724–9. doi:10.1136/jnnp.47.7.724. PMC . PMID 6747647.
- Fujii A, Yoneda M, Ito T, Yamamura O, Satomi S, Higa H, Kimura A, Suzuki M, Yamashita M, Yuasa T, Suzuki H, Kuriyama M (May 2005). "Autoantibodies against the amino terminal of alpha-enolase are a useful diagnostic marker of Hashimoto's encephalopathy". Journal of Neuroimmunology. 162 (1-2): 130–6. doi:10.1016/j.jneuroim.2005.02.004. PMID 15833368.
- Anderson VE, Weiss PM, Cleland WW (June 1984). "Reaction intermediate analogues for enolase". Biochemistry. 23 (12): 2779–86. PMID 6380574.
- Jung DW, Kim WH, Park SH, Lee J, Kim J, Su D, Ha HH, Chang YT, Williams DR. (April 2, 2013). "A unique small molecule inhibitor of enolase clarifies its role in fundamental biological processes.". ACS Chemical Biology. 8 (6): 1271–1282. doi:10.1021/cb300687k. PMID 23547795.
- Poyner RR, Reed GH (August 1992). "Structure of the bis divalent cation complex with phosphonoacetohydroxamate at the active site of enolase". Biochemistry. 31 (31): 7166–73. PMID 1322695.
- Zhang E, Hatada M, Brewer JM, Lebioda L (May 1994). "Catalytic metal ion binding in enolase: the crystal structure of an enolase-Mn2+-phosphonoacetohydroxamate complex at 2.4-A resolution". Biochemistry. 33 (20): 6295–300. PMID 8193144.
- Muller FL, Colla S, Aquilanti E, Manzo VE, Genovese G, Lee J, Eisenson D, Narurkar R, Deng P, Nezi L, Lee MA, Hu B, Hu J, Sahin E, Ong D, Fletcher-Sananikone E, Ho D, Kwong L, Brennan C, Wang YA, Chin L, DePinho RA (August 2012). "Passenger deletions generate therapeutic vulnerabilities in cancer". Nature. 488 (7411): 337–42. doi:10.1038/nature11331. PMID 22895339.
- Watanabe H, Yoshida J, Tanaka E, Ito M, Miyadoh S, Shomura T. (1986). "Studies on a new phosphonic acid antibiotic, SF-2312.". Sci Rep Meiji Seika Kaisha. 25: 12–17.
- Leonard PG, Satani N, Maxwell D, Lin YH, Hammoudi N, Peng Z, Pisaneschi F, Link TM, Lee GR, Sun D, Prasad BA, Di Francesco ME, Czako B, Asara JM, Wang YA, Bornmann W, DePinho RA, Muller FL (December 2016). "SF2312 is a natural phosphonate inhibitor of enolase". Nature Chemical Biology. 12 (12): 1053–1058. doi:10.1038/nchembio.2195. PMID 27723749.
- Satani N, Lin YH, Hammoudi N, Raghavan S, Georgiou DK, Muller FL. (December 28, 2016). "ENOblock Does Not Inhibit the Activity of the Glycolytic Enzyme Enolase.". PLoS One. 11 (12). doi:10.1371/journal.pone.0168739. PMID 28030597.
- "Populations receiving optimally fluoridated public drinking water--United States, 2000". MMWR. Morbidity and Mortality Weekly Report. 51 (7): 144–7. February 2002. PMID 11905481.
- Hüther FJ, Psarros N, Duschner H (April 1990). "Isolation, characterization, and inhibition kinetics of enolase from Streptococcus rattus FA-1". Infection and Immunity. 58 (4): 1043–7. PMC . PMID 2318530.
- Holt A, Wold F (December 1961). "The isolation and characterization of rabbit muscle enolase". The Journal of Biological Chemistry. 236: 3227–31. PMID 13908561.
- Boyer, P.D., Lardy, H. and Myrback, K. (Eds.), The Enzymes, 2nd ed., vol. 5, Academic Press, New York, 1961, p. 471-494.
- Westhead EW, Mclain G (August 1964). "A purification of brewers' and bakers' yeast enolase yielding a single active component". The Journal of Biological Chemistry. 239: 2464–8. PMID 14235523.
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.
Enolase, C-terminal TIM barrel domain Provide feedback
No Pfam abstract.
Internal database links
|SCOOP:||MAAL_C GhoS MR_MLE_C|
|Similarity to PfamA using HHSearch:||MR_MLE_C|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR020810
Enolase (2-phospho-D-glycerate hydrolase) is an essential glycolytic enzyme that catalyses the interconversion of 2-phosphoglycerate and phosphoenolpyruvate [PUBMED:1859865, PUBMED:1840492]. In vertebrates, there are 3 different, tissue-specific isoenzymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue. The functional enzyme exists as a dimer of any 2 isoforms. In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer [PUBMED:3390159]. The tissue specific forms display minor kinetic differences. Tau-crystallin, one of the major lens proteins in some fish, reptiles and birds, has been shown [PUBMED:3589669] to be evolutionary related to enolase.
Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke. Several tumour cells have also been found positive for neuron-specific enolase. Beta-enolase deficiency is associated with glycogenosis type XIII defect.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||phosphopyruvate hydratase complex (GO:0000015)|
|Molecular function||magnesium ion binding (GO:0000287)|
|phosphopyruvate hydratase activity (GO:0004634)|
|Biological process||glycolytic process (GO:0006096)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Number in seed:||9|
|Number in full:||4380|
|Average length of the domain:||273.00 aa|
|Average identity of full alignment:||48 %|
|Average coverage of the sequence by the domain:||65.58 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||20|
|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.
There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Enolase_C domain has been found. There are 152 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...