Summary: Luciferase/LBP N-terminal 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 "Luciferase". 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 email@example.com 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.
Luciferase Edit Wikipedia article
Structure of Photinus pyralis firefly luciferase.
|PDB||1LCI More structures|
|Bacterial Luciferase monooxygenase family|
|Dinoflagellate Luciferase catalytic domain|
crystal structure of a luciferase domain from the dinoflagellate Lingulodinium polyedrum
|Dinoflagellate Luciferase/LBP N-terminal domain|
|Dinoflagellate Luciferase helical bundle domain|
crystal structure of a Dinoflagellate luciferase domain from the dinoflagellate Lingulodinium polyedrum
Luciferase is a generic term for the class of oxidative enzymes that produce bioluminescence, and is usually distinguished from a photoprotein. The name was first used by Raphaël Dubois who invented the words luciferin and luciferase, for the substrate and enzyme, respectively. Both words are derived from the Latin word lucifer - meaning lightbringer.
Luciferases are widely used in biotechnology, for microscopy and as reporter genes, for many of the same applications as fluorescent proteins. However, unlike fluorescent proteins, luciferases do not require an external light source, but do require addition of luciferin, the consumable substrate.
A variety of organisms regulate their light production using different luciferases in a variety of light-emitting reactions. The majority of studied luciferases have been found in animals, including fireflies, and many marine animals such as copepods, jellyfish, and the sea pansy. However, luciferases have been studied in luminous fungi, like the Jack-O-Lantern mushroom, as well as examples in other kingdoms including luminous bacteria, and dinoflagellates.
Firefly and click beetle
The luciferases of fireflies - of which there are over 2000 species - and of the other Elateroidea (click beetles and relatives in general) are diverse enough to be useful in molecular phylogeny. In fireflies, the oxygen required is supplied through a tube in the abdomen called the abdominal trachea. One well-studied luciferase is that of the Photinini firefly Photinus pyralis, which has an optimum pH of 7.8.
Newer luciferases have recently been identified that, unlike other luciferases above, are naturally secreted molecules. One such example is the Metridia luciferase (MetLuc) that is derived from the marine copepod Metridia longa. The Metridia longa secreted luciferase gene encodes a 24 kDa protein containing an N-terminal secretory signal peptide of 17 amino acid residues. The sensitivity and high signal intensity of this luciferase molecule proves advantageous in many reporter studies. Some of the benefits of using a secreted reporter molecule like MetLuc is its no-lysis protocol that allows one to be able to conduct live cell assays and multiple assays on the same cell.
Also well studied is the fancy sea pansy, Renilla reniformis. In this organism, the luciferase (Renilla-luciferin 2-monooxygenase) is closely associated with a luciferin-binding protein as well as a green fluorescent protein (GFP). Calcium triggers release of the luciferin (coelenterazine) from the luciferin binding protein. The substrate is then available for oxidation by the luciferase, where it is degraded to coelenteramide with a resultant release of energy. In the absence of GFP, this energy would be released as a photon of blue light (peak emission wavelength 482 nm). However, due to the closely associated GFP, the energy released by the luciferase is instead coupled through resonance energy transfer to the fluorophore of the GFP, and is subsequently released as a photon of green light (peak emission wavelength 510 nm). The catalyzed reaction is:
Bacterial bioluminescence is seen in Photobacterium species, Vibrio fischeri, Vibrio haweyi, and Vibrio harveyi. Light emission in some bioluminescent bacteria utilizes 'antenna' such as 'lumazine protein' to accept the energy from the primary excited state on the luciferase, resulting in an excited lulnazine chromophore which emits light that is of a shorter wavelength (more blue), while in others use a yellow fluorescent protein (YFP) with FMN as the chromophore and emits light that is red-shifted relative to that from luciferase.
Dinoflagellate luciferase is a multi-domain protein, consisting of an N-terminal domain, and three catalytic domains, each of which preceded by a helical bundle domain. The structure of the dinoflagellate luciferase catalytic domain has been solved. The core part of the domain is a 10 stranded beta barrel that is structurally similar to lipocalins and FABP. The N-terminal domain is conserved between dinoflagellate luciferase and luciferin binding proteins (LBPs). It has been suggested that this region may mediate an interaction between LBP and luciferase or their association with the vacuolar membrane. The helical bundle domain has a three helix bundle structure that holds four important histidines that are thought to play a role in the pH regulation of the enzyme. There is a large pocket in the β-barrel of the dinoflagellate luciferase at pH 8 to accommodate the tetrapyrrole substrate but there is no opening to allow the substrate to enter. Therefore, a significant conformational change must occur to provide access and space for a ligand in the active site and the source for this change is through the four N-terminal histidine residues. At pH 8, it can be seen that the unprotonated histidine residues are involved in a network of hydrogen bonds at the interface of the helices in the bundle that block substrate access to the active site and disruption of this interaction by protonation (at pH 6.3) or by replacement of the histidine residues by alanine causes a large molecular motion of the bundle, separating the helices by 11Å and opening the catalytic site. Logically, the histidine residues cannot be replaced by alanine in nature but this experimental replacement further confirms that the larger histidine residues block the active site. Additionally, three Gly-Gly sequences, one in the N-terminal helix and two in the helix-loop-helix motif, could serve as hinges about which the chains rotate in order to further open the pathway to the catalytic site and enlarge the active site.
A dinoflagellate luciferase is capable of emitting light due to its interaction with its substrate (luciferin) and the luciferin-binding protein (LBP) in the scintillon organelle found in dinoflagellates. The luciferase acts in accordance with luciferin and LBP in order to emit light but each component functions at a different pH. Luciferase and its domains are not active at pH 8 but they are extremely active at the optimum pH of 6.3 whereas LBP binds luciferin at pH 8 and releases it at pH 6.3. Consequently, luciferin is only released to react with an active luciferase when the scintillon is acidified to pH 6.3. Therefore, in order to lower the pH, voltage-gated channels in the scintillon membrane are opened to allow the entry of protons from a vacuole possessing an action potential produced from a mechanical stimulation. Hence, it can be seen that the action potential in the vacuolar membrane leads to acidification and this in turn allows the luciferin to be released to react with luciferase in the scintillon, producing a flash of blue light.
Mechanism of reaction
All luciferases are classified as oxidoreductases (EC 1.13.12.-), meaning they act on single donors with incorporation of molecular oxygen. Because luciferases are from many diverse protein families that are unrelated, there is no unifying mechanism, as any mechanism depends on the luciferase and luciferin combination. However, all characterised luciferase-luciferin reactions to date have been shown to require molecular oxygen at some stage.
The reaction catalyzed by bacterial luciferase is also an oxidative process:
- FMNH2 + O2 + RCHO → FMN + RCOOH + H2O + light
In the reaction, a reduced flavin mononucleotide oxidizes a long-chain aliphatic aldehyde to an aliphatic carboxylic acid. The reaction forms an excited hydroxyflavin intermediate, which is dehydrated to the product FMN to emit blue-green light.
Nearly all of the energy input into the reaction is transformed into light. The reaction is 80% to 90% efficient. As a comparison, the incandescent light bulb only converts about 10% of its energy into light. and a 150 lumen per Watt (lm/W) LED converts 20% of input energy to visible light.
Luciferases can be produced in the lab through genetic engineering for a number of purposes. Luciferase genes can be synthesized and inserted into organisms or transfected into cells. Mice, silkworms, and potatoes are just a few of the organisms that have already been engineered to produce the protein.
In the luciferase reaction, light is emitted when luciferase acts on the appropriate luciferin substrate. Photon emission can be detected by light sensitive apparatus such as a luminometer or modified optical microscopes. This allows observation of biological processes. Since light excitation is not needed for luciferase bioluminescence, there is minimal autofluorescence and therefore virtually background-free fluorescence. Therefore, as little as 0.02pg can still be accurately measured using a standard scintillation counter.
In biological research, luciferase is commonly used as a reporter to assess the transcriptional activity in cells that are transfected with a genetic construct containing the luciferase gene under the control of a promoter of interest. Additionally proluminescent molecules that are converted to luciferin upon activity of a particular enzyme can be used to detect enzyme activity in coupled or two-step luciferase assays. Such substrates have been used to detect caspase activity and cytochrome P450 activity, among others.
Luciferase can also be used to detect the level of cellular ATP in cell viability assays or for kinase activity assays. Luciferase can act as an ATP sensor protein through biotinylation. Biotinylation will immobilize luciferase on the cell-surface by binding to a streptavidin-biotin complex. This allows luciferase to detect the efflux of ATP from the cell and will effectively display the real-time release of ATP through bioluminescence. Luciferase can additionally be made more sensitive for ATP detection by increasing the luminescence intensity by changing certain amino acid residues in the sequence of the protein.
Whole animal imaging (referred to as in vivo or, occasionally, ex vivo imaging) is a powerful technique for studying cell populations in live animals, such as mice. Different types of cells (e.g. bone marrow stem cells, T-cells) can be engineered to express a luciferase allowing their non-invasive visualization inside a live animal using a sensitive charge-couple device camera (CCD camera).This technique has been used to follow tumorigenesis and response of tumors to treatment in animal models. However, environmental factors and therapeutic interferences may cause some discrepancies between tumor burden and bioluminescence intensity in relation to changes in proliferative activity. The intensity of the signal measured by in vivo imaging may depend on various factors, such as D-luciferin absorption through the peritoneum, blood flow, cell membrane permeability, availability of co-factors, intracellular pH and transparency of overlying tissue, in addition to the amount of luciferase.
Luciferase is a heat-sensitive protein that is used in studies on protein denaturation, testing the protective capacities of heat shock proteins. The opportunities for using luciferase continue to expand.
- Gould SJ, Subramani S (Nov 1988). "Firefly luciferase as a tool in molecular and cell biology". Analytical Biochemistry. 175 (1): 5–13. PMID 3072883. doi:10.1016/0003-2697(88)90353-3.
- Steghens JP, Min KL, Bernengo JC (Nov 1998). "Firefly luciferase has two nucleotide binding sites: effect of nucleoside monophosphate and CoA on the light-emission spectra". The Biochemical Journal. 336 ( Pt 1) (1): 109–13. PMC . PMID 9806891.
- Huh S, Lee J, Jung E, Kim SC, Kang JI, Lee J, Kim YW, Sung YK, Kang HK, Park D (Jun 2009). "A cell-based system for screening hair growth-promoting agents". Archives of Dermatological Research. 301 (5): 381–85. PMID 19277688. doi:10.1007/s00403-009-0931-0.
- Shimomura O (1985). "Bioluminescence in the sea: photoprotein systems". Symposia of the Society for Experimental Biology. 39: 351–72. PMID 2871634.
- Baldwin TO, Christopher JA, Raushel FM, Sinclair JF, Ziegler MM, Fisher AJ, Rayment I (Dec 1995). "Structure of bacterial luciferase". Current Opinion in Structural Biology. 5 (6): 798–809. PMID 8749369. doi:10.1016/0959-440x(95)80014-x.
- Schultz LW, Liu L, Cegielski M, Hastings JW (Feb 2005). "Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole". Proceedings of the National Academy of Sciences of the United States of America. 102 (5): 1378–83. PMC . PMID 15665092. doi:10.1073/pnas.0409335102.
- Okamoto OK, Liu L, Robertson DL, Hastings JW (Dec 2001). "Members of a dinoflagellate luciferase gene family differ in synonymous substitution rates". Biochemistry. 40 (51): 15862–68. PMID 11747464. doi:10.1021/bi011651q.
- Fisher AJ, Thompson TB, Thoden JB, Baldwin TO, Rayment I (Sep 1996). "The 1.5-A resolution crystal structure of bacterial luciferase in low salt conditions". The Journal of Biological Chemistry. 271 (36): 21956–68. PMID 8703001. doi:10.1074/jbc.271.36.21956.
- Elizabeth Wilson (Jan 18, 1999). "What's That Stuff?". Chemical and Engineering News. 77 (3): 65. doi:10.1021/cen-v077n003.p065.
- Vanessa Knivett (2009). "Lighting the way". EE times.
- General Electric TP-110, p. 23, table.
- Contag CH, Bachmann MH (2002). "Advances in in vivo bioluminescence imaging of gene expression". Annual Review of Biomedical Engineering. 4: 235–60. PMID 12117758. doi:10.1146/annurev.bioeng.4.111901.093336.
- "Introduction to Bioluminescence Assays". Promega Corporation. Retrieved 2009-03-07.
- Williams TM, Burlein JE, Ogden S, Kricka LJ, Kant JA (Jan 1989). "Advantages of firefly luciferase as a reporter gene: application to the interleukin-2 gene promoter". Analytical Biochemistry. 176 (1): 28–32. PMID 2785354. doi:10.1016/0003-2697(89)90267-4.
- Nguyen VT, Morange M, Bensaude O (Jun 1988). "Firefly luciferase luminescence assays using scintillation counters for quantitation in transfected mammalian cells". Analytical Biochemistry. 171 (2): 404–08. PMID 3407940. doi:10.1016/0003-2697(88)90505-2.
- Fan F, Wood KV (Feb 2007). "Bioluminescent assays for high-throughput screening". ASSAY and Drug Development Technologies. 5 (1): 127–36. PMID 17355205. doi:10.1089/adt.2006.053.
- Meisenheimer PL, O'Brien MA, Cali JJ (September 2008). "Luminogenic enzyme substrates: The basis for a new paradigm in assay design." (PDF). Promega Notes. 100: 22–26.
- Nakamura M, Mie M, Funabashi H, Yamamoto K, Ando J, Kobatake E (May 2006). "Cell-surface-localized ATP detection with immobilized firefly luciferase". Analytical Biochemistry. 352 (1): 61–67. PMID 16564487. doi:10.1016/j.ab.2006.02.019.
- Fujii H, Noda K, Asami Y, Kuroda A, Sakata M, Tokida A (Jul 2007). "Increase in bioluminescence intensity of firefly luciferase using genetic modification". Analytical Biochemistry. 366 (2): 131–36. PMID 17540326. doi:10.1016/j.ab.2007.04.018.
- Greer LF, Szalay AA (2002). "Imaging of light emission from the expression of luciferases in living cells and organisms: a review". Luminescence. 17 (1): 43–74. PMID 11816060. doi:10.1002/bio.676.
- Lyons SK, Meuwissen R, Krimpenfort P, Berns A (Nov 2003). "The generation of a conditional reporter that enables bioluminescence imaging of Cre/loxP-dependent tumorigenesis in mice". Cancer Research. 63 (21): 7042–46. PMID 14612492.
- Becher OJ, Holland EC (Apr 2006). "Genetically engineered models have advantages over xenografts for preclinical studies". Cancer Research. 66 (7): 3355–58, discussion 3358–59. PMID 16585152. doi:10.1158/0008-5472.CAN-05-3827.
- Inoue Y, Tojo A, Sekine R, Soda Y, Kobayashi S, Nomura A, Izawa K, Kitamura T, Okubo T, Ohtomo K (May 2006). "In vitro validation of bioluminescent monitoring of disease progression and therapeutic response in leukaemia model animals". European Journal of Nuclear Medicine and Molecular Imaging. 33 (5): 557–65. PMID 16501974. doi:10.1007/s00259-005-0048-4.
- Massoud TF, Paulmurugan R, De A, Ray P, Gambhir SS (Feb 2007). "Reporter gene imaging of protein-protein interactions in living subjects". Current Opinion in Biotechnology. 18 (1): 31–37. PMID 17254764. doi:10.1016/j.copbio.2007.01.007.
- Media related to Luciferase at Wikimedia Commons
- Trimmer B, Zayas R, Qazi S, Lewis S, Michel T, Dudzinski D, Aprille J, Lagace C (2001-06-28). "Firefly flashes and Nitric Oxide". Tufts University. Retrieved 2008-10-02.
- "Trends in development of reporter genes". reportergene.com. Retrieved 2009-03-07.
- "BL Web: Luciferin types". The Bioluminescence Web Page. University of California, Santa Barbara. Retrieved 2009-03-07.
- "Bioluminescence Reporters Protocols and Applications Guide". Protocols and applications. Promega Corporation. Retrieved 2009-03-07.
- "BL Web: Luciferin types". ISCID Encyclopedia of Science and Philosophy. ISCID. Retrieved 2010-04-20.
- David Goodsell. "Luciferase". Molecule of the Month. Protein Data Bank. Retrieved 2013-01-15.
This article incorporates text from the public domain Pfam and InterPro IPR018804 This article incorporates text from the public domain Pfam and InterPro IPR007959 This article incorporates text from the public domain Pfam and InterPro IPR018475
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.
Luciferase/LBP N-terminal domain Provide feedback
This family consists of a presumed N-terminal domain that is conserved between dinoflagellate luciferase and luciferin binding proteins. Luciferase is involved in catalysing the light emitting reaction in bioluminescence and luciferin binding protein (LBP) is known to bind to luciferin (the substrate for luciferase) to stop it reacting with the enzyme and therefore switching off the bioluminescence function. The expression of these two proteins is controlled by a circadian clock at the translational level, with synthesis and degradation occurring on a daily basis . However This domain is not the catalytic part of the protein. It has been suggested that this region may mediate an interaction between LBP and Luciferase or their association with the vacuolar membrane .
Okamoto OK, Liu L, Robertson DL, Hastings JW; , Biochemistry 2001;40:15862-15868.: Members of a dinoflagellate luciferase gene family differ in synonymous substitution rates. PUBMED:11747464 EPMC:11747464
This tab holds annotation information from the InterPro database.
InterPro entry IPR007959
Proteins in this entry belong to a family of dinoflagellate luciferase and luciferin binding proteins. Luciferase is involved in catalysing the light emitting reaction in bioluminescence and luciferin binding protein (LBP) is known to bind to luciferin (the substrate for luciferase) to stop it reacting with the enzyme and therefore switching off the bioluminescence function. The expression of these two proteins is controlled by a circadian clock at the translational level, with synthesis and degradation occurring on a daily basis [PUBMED:11747464].
This entry consists of a presumed N-terminal domain that is conserved between dinoflagellate luciferase and luciferin binding proteins. This domain is not, however, the catalytic part of the protein. It has been suggested that this region may mediate an interaction between LBP and Luciferase or their association with the vacuolar membrane [PUBMED:11747464].
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.
|Seed source:||Pfam-B_7906 (release 7.7)|
|Author:||Moxon SJ, Bateman A|
|Number in seed:||13|
|Number in full:||0|
|Average length of the domain:||0.00 aa|
|Average identity of full alignment:||0 %|
|Average coverage of the sequence by the domain:||0.00 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|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.