Summary: Insect antifreeze protein repeat
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 "Antifreeze protein". 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.
Antifreeze protein Edit Wikipedia article
|Insect antifreeze protein repeat|
|Choristoneura fumiferana antifreeze protein (CfAFP)|
Structure of Choristoneura fumiferana (spruce budworm) beta-helical antifreeze protein
Antifreeze proteins (AFPs) or ice structuring proteins (ISPs) refer to a class of polypeptides produced by certain vertebrates, plants, fungi and bacteria that permit their survival in subzero environments. AFPs bind to small ice crystals to inhibit growth and recrystallization of ice that would otherwise be fatal. There is also increasing evidence that AFPs interact with mammalian cell membranes to protect them from cold damage. This work suggests the involvement of AFPs in cold acclimatization.
- 1 Non-colligative properties
- 2 Thermal hysteresis
- 3 Freeze tolerance versus freeze avoidance
- 4 Diversity
- 5 Evolution
- 6 Mechanisms of action
- 7 Binding to ice
- 8 Binding mechanism and antifreeze function
- 9 History
- 10 Name change
- 11 Commercial applications
- 12 Recent news
- 13 References
- 14 Further reading
- 15 External links
Unlike the widely used automotive antifreeze, ethylene glycol, AFPs do not lower freezing point in proportion to concentration. Rather, they work in a noncolligative manner. This phenomenon allows them to act as an antifreeze at concentrations 1/300th to 1/500th of those of other dissolved solutes. Their low concentration minimizes their effect on osmotic pressure. The unusual properties of AFPs are attributed to their affinity for specific ice crystal surfaces.
AFPs create a difference between the melting point and freezing point known as thermal hysteresis. The addition of AFPs at the interface between solid ice and liquid water inhibits the thermodynamically favored growth of the ice crystal. Ice growth is kinetically inhibited by the AFPs covering the water-accessible surfaces of ice.
Thermal hysteresis is easily measured in the lab with a nanolitre osmometer. Organisms differ in their values of thermal hysteresis. The maximum level of thermal hysteresis shown by fish AFP is approximately -1.5Â°C (29.3Â°F). However, insect antifreeze proteins are 10â30 times more active than fish proteins. This difference probably reflects the lower temperatures encountered by insects on land. In contrast, aquatic organisms are exposed only to â1 to â2Â°C below freezing. During the extreme winter months, the spruce budworm resist freezing at temperatures approaching â30 Â°C. The Alaskan beetle Upis ceramboides can survive in a temperature of â60 Â°C by using antifreeze agents that are not proteins.
The rate of cooling can influence the thermal hysteresis value of AFPs. Rapid cooling can substantially decrease the nonequilibrium freezing point, and hence the thermal hysteresis value. Consequently, organisms cannot necessarily adapt to their subzero environment if the temperature drops abruptly.
Freeze tolerance versus freeze avoidance
Species containing AFPs may be classified as
Freeze avoidant: These species are able to prevent their body fluids from freezing altogether. Generally, the AFP function may be overcome at extremely cold temperatures, leading to rapid ice growth and death.
Freeze tolerant: These species are able to survive body fluid freezing. Some freeze tolerant species are thought to use AFPs as cryoprotectants to prevent the damage of freezing, but not freezing altogether. The exact mechanism is still unknown. However, it is thought AFPs may inhibit recrystallization and stabilize cell membranes to prevent damage by ice. They may work in conjunction with protein ice nucleators (PINs) to control the rate of ice propagation following freezing.
There are many known nonhomologous types of AFPs.
Type I AFP is found in winter flounder, longhorn sculpin and shorthorn sculpin. It is the best documented AFP because it was the first to have its three dimensional structure determined. Type I AFP consists of a single, long, amphipathic alpha helix, about 3.3-4.5 kD in size. There are three faces to the 3D structure: the hydrophobic, hydrophilic, and Thr-Asx face.
Type I-hyp AFP (where hyp stands for hyperactive) are found in several righteye flounders. It is approximately 32 kD (two 17 kD dimeric molecules). The protein was isolated from the blood plasma of winter flounder. It is considerably better at depressing freezing temperature than most fish AFPs.
Type IV AFPs are found in longhorn sculpins. They are alpha helical proteins rich in glutamate and glutamine. This protein is approximately 12KDa in size and consists of a 4-helix bundle. Its only posttranslational modification is a pyroglutamate residue, a cyclized glutamine residue at its N-terminus. Scientists at the University of Guelph in Canada are currently examining the role of this pyroglutame residue in the antifreeze activity of type IV AFP from the longhorn sculpin.
The classification of AFPs became more complicated when antifreeze proteins from plant were discovered. Plant AFPs are rather different from the other AFPs in the following aspects:
- They have much weaker thermal hysteresis activity when compared to other AFPs.
- Their physiological function is likely in inhibiting the recrystallization of ice rather than in the preventing ice formation.
- Most of them are evolved pathogenesis-related proteins, sometimes retaining antifungal properties.
See also dehydrin
There are two types of insect antifreeze proteins, Tenebrio and Dendroides AFPs which are both in different insect families. They are similar to one another, both being hyperactive (i.e. greater thermal hysteresis value) and consist of varying numbers of 12- or 13-mer repeats of approximately 8.3 to 12.5 kD. Throughout the length of the protein, at least every sixth residue is a cysteine.
Sea ice organisms AFPs
AFPs were also found in microorganisms living in sea ice. The diatoms Fragilariopsis cylindrus and F. curta play a key role in polar sea ice communities, dominating the assemblages of both platelet layer and within pack ice. AFPs are widespread in these species, and the presence of AFP genes as a multigene family indicates the importance of this group for the genus Fragilariopsis. AFPs identified in F. cylindrus belong to an AFP family which is represented in different taxa and can be found in other organisms related to sea ice (Colwellia spp., Navicula glaciei, Chaetoceros neogracile and Stephos longipes and Leucosporidium antarcticum) and Antarctic inland ice bacteria (Flavobacteriaceae), as well as in cold-tolerant fungi (Typhula ishikariensis, Lentinula edodes and Flammulina populicola.)
The remarkable diversity and distribution of AFPs suggest the different types evolved recently in response to sea level glaciation occurring 1-2 million years ago in the Northern hemisphere and 10-30 million years ago in Antarctica. This independent development of similar adaptations is referred to as convergent evolution. There are two reasons why many types of AFPs are able to carry out the same function despite their diversity:
- Although ice is uniformly composed of oxygen and hydrogen, it has many different surfaces exposed for binding. Different types of AFPs may interact with different surfaces.
- Although the five types of AFPs differ in their primary sequence of amino acids, when each folds into a functioning protein, they may share similarities in their three dimensional or tertiary structure that facilitates the same interactions with ice.
Mechanisms of action
AFPs are thought to inhibit growth by an adsorptionâinhibition mechanism. They adsorb to nonbasal planes of ice, inhibiting thermodynamically favored ice growth. The presence of a flat, rigid surface in some AFPs seems to facilitate its interaction with ice via Van der Waals force surface complementarity.
Binding to ice
Normally, ice crystals grown in solution only exhibit the basal (0001) and prism faces (1010), and appear as round and flat discs. However, it appears the presence of AFPs exposes other faces. It now appears the ice surface 2021 is the preferred binding surface, at least for AFP type I. Through studies on type I AFP, ice and AFP were initially thought to interact through hydrogen bonding (Raymond and DeVries, 1977). However, when parts of the protein thought to facilitate this hydrogen bonding were mutated, the hypothesized decrease in antifreeze activity was not observed. Recent data suggest hydrophobic interactions could be the main contributor. It is difficult to discern the exact mechanism of binding because of the complex water-ice interface. Currently, attempts to uncover the precise mechanism are being made through use of molecular modelling programs (molecular dynamics or the Monte Carlo method).
Binding mechanism and antifreeze function
According to the structure and function study on the antifreeze protein from the fish winter flounder, the antifreeze mechanism of the type-I AFP molecule was shown to be due to the binding to an ice nucleation structure in a zipper-like fashion through hydrogen bonding of the hydroxyl groups of its four Thr residues to the oxygens along the direction in ice lattice, subsequently stopping or retarding the growth of ice pyramidal planes so as to depress the freeze point.
The above mechanism can be used to elucidate the structure-function relationship of other antifreeze proteins with the following two common features:
- recurrence of a Thr residue (or any other polar amino acid residue whose side-chain can form a hydrogen bond with water) in an 11-amino-acid period along the sequence concerned, and
- a high percentage of an Ala residue component therein.
In the 1950s, Canadian scientist Scholander set out to explain how Arctic fish can survive in water colder than the freezing point of their blood. His experiments led him to believe there was âantifreezeâ in the blood of Arctic fish. Then in the late 1960s, animal biologist Arthur DeVries was able to isolate the antifreeze protein through his investigation of Antarctic fish. These proteins were later called antifreeze glycoproteins (AFGPs) or antifreeze glycopeptides to distinguish them from newly discovered nonglycoprotein biological antifreeze agents (AFPs). DeVries worked with Robert Feeney (1970) to characterize the chemical and physical properties of antifreeze proteins. In 1992, Griffith et al. documented their discovery of AFP in winter rye leaves. Around the same time, Urrutia, Duman and Knight (1992) documented thermal hysteresis protein in angiosperms. The next year, Duman and Olsen noted AFPs had also been discovered in over 23 species of angiosperms, including ones eaten by humans. As well, they reported their presence in fungi and bacteria.
Recent attempts have been made to relabel antifreeze proteins as ice structuring proteins to more accurately represent their function and to dispose of any assumed negative relation between AFPs and automotive antifreeze, ethylene glycol. These two things are completely separate entities, and show loose similarity only in their function.
Commercially, there appear to be countless applications for antifreeze proteins. Numerous fields would be able to benefit from the protection of tissue damage by freezing. Businesses are currently investigating the use of these proteins in:
- increasing freeze tolerance of crop plants and extending the harvest season in cooler climates
- improving farm fish production in cooler climates
- lengthening shelf life of frozen foods
- improving cryosurgery
- enhancing preservation of tissues for transplant or transfusion in medicine
- therapy for hypothermia
One recent, successful business endeavor has been the introduction of AFPs into ice cream and yogurt products. This ingredient, labelled ice-structuring protein, has been approved by the Food and Drug Administration. The proteins are isolated from fish and replicated, on a larger scale, in yeast.
There is concern from organizations opposed to genetically modified organisms (GMOs), arguing modified antifreeze proteins may cause inflammation. Intake of AFPs in diet is likely substantial in most northerly and temperate regions already. Given the known historic consumption of AFPs, it is safe to conclude their functional properties do not impart any toxicologic or allergenic effects in humans.
As well, the transgenic process of ISP production is widely used in society already. Insulin is produced using this technology. The process does not impact the product; it merely makes production more efficient and prevents the death of many fish who would, otherwise, be killed for the extraction of such protein.
Currently, Unilever incorporates AFPs into some of its American products, including some popsicles and a new line of Breyers Light Double Churned ice cream bars. In ice cream, AFPs allow the production of very creamy, dense, reduced fat ice cream with fewer additives. They control ice crystal growth brought on by thawing on the loading dock or kitchen table which drastically reduces texture quality.
In November 2009, the Proceedings of the National Academy of Sciences published the discovery of a molecule in an Alaskan beetle that behaves like AFPs, but is composed of saccharides and fatty acids.
A 2010 study demonstrated the stability of superheated water ice crystals in an AFP solution, showing while the proteins can inhibit freezing, they can also inhibit melting.
- Daley ME, Spyracopoulos L, Jia Z, Davies PL, Sykes BD (April 2002). "Structure and dynamics of a beta-helical antifreeze protein". Biochemistry 41 (17): 5515â25. doi:10.1021/bi0121252. PMID 11969412.
- Leinala EK, Davies PL, Doucet D, Tyshenko MG, Walker VK, Jia Z (September 2002). "A beta-helical antifreeze protein isoform with increased activity. Structural and functional insights". J. Biol. Chem. 277 (36): 33349â52. doi:10.1074/jbc.M205575200. PMID 12105229.
- Fletcher GL, Hew CL, Davies PL (2001). "Antifreeze proteins of teleost fishes". Annu. Rev. Physiol. 63: 359â90. doi:10.1146/annurev.physiol.63.1.359. PMID 11181960.
- Jorov A, Zhorov BS, Yang DS (June 2004). "Theoretical study of interaction of winter flounder antifreeze protein with ice". Protein Sci. 13 (6): 1524â37. doi:10.1110/ps.04641104. PMC 2279984. PMID 15152087.
- Walters KR Jr, Serianni AS, Sformo T, Barnes BM, Duman JG (2009). "A nonprotein thermal hysteresis-producing xylomannan antifreeze in the freeze-tolerant Alaskan beetle Upis ceramboides". PNAS 106 (48): 20210â5. doi:10.1073/pnas.0909872106. PMC 2787118. PMID 19934038.
- Duman JG (2001). "Antifreeze and ice nucleator proteins in terrestrial arthropods". Annu. Rev. Physiol. 63: 327â57. doi:10.1146/annurev.physiol.63.1.327. PMID 11181959.
- Crevel RW, Fedyk JK, Spurgeon MJ (July 2002). "Antifreeze proteins: characteristics, occurrence and human exposure". Food Chem. Toxicol. 40 (7): 899â903. doi:10.1016/S0278-6915(02)00042-X. PMID 12065210.
- Duman JG, de Vries AL (1976). "Isolation, characterization, and physical properties of protein antifreezes from the winter flounder, Pseudopleuronectes americanus". Comp. Biochem. Physiol., B 54 (3): 375â80. PMID 1277804.
- Scotter AJ, Marshall CB, Graham LA, Gilbert JA, Garnham CP, Davies PL (October 2006). "The basis for hyperactivity of antifreeze proteins". Cryobiology 53 (2): 229â39. doi:10.1016/j.cryobiol.2006.06.006. PMID 16887111.
- Ng NF, Hew CL (August 1992). "Structure of an antifreeze polypeptide from the sea raven. Disulfide bonds and similarity to lectin-binding proteins". J. Biol. Chem. 267 (23): 16069â75. PMID 1644794.
- Deng G, Andrews DW, Laursen RA (January 1997). "Amino acid sequence of a new type of antifreeze protein, from the longhorn sculpin Myoxocephalus octodecimspinosis". FEBS Lett. 402 (1): 17â20. doi:10.1016/S0014-5793(96)01466-4. PMID 9013849.
- Griffith M, Ala P, Yang DS, Hon WC, Moffatt BA (October 1992). "Antifreeze protein produced endogenously in winter rye leaves". Plant Physiol. 100 (2): 593â6. doi:10.1104/pp.100.2.593. PMC 1075599. PMID 16653033.
- Griffith M, Yaish MW (August 2004). "Antifreeze proteins in overwintering plants: a tale of two activities". Trends Plant Sci. 9 (8): 399â405. doi:10.1016/j.tplants.2004.06.007. PMID 15358271.
- Graham LA, Liou YC, Walker VK, Davies PL (August 1997). "Hyperactive antifreeze protein from beetles". Nature 388 (6644): 727â8. doi:10.1038/41908. PMID 9285581.
- Bayer-Giraldi M, Uhlig C, John U, Mock T, Valentin K (April 2010). "Antifreeze proteins in polar sea ice diatoms: diversity and gene expression in the genus Fragilariopsis". Environ. Microbiol. 12 (4): 1041â52. doi:10.1111/j.1462-2920.2009.02149.x. PMID 20105220.
- Raymond JA, Fritsen C, Shen K (August 2007). "An ice-binding protein from an Antarctic sea ice bacterium". FEMS Microbiol. Ecol. 61 (2): 214â21. doi:10.1111/j.1574-6941.2007.00345.x. PMID 17651136.
- Kiko, R. (2010): Acquisition of freeze protection in a sea-ice crustacean through horizontal gene transfer? Polar Biology (33) 543-556.
- Raymond JA, Christner BC, Schuster SC (September 2008). "A bacterial ice-binding protein from the Vostok ice core". Extremophiles 12 (5): 713â7. doi:10.1007/s00792-008-0178-2. PMID 18622572.
- Hoshino, T., Kiriaki, M., Ohgiya, S., Fujiwara, M., Kondo, H., Nishimiya, Y., et al. (2003) Antifreeze proteins from snow mold fungi. Can J Bot 81: 1175â1181.
- Raymond JA, Janech MG (April 2009). "Ice-binding proteins from enoki and shiitake mushrooms". Cryobiology 58 (2): 151â6. doi:10.1016/j.cryobiol.2008.11.009. PMID 19121299.
- Chen L, DeVries AL, Cheng CH (April 1997). "Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod". Proc. Natl. Acad. Sci. U.S.A. 94 (8): 3817â22. doi:10.1073/pnas.94.8.3817. PMC 20524. PMID 9108061.
- Raymond JA, DeVries AL (June 1977). "Adsorption inhibition as a mechanism of freezing resistance in polar fishes". Proc. Natl. Acad. Sci. U.S.A. 74 (6): 2589â93. doi:10.1073/pnas.74.6.2589. PMC 432219. PMID 267952.
- Raymond JA, Wilson P, DeVries AL (February 1989). "Inhibition of growth of non basal planes in ice by fish antifreezes". Proc. Natl. Acad. Sci. U.S.A. 86 (3): 881â5. doi:10.1073/pnas.86.3.881. PMC 286582. PMID 2915983.
- Yang DS, Hon WC, Bubanko S, Xue Y, Seetharaman J, Hew CL, Sicheri F (May 1998). "Identification of the ice-binding surface on a type III antifreeze protein with a "flatness function" algorithm". Biophys. J. 74 (5): 2142â51. doi:10.1016/S0006-3495(98)77923-8. PMC 1299557. PMID 9591641.
- Knight CA, Cheng CC, DeVries AL (February 1991). "Adsorption of alpha-helical antifreeze peptides on specific ice crystal surface planes". Biophys. J. 59 (2): 409â18. doi:10.1016/S0006-3495(91)82234-2. PMC 1281157. PMID 2009357.
- Haymet AD, Ward LG, Harding MM, Knight CA (July 1998). "Valine substituted winter flounder 'antifreeze': preservation of ice growth hysteresis". FEBS Lett. 430 (3): 301â6. doi:10.1016/S0014-5793(98)00652-8. PMID 9688560.
- Chou KC (January 1992). "Energy-optimized structure of antifreeze protein and its binding mechanism". J. Mol. Biol. 223 (2): 509â17. doi:10.1016/0022-2836(92)90666-8. PMID 1738160.
- DeVries AL, Wohlschlag DE (March 1969). "Freezing resistance in some Antarctic fishes". Science 163 (3871): 1073â5. doi:10.1126/science.163.3871.1073. PMID 5764871.
- DeVries AL, Komatsu SK, Feeney RE (June 1970). "Chemical and physical properties of freezing point-depressing glycoproteins from Antarctic fishes". J. Biol. Chem. 245 (11): 2901â8. PMID 5488456.
- Duman JG, Olsen TM (1993). "Thermal hysteresis protein activity in bacteria, fungi and phylogenetically diverse plants". Cryobiology 30 (3): 322â328. doi:10.1006/cryo.1993.1031.
- Clarke CJ, Buckley SL, Lindner N (2002). "Ice structuring proteins - a new name for antifreeze proteins". Cryo Letters 23 (2): 89â92. PMID 12050776.
- Antifreeze proteins and their genes: From basic research to business opportunity
- Science Daily
- Dortch, Eloise. (2006). Fishy GM yeast used to make ice-cream. Network of Concerned Farmers. Retrieved October 09, 2006
- Creamy, Healthier Ice Cream? Whatâs the Catch?
- Regand A, Goff HD (January 2006). "Ice recrystallization inhibition in ice cream as affected by ice structuring proteins from winter wheat grass". J. Dairy Sci. 89 (1): 49â57. doi:10.3168/jds.S0022-0302(06)72068-9. PMID 16357267.
- Celik, Y; Graham, LA; Mok, YF; Bar, M; Davies, PL; Braslavsky, I (2010). "Superheating of Ice in the Presence of Ice Binding Proteins". Biophysical Journal 98 (3): 245a. doi:10.1016/j.bpj.2009.12.1331. Lay summary â Physorg.com.
- Haymett, A.; Ward, L.; Harding, M. (1999). "Winter Flounder 'anti-freeze' proteins: Synthesis and ice growth inhibition of analogues that probe the relative importance of hydrophobic and hydrogen bonding interactions". Journal of the American Chemical Society 121 (5): 941â948. doi:10.1021/ja9801341. ISSN 00027863.
- Sicheri, F.; Yang, D. S. (1995). "Ice-binding structure and mechanism of an antifreeze protein from winter flounder". Nature 375 (6530): 427â431. doi:10.1038/375427a0. PMID 7760940.
- Cold, Hard Fact: Fish Antifreeze Produced in Pancreas
- Antifreeze Proteins: Molecule of the Month, by David Goodsell, RCSB Protein Data Bank
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.
Insect antifreeze protein repeat Provide feedback
This family of extracellular proteins is involved in stopping the formation of ice crystals at low temperatures. The proteins are composed of a 12 residue repeat that forms a structural repeat. The structure of the repeats is a beta helix . Each repeat contains two cys residues that form a disulphide bridge.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003460
Antifreeze proteins (AFPs) are a class of proteins that are able to bind to and inhibit the growth of macromolecular ice, thereby permitting an organism to survive subzero temperatures by decreasing the probability of ice nucleation in their bodies [PUBMED:15291806]. These proteins have been characterised from a variety of organisms, including fish, plants, bacteria, fungi and arthropods. This entry represents insect AFPs of the type found in Tenebrio molitor (Yellow mealworm) and in Dendroides canadensis (Pyrochroid beetle).
The structure of these AFPs consists of a right-handed beta-helix with 12 residues per coil. Each 12 residue-repeat contains two cys residues that form a disulphide bridge. The beta-helices of insect AFPs present a highly rigid array of threonine residues and bound water molecules that can effectively mimic the ice lattice. As such, beta-helical AFPs provide a more effective coverage of the ice surface compared to the alpha-helical fish AFPs [PUBMED:10917536].
A second insect antifreeze from Choristoneura fumiferana (Spruce budworm) (INTERPRO) also consists of beta-helices, however in these proteins the helices form a left-handed twist; these proteins show no sequence homology to the current entry, but may act by a similar mechanism. The beta-helix motif may be used as an AFP structural motif in non-homologous proteins from other (non-fish) organisms as well.
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:||9|
|Number in full:||502|
|Average length of the domain:||11.70 aa|
|Average identity of full alignment:||45 %|
|Average coverage of the sequence by the domain:||80.61 %|
|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:||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.
There is 1 interaction 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 AFP domain has been found. There are 21 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...