Summary: Phospholipase A2
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 "Phospholipase A2". 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.
Phospholipase A2 Edit Wikipedia article
Phospholipase Cleavage Sites. Note that an enzyme that displays both PLA1 and PLA2 activities is called a Phospholipase B
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
Bee venom phospholipase A2 sPLA2. Middle plane of the lipid bilayer - black dots. Boundary of the hydrocarbon core region - red dots (extracellular side). Layer of lipid phosphates - yellow dots.
Phospholipases A2 (PLA2s) EC 126.96.36.199 are enzymes that release fatty acids from the second carbon group of glycerol. This particular phospholipase specifically recognizes the sn-2 acyl bond of phospholipids and catalytically hydrolyzes the bond releasing arachidonic acid and lysophosphatidic acid. Upon downstream modification by cyclooxygenases, arachidonic acid is modified into active compounds called eicosanoids. Eicosanoids include prostaglandins and leukotrienes, which are categorized as anti-inflammatory and inflammatory mediators.
PLA2 enzymes are commonly found in mammalian tissues as well as arachnid, insect and snake venom. Venom from both snakes and insects is largely composed of melittin, which is a stimulant of PLA2. Due to the increased presence and activity of PLA2 resulting from a snake or insect bite, arachidonic acid is released from the phospholipid membrane disproportionately. As a result, inflammation and pain occur at the site. There are also prokaryotic A2 phospholipases.
Phospholipases A2 include several unrelated protein families with common enzymatic activity. Two most notable families are secreted and cytosolic phospholipases A2. Other families include Ca2+ independent PLA2 (iPLA2) and lipoprotein-associated PLA2s (lp-PLA2), also known as platelet activating factor acetylhydrolase (PAF-AH).
Secreted phospholipases A2 (sPLA2)
The extracellular forms of phospholipases A2 have been isolated from different venoms (snake, bee, and wasp), from virtually every studied mammalian tissue (including pancreas and kidney) as well as from bacteria. They require Ca2+ for activity.
sPLA2 has been shown to promote inflammation in mammals by catalyzing the first step of the arachidonic acid pathway by breaking down phospholipids, resulting in the formation of fatty acids including arachidonic acid. This arachidonic acid is then metabolized to form several inflammatory and thrombogenic molecules. Excess levels of sPLA2 is thought to contribute to several inflammatory diseases, and has been shown to promote vascular inflammation correlating with coronary events in coronary artery disease and acute coronary syndrome, and possibly leading to acute respiratory distress syndrome and progression of tonsillitis.
Increased sPLA2 activity is observed in the cerebrospinal fluid of humans with Alzheimer's disease and multiple sclerosis, and may serve as a marker of increases in permeability of the blood-cerebrospinal fluid barrier.
There are atypical members of the phospholipase A2 family, such as PLA2G12B, that have no phospholipase activity with typical phospholipase substrate. The lack of enzymatic activity of PLA2G12B indicates that it may have unique function distinctive from other sPLA2s. It has been shown that in PLA2G12B null mice VLDL levels were greatly reduced, suggesting it could have an effect in lipoprotein secretion
Cytosolic phospholipases A2 (cPLA2)
The intracellular, group IV PLA2 are also Ca-dependent, but they have a different 3D structure and are significantly larger than secreted PLA2 (more than 700 residues). They include a C2 domain and a large catalytic domain.
These phospholipases are involved in cell signaling processes, such as inflammatory response. They release arachidonic acid from membrane phospholipids. Arachidonic acid is both a signaling molecule and the precursor for the synthesis of other signaling molecules termed eicosanoids. These include leukotrienes and prostaglandins. Some eicosanoids are synthesized from diacylglycerol, released from the lipid bilayer by phospholipase C (see below).
Phospholipases A2 can be classified based on sequence homology.
Lipoprotein-associated PLA2s (lp-PLA2)
The suggested catalytic mechanism of pancreatic sPLA2 is initiated by a His-48/Asp-99/calcium complex within the active site. The calcium ion polarizes the sn-2 carbonyl oxygen while also coordinating with a catalytic water molecule, w5. His-48 improves the nucleophilicity of the catalytic water via a bridging second water molecule, w6. It has been suggested that two water molecules are necessary to traverse the distance between the catalytic histidine and the ester. The basicity of His-48 is thought to be enhanced through hydrogen bonding with Asp-99. An asparagine substitution for His-48 maintains wild-type activity, as the amide functional group on asparagine can also function to lower the pKa, or acid dissociation constant, of the bridging water molecule. The rate limiting state is characterized as the degradation of the tetrahedral intermediate composed of a calcium coordinated oxyanion. The role of calcium can also be duplicated by other relatively small cations like cobalt and nickel. Before becoming active in digestion, the proform of PLA2 is activated by Trypsin.
PLA2 can also be characterized as having a channel featuring a hydrophobic wall in which hydrophobic amino acid residues such as Phe, Leu, and Tyr serve to bind the substrate. Another component of PLA2 is the seven disulfide bridges that are influential in regulation and stable protein folding.
Due to the importance of PLA2 in inflammatory responses, regulation of the enzyme is essential. PLA2 is regulated by phosphorylation and calcium concentrations. PLA2 is phosphorylated by a MAPK at Serine-505. When phosphorylation is coupled with an influx of calcium ions, PLA2 becomes stimulated and can translocate to the membrane to begin catalysis.
Phosphorylation of PLA2 may be a result of ligand binding to receptors, including:
In the case of an inflammation, the application of glucocorticoids up-regulate (mediated at the gene level) the production of the protein lipocortin which will inhibit PLA2 and reduce the inflammatory response.
Relevance in neurological disorders
In normal brain cells, PLA2 regulation accounts for a balance between arachidonic acid's conversion into proinflammatory mediators and its reincorporation into the membrane. In the absence of strict regulation of PLA2 activity, a disproportionate amount of proinflammatory mediators are produced. The resulting induced oxidative stress and neuroinflammation is analogous to neurological diseases such as Alzheimer's disease, epilepsy, multiple sclerosis, ischemia. Lysophospholipids are another class of molecules released from the membrane that are upstream predecessors of platelet activating factors (PAF). Abnormal levels of potent PAF are also associated with neurological damage. An optimal enzyme inhibitor would specifically target PLA2 activity on neural cell membranes already under oxidative stress and potent inflammation. Thus, specific inhibitors of brain PLA2 could be a pharmaceutical approach to treatment of several disorders associated with neural trauma.
Increase in phospholipase A2 activity is an acute-phase reaction that rises during inflammation, which is also seen to be exponentially higher in low back disc herniations compared to rheumatoid arthritis. It is a mixture of inflammation and substance P that are responsible for pain.
Increased phospholipase A2 has also been associated with neuropsychiatric disorders such as schizophrenia and pervasive developmental disorders (such as autism), though the mechanisms involved are not known.
Human phospholipase A2 isozymes include:
- Group I: PLA2G1B
- Group II: PLA2G2A, PLA2G2C, PLA2G2D, PLA2G2E, PLA2G2F
- Group III: PLA2G3
- Group IV: PLA2G4A, PLA2G4B, PLA2G4C, PLA2G4D, PLA2G4E, PLA2G4F
- Group V: PLA2G5
- Group VI: PLA2G6
- Group VII: PLA2G7
- Group X: PLA2G10
- Group XII: PLA2G12A, PLA2G12B
In addition, the following human proteins contain the phospholipase A2 domain:
- Dennis EA (May 1994). "Diversity of group types, regulation, and function of phospholipase A2". The Journal of Biological Chemistry. 269 (18): 13057–60. PMID 8175726.
- Nicolas JP, Lin Y, Lambeau G, Ghomashchi F, Lazdunski M, Gelb MH (Mar 1997). "Localization of structural elements of bee venom phospholipase A2 involved in N-type receptor binding and neurotoxicity". The Journal of Biological Chemistry. 272 (11): 7173–81. doi:10.1074/jbc.272.11.7173. PMID 9054413.
- Argiolas A, Pisano JJ (Nov 1983). "Facilitation of phospholipase A2 activity by mastoparans, a new class of mast cell degranulating peptides from wasp venom". The Journal of Biological Chemistry. 258 (22): 13697–702. PMID 6643447.
- Cox, Michael; Nelson, David R.; Lehninger, Albert L (2005). Lehninger principles of biochemistry (4th ed.). San Francisco: W.H. Freeman. ISBN 0-7167-4339-6.
- Sato H, Taketomi Y, Isogai Y, Miki Y, Yamamoto K, Masuda S, Hosono T, Arata S, Ishikawa Y, Ishii T, Kobayashi T, Nakanishi H, Ikeda K, Taguchi R, Hara S, Kudo I, Murakami M (May 2010). "Group III secreted phospholipase A2 regulates epididymal sperm maturation and fertility in mice". The Journal of Clinical Investigation. 120 (5): 1400–14. doi:10.1172/JCI40493. PMC . PMID 20424323.
- Escoffier J, Jemel I, Tanemoto A, Taketomi Y, Payre C, Coatrieux C, Sato H, Yamamoto K, Masuda S, Pernet-Gallay K, Pierre V, Hara S, Murakami M, De Waard M, Lambeau G, Arnoult C (May 2010). "Group X phospholipase A2 is released during sperm acrosome reaction and controls fertility outcome in mice". The Journal of Clinical Investigation. 120 (5): 1415–28. doi:10.1172/JCI40494. PMC . PMID 20424324.
- Mallat Z, Lambeau G, Tedgui A (Nov 2010). "Lipoprotein-associated and secreted phospholipases A₂ in cardiovascular disease: roles as biological effectors and biomarkers". Circulation. 122 (21): 2183–200. doi:10.1161/CIRCULATIONAHA.110.936393. PMID 21098459.
- De Luca D, Minucci A, Cogo P, Capoluongo ED, Conti G, Pietrini D, Carnielli VP, Piastra M (Jan 2011). "Secretory phospholipase A₂ pathway during pediatric acute respiratory distress syndrome: a preliminary study". Pediatric Critical Care Medicine. 12 (1): e20–4. doi:10.1097/PCC.0b013e3181dbe95e. PMID 20351613.
- Ezzeddini R, Darabi M, Ghasemi B, Jabbari Moghaddam Y, Jabbari Y, Abdollahi S, Rashtchizadeh N, Gharahdaghi A, Darabi M, Ansarin M, Shaaker M, Samadi A, Karamravan J (Apr 2012). "Circulating phospholipase-A2 activity in obstructive sleep apnea and recurrent tonsillitis". International Journal of Pediatric Otorhinolaryngology. 76 (4): 471–4. doi:10.1016/j.ijporl.2011.12.026. PMID 22297210.
- Henderson WR, Oslund RC, Bollinger JG, Ye X, Tien YT, Xue J, Gelb MH (Aug 2011). "Blockade of human group X secreted phospholipase A2 (GX-sPLA2)-induced airway inflammation and hyperresponsiveness in a mouse asthma model by a selective GX-sPLA2 inhibitor". The Journal of Biological Chemistry. 286 (32): 28049–55. doi:10.1074/jbc.M111.235812. PMC . PMID 21652694.
- Wei Y, Epstein SP, Fukuoka S, Birmingham NP, Li XM, Asbell PA (Jun 2011). "sPLA2-IIa amplifies ocular surface inflammation in the experimental dry eye (DE) BALB/c mouse model". Investigative Ophthalmology & Visual Science. 52 (7): 4780–8. doi:10.1167/iovs.10-6350. PMC . PMID 21519031.
- Chalbot S; Zetterberg H; Blennow K; Fladby T; Andreasen N; Grundke-Iqbal I; Iqbal K (January 2011). "Blood-cerebrospinal fluid barrier permeability in Alzheimer's disease". Journal of Alzheimer's Disease. 25 (3): 505–15. doi:10.3233/JAD-2011-101959. PMC . PMID 21471645.
- Aleksandra Aljakna; Seungbum Choi; Holly Savage; Rachael Hageman Blair; Tongjun Gu; Karen L. Svenson; Gary A. Churchill; Matt Hibbs; Ron Korstanje (August 2012). "Pla2g12b and Hpn Are Genes Identified by Mouse ENU Mutagenesis That Affect HDL Cholesterol". PLOS ONE. 7 (8): e43139. doi:10.1371/journal.pone.0043139. PMC . PMID 22912808.
- Guan M, Qu L, Tan W, Chen L, Wong CW (Feb 2011). "Hepatocyte Nuclear Factor-4 Alpha Regulates Liver Triglyceride Metabolism in Part Through Secreted Phospholipase A2 GXIIB". Hepatology. 53 (2): 458–466. doi:10.1002/hep.24066. PMID 21274867.
- Li X, Jiang H, Qu L, Yao W, Cai H, Chen L, Peng T (Jan 2014). "Hepatocyte nuclear factor 4α and downstream secreted phospholipase A2 GXIIB regulate production of infectious hepatitis C virus". J Virol. 88 (1): 612–627. doi:10.1128/JVI.02068-13. PMC . PMID 24173221.
- Six DA, Dennis EA (Oct 2000). "The expanding superfamily of phospholipase A(2) enzymes: classification and characterization". Biochimica et Biophysica Acta. 1488 (1-2): 1–19. doi:10.1016/S1388-1981(00)00105-0. PMID 11080672.
- Wilensky RL, Shi Y, Mohler ER, Hamamdzic D, Burgert ME, Li J, Postle A, Fenning RS, Bollinger JG, Hoffman BE, Pelchovitz DJ, Yang J, Mirabile RC, Webb CL, Zhang L, Zhang P, Gelb MH, Walker MC, Zalewski A, Macphee CH (Oct 2008). "Inhibition of lipoprotein-associated phospholipase A2 reduces complex coronary atherosclerotic plaque development". Nature Medicine. 14 (10): 1059–66. doi:10.1038/nm.1870. PMC . PMID 18806801.
- Berg OG, Gelb MH, Tsai MD, Jain MK (Sep 2001). "Interfacial enzymology: the secreted phospholipase A(2)-paradigm". Chemical Reviews. 101 (9): 2613–54. doi:10.1021/cr990139w. PMID 11749391.
See page 2640
- doi:10.1021/bi002514g. PMID 11170377.; Pan YH, Epstein TM, Jain MK, Bahnson BJ (January 2001). "Five coplanar anion binding sites on one face of phospholipase A2: relationship to interface binding". Biochemistry. 40 (3): 609–17.
- Choi SH1, Sakamoto T, Fukutomi O, Inagaki N, Matsuura N, Nagai H, Koda A. "Pharmacological study of phospholipase A2-induced histamine release from rat peritoneal mast cells". J Pharmacobiodyn. 1989 Sep;12(9):517-22.
- Morita Y, Aida N, Miyamoto T. "Role of phospholipase A2 activation in histamine release from human basophils". Allergy. 1983 Aug;38(6):413-8.
- Leslie CC (Jul 1997). "Properties and regulation of cytosolic phospholipase A2". The Journal of Biological Chemistry. 272 (27): 16709–12. doi:10.1074/jbc.272.27.16709. PMID 9201969.
- Walter F. Boron (2003). Medical Physiology: A Cellular And Molecular Approaoch. Elsevier/Saunders. p. 103. ISBN 1-4160-2328-3.
- Farooqui AA, Ong WY, Horrocks LA (Sep 2006). "Inhibitors of brain phospholipase A2 activity: their neuropharmacological effects and therapeutic importance for the treatment of neurologic disorders". Pharmacological Reviews. 58 (3): 591–620. doi:10.1124/pr.58.3.7. PMID 16968951.
- Bell JG, MacKinlay EE, Dick JR, MacDonald DJ, Boyle RM, Glen AC (Oct 2004). "Essential fatty acids and phospholipase A2 in autistic spectrum disorders". Prostaglandins, Leukotrienes, and Essential Fatty Acids. 71 (4): 201–4. doi:10.1016/j.plefa.2004.03.008. PMID 15301788.
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.
Phospholipase A2 Provide feedback
Phospholipase A2 releases fatty acids from the second carbon group of glycerol. Perhaps the best known members are secreted snake venoms, but also found in secreted pancreatic and membrane-associated forms. Structure is all-alpha, with two core disulfide-linked helices and a calcium-binding loop. This alignment represents the major family of PLA2s. A second minor family, defined by the honeybee venom PLA2 PDB:1POC and related sequences from Gila monsters (Heloderma), is not recognised. This minor family conserves the core helix pair but is substantially different elsewhere. The PROSITE pattern PA2_HIS, specific to the first core helix, recognises both families.
Internal database links
|Similarity to PfamA using HHSearch:||Phospholip_A2_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR016090
This entry represents eukaryotic and prokaryotic phospholipase A2 enzymes (PLA2; EC), small lipolytic enzymes that releases fatty acids from the second carbon group of glycerol, usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA) [PUBMED:11872155]. The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks [PUBMED:10331081]. These enzymes enable the of fatty acids and lysophospholipid by hydrolysing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. In eukaryotes, PLA2 plays a pivotal role in the biosynthesis of prostaglandin and other mediators of inflammation. These enzymes are either secreted or cytosolic; the latter are either Ca dependent or Ca independent. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors [PUBMED:11293116]. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids [PUBMED:11212293]. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters [PUBMED:16805767,PUBMED:10838563,PUBMED:16339444].
The phospholipase domain adopts an alpha-helical secondary structure, consisting of five alpha-helices and two helical segments. PLA2 may form dimers or oligomers [PUBMED:11080675,PUBMED:11897785,PUBMED:12161451].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||phospholipase A2 activity (GO:0004623)|
|Biological process||arachidonic acid secretion (GO:0050482)|
|phospholipid metabolic process (GO:0006644)|
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:||Overington and HMM_iterative_training|
|Number in seed:||145|
|Number in full:||1241|
|Average length of the domain:||103.90 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||57.54 %|
|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:||18|
|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 Phospholip_A2_1 domain has been found. There are 464 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 sequence.
Loading structure mapping...