Summary: Leukocidin/Hemolysin toxin family
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 "Hemolysin". 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.
Hemolysin Edit Wikipedia article
||This article may lend undue weight to certain ideas, incidents, controversies or matters relative to the article subject as a whole. (January 2013)|
Hemolysins (UK spelling: haemolysins) are certain proteins and lipids that cause lysis of red blood cells by damaging their cell membrane. Although the lytic activity of some microbial hemolysins on red blood cells may be important for nutrient acquisition or for causing certain conditions such as anemia, many hemolysin-producing pathogens do not cause significant lysis of red blood cells during infection. Although hemolysins are able to lyse red blood cells in vitro, the ability of hemolysins to target other cells, including white blood cells, often accounts for the effects of hemolysins during infection.
- 1 Properties
- 2 Mechanism
- 3 Structure
- 4 Role during infection
- 5 Treatment
- 6 Applications
- 7 See also
- 8 References
- 9 External links
Many bacteria produce hemolysins that can be detected in the laboratory. It is now believed that many clinically relevant fungi also produce hemolysins. Hemolysins can be identified by their ability to lyse red blood cells in vitro.
Not only are the erythrocytes affected by hemolysins, but there are also some effects among other blood cells, such as leucocytes (white blood cells). Escherichia coli hemolysin is potentially cytotoxic to monocytes, lymphocytes and macrophages, leading them to autolysis and death.
Visualization of hemolysis (UK: haemolysis) of red blood cells in agar plates facilitates the categorization of Streptococcus.
In the next image we can see the process of hemolysis by a Streptococcus:
Due to the importance of hemolysins and the formation of pores, this part looks forward to enhance some more aspects of the process. Many hemolysins are pore-forming toxins (PFT), which are capable to cause the lysis of erythrocytes, leukocytes, and platelets by producing pores on the cytoplasmic membrane.
But, in which way does this kind of protein carry out this process?
Hemolysin is normally secreted by the bacteria in a water-resoluble way. These monomers diffuse to the target cells and are attached to them by specific receivers. After this is already done, they oligomerize, creating ring-shaped heptamer complexes.
Hemolysin can be segregated by many different kinds of bacteria such as Staphylococcus aureus, Escherichia coli or Vibrio parahemolyticus among other pathogens. We can take a look at the bacterium Staphylococcus aureus to study more precisely the formation of this pores. Staphylococcus aureus is a pathogen that causes many infectious diseases such as pneumonia and sepsis. This ring-shaped complex we’ll take a look at, is called staphylococcal alpha-hemolysin pore. In nature, what happens with these pathogens is that, in its fight for resources, bacterium Staphylococcus aureus secretes alpha-hemolysin monomers that bind to the outer membrane of susceptible cells. Upon binding, the monomers oligomerize to form a water-filled transmembrane channel that facilitates uncontrolled permeation of water, ions, and small organic molecules. Rapid discharge of vital molecules such as ATP, dissipation of the membrane potential and ionic gradients, and irreversible osmotic swelling leading to the cell wall rupture (lysis) can cause death of the host cell.
This pore consists of seven alpha-hemolysin subunits, which represent the major cytotoxic agent that is freed by this kind of bacterium. These subunits are attached to the target cells, the way we have already explained, and extend the lipid bilayer, forming the pore structures. These pores in the cellular membrane will eventually end up causing cell death, since it allows the exchange of monovalent ions that would cause the DNA fragmentation.
Some hemolysins damage the erythrocyte membrane by cleaving the phospholipids in the membrane.
Staphylococcus aureus hemolysins
Secreted by Staphylococcus aureus, this toxin causes cell death by binding with the outer membrane, with subsequent oligomerization of the toxin monomer and water-filled channels. These are responsible for osmotic phenomena, cell depolarization, and loss of vital molecules (v.gr. ATP), leading to its demise.
Upon investigating sheep erythrocytes, its toxic mechanism was discovered to be the hydrolysis of a specific membrane lipid, sphingomyelin, which accounts for 50% of the cell’s membrane. This degradation was followed by a noticeable rise of phosphoryl choline due to the release of organic phosphorus from sphingomyelin and ultimately caused cell lysis.
Unlike beta-hemolysin, it has a higher affinity for phosphocholines with short saturated acyl chains, especially if they have a conical form, whereas cylindrical lipids (e.g., sphingomyelin) hinder its activity. The lytic process, most commonly seen in leucocytes, is caused by pore formation induced by an oligomerized octamer that organizes in a ring structure. Once the prepore is formed, a more stable one ensues, named β-barrel. In this final part, the octamer binds with phosphatidylcholine.
The structure of several hemolysins has been solved by X-ray crystallography in the soluble and pore-forming conformations. For example, α-hemolysin of Staphylococcus aureus forms a homo-heptameric β-barrel in biological membranes. The Vibrio cholerae cytolysin also forms a heptameric pore, however Staphylococcus aureus γ-hemolysin forms a pore that is octomeric.
Thanks to latest research on the field of hemolysin's structure, we do know that the structure of the Staphylococcus aureus α-hemolysin pore has been determined to 1.9 Å resolution. Contained within the mushroom-shaped homo-oligomeric heptamer is a solvent-filled channel, 100 Å in length, that runs along the sevenfold axis and ranges from 14 Å to 46 Å in diameter. Furthermore, the structure proves the heptameric subunit stoichiometry of the α-hemolysin oligomer, shows that a glycine-rich and solvent-exposed region of a water-soluble protein can self-assemble to form a transmembrane pore of defined structure, and provides insight into the principles of membrane interaction and transport activity of β barrel pore-forming toxins.
The structure of the detergent-solubilized heptamer has been determined by X-ray crystallography to 1.9 Å resolution. The heptamer has a mushroom-like shape and measures up to 100 Å in diameter and 100 Å in height. Spanning the length of the molecule and coincident with the molecular sevenfold axis is a water-filled channel that ranges in diameter from 16 to 46 Å. A 14 strand antiparallel β barrel. On the exterior of the β barrel there is a hydrophobic belt approximately 30 Å in width that provides a surface complementary to the nonpolar portion of the lipid bilayer. The interfaces are composed of both salt-links and hydrogen bonds, as well as hydrophobic interactions, and these contacts provide a molecular stability for the heptamer in SDS solutions even up to 65°C.
Role during infection
Hemolysins are thought to be responsible for many events in host cells. For example, iron may be a limiting factor in the growth of various pathogenic bacteria. Since free iron may generate damaging free radicals, free iron is typically maintained at low concentrations within the body. Red blood cells are rich in iron-containing heme. Lysis of these cells releases heme into the surroundings, allowing the bacteria to take up the free iron. But hemolysin is related to bacteria not only in this way but also in some others.
As mentioned before, hemolysin is a potential virulence factor produced by microorganisms, which can put a human's health at risk. Despite causing some severe pathologies, lots of cases of hemolysis do not suppose a health hazard. But the fact that hemolysins (produced by pathogenic microorganisms during infections) are combined with other virulence factors may threaten a human's life to a greater extent.
The main consequence of hemolysis is hemolytic anemia, condition that involves the destruction of erythrocytes and their later removal from the bloodstream, earlier than expected in a normal situation. As the bone marrow cannot make erythrocytes fast enough to meet the body’s needs, oxygen does not arrive to body tissues properly. As a consequence, some symptoms may appear, such as fatigue, pain, arrhythmias, an enlarged heart or even heart failure, among others.
Depending on the type of hemolysin and the microorganism that produces it, manifestation of symptoms and diseases may differ from one case to the other:
- Alpha-hemolysin from uropathogenic E. coli produces extra-intestinal infections and can cause cystitis, pyelonephritis, and septicemia. Alpha-hemolysin from Staphylococcus aureus can cause severe diseases, such as pneumonia.
- Aerolysin from Aeromonas sobria infects the intestinal tract, but it might also cause septicemia and meningitis.
(Both hemolysins mentioned above are synthetized by extracellular bacteria, which infect specific tissue surfaces.)
- Listeriolysin from Listeria monocytogenes (a facultative intracellular bacterium that thrives within host cells, mainly macrophages and monocytes) causes the degradation of phagosome membranes, but they are not a potential danger for the cell’s plasmatic membrane.
Hemolysins have proved to be a damaging factor for vital organs, through the activity of Staphylococcus aureus. S.aureus is a dangerous pathogen that may lead cells to necrotizing infections usually recognized by a massive inflammatory response leading to tissue damage or even tissue destruction. There is a clear example of this: the pneumonia produced by S.aureus. In this case, it has been proven that alpha-hemolysin takes part in inducing necrotic pulmonary injury by the use of the NLRP3 inflammasome, which is responsible for inflammatory processes and of pyroptosis. Pneumonia caused by S.aureus is a common disease in some areas, which is the reason for the many studies in the field of immunology aimed at developing new farmacs to cure easily or prevent this kind of pneumonia. At the moment, apiegnin and beta-cyclodextrin are thought to alleviate S.aureus pneumonia, whereas the antibodies of anti alpha-hemlysin are thought to give protection.
Further findings show that the main virulence factor of S. aureus, the pore-forming toxin α-hemolysin (Hla), is the secreted factor responsible for the activation of an alternative autophagic pathway. It has been demonstrated that this autophagic response is inhibited by artificially elevating the intracellular levels of cAMP. This process is also mediated by the exchange factors RAPGEF3 and RAP2B.
Another interesting point is that pretreatment of leukocytes with doses of alpha-hemolysin at which nearly 80% of the cells survived decreased the ability of the cells to phagocytize bacteria and particles and to undergo chemotaxis. Premature activation of leukocytes and inhibition of phagocytosis and chemotaxis by alpha-hemolysin, if they occur in vivo, would greatly enhance the survival of an E. coli attack.
Regulation of gene expression
The regulation of gene expression of hemolysins (such as streptolysin S) is a system repressed in the presence of iron. This ensures that hemolysin is produced only when needed. The regulation of the production of hemolysin in S.aureus(expression of hemolysin) is now possible due to in-vitro mutations that are related to serine/threonine kinase and phosphatase.
As hemolysins are produced by pathogenic organisms, the main treatment is the intake of antibiotics specific to the pathogen that have caused the infection. Moreover, some hemolysins may be neutralized by the action of anti-hemolysin antibodies, preventing a longer and more dangerous effect of hemolysis within the body.
When blood cells are being destroyed too fast, extra folic acid and iron supplements may be given or, in case of emergencies, a blood transfusion. In rare cases, the spleen must be removed because it filters blood and removes from the bloodstream dead or damaged cells, worsening the lack of erythrocytes.
The hemolysin TDH, or Thermoestable Direct Hemolysin, is now being studied in the field of oncology. It is now said that Thermostable Direct Hemolysin (TDH), produced by Vibrio parahaemolyticus, regulates cell proliferation in colon carcinoma cells. TDH induces Ca2+ influx from an extracellular environment accompanied by protein kinase C phosphorylation. Activated protein kinase C inhibits the tyrosine kinase activity of epidermal growth factor receptor (EGFR), the rational target of anti-colorectal cancer therapy.
α-Hemolysin has been utilized to conduct nanopore sequencing of DNA.
- Stipcevic T, Piljac T, Isseroff RR (November 2005). "Di-rhamnolipid from Pseudomonas aeruginosa displays differential effects on human keratinocyte and fibroblast cultures". J. Dermatol. Sci. 40 (2): 141–3. doi:10.1016/j.jdermsci.2005.08.005. PMC 1592130. PMID 16199139.
- Vesper SJ, Vesper MJ (2004). "Possible role of fungal hemolysins in sick building syndrome". Adv. Appl. Microbiol. 55: 191–213. doi:10.1016/S0065-2164(04)55007-4. PMID 15350795.
- Chalmeau J, Monina N, Shin J, Vieu C, Noireaux V (January 2011). "α-Hemolysin pore formation into a supported phospholipid bilayer using cell-free expression". Biochim. Biophys. Acta 1808 (1): 271–8. doi:10.1016/j.bbamem.2010.07.027. PMID 20692229.
- Bhakdi S, Mackman N, Menestrina G, Gray L, Hugo F, Seeger W, Holland IB (June 1988). "The hemolysin of Escherichia coli". Eur. J. Epidemiol. 4 (2): 135–43. doi:10.1007/BF00144740. PMID 3042445.
- Thompson JR, Cronin B, Bayley H, Wallace MI (December 2011). "Rapid assembly of a multimeric membrane protein pore". Biophys. J. 101 (11): 2679–83. doi:10.1016/j.bpj.2011.09.054. PMID 22261056.
- McGillivray DJ, Heinrich F, Valincius G, Ignatjev I, Vanderah DJ, Lösche M, Kasianowicz JJ. "Membrane Association of α-Hemolysin: Proteins Functionally Reconstituted in tBLMs". Carnegie Mellon University.
- Maheswaran SK, Lindorfer RK (November 1967). "Staphylococcal beta-hemolysin. II. Phospholipase C activity of purified beta-hemolysin". J. Bacteriol. 94 (5): 1313–9. PMC 276826. PMID 4964474.
- Dalla Serra M, Coraiola M, Viero G, Comai M, Potrich C, Ferreras M, Baba-Moussa L, Colin DA, Menestrina G, Bhakdi S, Prévost G (2005). "Staphylococcus aureus bicomponent gamma-hemolysins, HlgA, HlgB, and HlgC, can form mixed pores containing all components". J Chem Inf Model 45 (6): 1539–45. doi:10.1021/ci050175y. PMID 16309251.
- Song L, Hobaugh MR, Shustak C, Cheley S, Bayley H, Gouaux JE (December 1996). "Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore". Science 274 (5294): 1859–66. doi:10.1126/science.274.5294.1859. PMID 8943190.
- PDB 3o44; De S, Olson R (May 2011). "Crystal structure of the Vibrio cholerae cytolysin heptamer reveals common features among disparate pore-forming toxins". Proc. Natl. Acad. Sci. U.S.A. 108 (18): 7385–90. doi:10.1073/pnas.1017442108. PMC 3088620. PMID 21502531.
- PDB 3b07; Yamashita K, Kawai Y, Tanaka Y, Hirano N, Kaneko J, Tomita N, Ohta M, Kamio Y, Yao M, Tanaka I (October 2011). "Crystal structure of the octameric pore of staphylococcal γ-hemolysin reveals the β-barrel pore formation mechanism by two components". Proc. Natl. Acad. Sci. U.S.A. 108 (42): 17314–9. doi:10.1073/pnas.1110402108. PMC 3198349. PMID 21969538.
- Gouaux E (1998). "α-Hemolysin from Staphylococcus aureus: an archetype of β-barrel, channel-forming toxins". J. Struct. Biol. 121 (2): 110–22. doi:10.1006/jsbi.1998.3959. PMID 9615434.
- Sritharan M (July 2006). "Iron and bacterial virulence". Indian J Med Microbiol 24 (3): 163–4. PMID 16912433.
- "What Is Hemolytic Anemia? - NHLBI, NIH". United States National Institutes of Health. 2011-04-01. Retrieved 2012-11-24.
- Kebaier C, Chamberland RR, Allen IC, Gao X, Broglie PM, Hall JD, Jania C, Doerschuk CM, Tilley SL, Duncan JA (March 2012). "Staphylococcus aureus α-hemolysin mediates virulence in a murine model of severe pneumonia through activation of the NLRP3 inflammasome". J. Infect. Dis. 205 (5): 807–17. doi:10.1093/infdis/jir846. PMID 22279123.
- Dong J, Qiu J, Wang J, Li H, Dai X, Zhang Y, Wang X, Tan W, Niu X, Deng X, Zhao S (October 2012). "Apigenin alleviates the symptoms of Staphylococcus aureus pneumonia by inhibiting the production of alpha-hemolysin". FEMS Microbiol. Lett. 338 (2): 124–31. doi:10.1111/1574-6968.12040. PMID 23113475.
- Mestre MB, Colombo MI (October 2012). "Staphylococcus aureus promotes autophagy by decreasing intracellular cAMP levels". Autophagy 8 (12). doi:10.4161/auto.22161. PMID 23047465.
- Cavalieri SJ, Snyder IS (September 1982). "Effect of Escherichia coli alpha-hemolysin on human peripheral leukocyte function in vitro". Infect. Immun. 37 (3): 966–74. PMC 347633. PMID 6752033.
- Griffiths BB, McClain O (1988). "The role of iron in the growth and hemolysin (Streptolysin S) production in Streptococcus pyogenes". J. Basic Microbiol. 28 (7): 427–36. doi:10.1002/jobm.3620280703. PMID 3065477.
- Burnside K, Lembo A, de Los Reyes M, Iliuk A, Binhtran NT, Connelly JE, Lin WJ, Schmidt BZ, Richardson AR, Fang FC, Tao WA, Rajagopal L (2010). "Regulation of hemolysin expression and virulence of Staphylococcus aureus by a serine/threonine kinase and phosphatase". PLoS ONE 5 (6): e11071. doi:10.1371/journal.pone.0011071. PMC 2884019. PMID 20552019.
- Ragle BE, Bubeck Wardenburg J (July 2009). "Anti-alpha-hemolysin monoclonal antibodies mediate protection against Staphylococcus aureus pneumonia". Infect. Immun. 77 (7): 2712–8. doi:10.1128/IAI.00115-09. PMC 2708543. PMID 19380475.
- Karmakar P, Chakrabarti MK (July 2012). "Thermostable direct hemolysin diminishes tyrosine phosphorylation of epidermal growth factor receptor through protein kinase C dependent mechanism". Biochim. Biophys. Acta 1820 (7): 1073–80. doi:10.1016/j.bbagen.2012.04.011. PMID 22543197.
- Hemolysins at the US National Library of Medicine Medical Subject Headings (MeSH)
- Hemolysin at eMedicine Dictionary
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.
Leukocidin/Hemolysin toxin family Provide feedback
No Pfam abstract.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001340
Staphylococcus aureus is a Gram-positive coccus that grows in clusters or pairs, and is the major cause of nosocomial infections due to its multiple antibiotic resistant nature. Patients who are immuno-compromised (e.g., those suffering from third degree burns or chronic illness) are at risk from deep staphylococcal infections, such as osteomyelitis and pneumonia. Most skin infections are also caused by this bacterium [PUBMED:9350200].
Many virulence mechanisms are employed by Staphylococci to induce pathogenesis: these can include polysaccharide capsules and exotoxins [PUBMED:9350200]. Examples of the latter are bi-component toxins, which involve the synergistic combination of an "S" and an "F" component [PUBMED:9804914]. These undergo conformational changes in their protein structure and form oligomeric pores in the target cell membrane upon recognition of certain host receptors. The main cells targeted are polymorphonuclear cells, monocytes, erythrocytes and macrophages. Examples of this protein family include: leucocidin, gamma-haemolysin and alpha-haemolysin.
Recently, the crystal structure of the S. aureus leucocidin "F" component (LukF) has been determined to 1.9A resolution [PUBMED:10048924]. This structure, which comprises a central 3-strand beta-sheet, with an N-terminal "latch", clarified the mechanism of virulence in the bi-component toxin. Further work using a different form of the leucocidin (LukF-PV) has suggested that it may be a representative fold for water-soluble transmembrane toxins [PUBMED:10368297].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||extracellular region (GO:0005576)|
|Biological process||cytolysis in other organism (GO:0051715)|
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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
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 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.
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
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.
MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
HMM 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:||19|
|Number in full:||1628|
|Average length of the domain:||237.50 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||70.82 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|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 2 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 Leukocidin domain has been found. There are 102 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...