Summary: Avidin 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 "Avidin". 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.
Avidin Edit Wikipedia article
|core-streptavidin mutant d128a at ph 4.5|
Avidin is a tetrameric or dimeric biotin-binding protein produced in the oviducts of birds, reptiles and amphibians deposited in the whites of their eggs. In chicken egg white, avidin makes up approximately 0.05% of total protein (approximately 1.8 mg per egg). The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of avidin is measured to be KD â 10â15 M, making it one of the strongest known non-covalent bonds.
In its tetrameric form, avidin is estimated to be between 66â69 kDa in size. Ten percent of the molecular weight is attributed to carbohydrate content composed of four to five mannose and three N-acetylglucosamine residues. The carbohydrate moieties of avidin contain at least three unique oligosaccharide structural types that are similar in structure and composition.
Functional avidin is found only in raw egg, as the biotin avidity of the protein is destroyed by cooking. The natural function of avidin in eggs is not known, although it has been postulated to be made in the oviduct as a bacterial growth-inhibitor, by binding biotin the bacteria need. As evidence for this, streptavidin, a loosely related protein with equal biotin affinity and a very similar binding site, is made by certain strains of Streptomyces bacteria, and is thought to serve to inhibit the growth of competing bacteria, in the manner of an antibiotic.
A non-glycosylated form of avidin has been isolated from commercially prepared product; however, it is not conclusive as to whether the non-glycosylated form occurs naturally or is a product of the manufacturing process.
 Discovery of avidin
Avidin was first discovered by Esmond Emerson Snell (1914â2003). The route to discovery began with the observation that chicks on a diet of raw egg-white were deficient in biotin, despite availability of the vitamin in their diet. It was concluded that a component of the egg-white was sequestering biotin which Snell verified in vitro using a yeast assay. Snell later isolated the component of egg white responsible for biotin binding, and, in collaboration with Paul Gyorgy, confirmed that the isolated egg protein was the cause of biotin deficiency or âegg white injuryâ. At the time the protein had been tentatively named avidalbumin (literally, hungry albumin) by the involved researchers at the University of Texas. The name of the protein was later revised to "avidin" based on its affinity for biotin (avid + biotin).
 Applications of avidin
Research in the 1970s helped establish the avidin-biotin system as a powerful tool in biological sciences. Aware of the strength and specificity of the avidin-biotin complex, researchers began to exploit avidin and streptavidin as probes and affinity matrixes in numerous research projects. Soon after, researchers Bayer and Wilchek developed new methods and reagents to biotinylate antibodies and other biomolecules, allowing the transfer of the avidin-biotin system to a range of biotechnological applications. Today, avidin is used in applications ranging from research and diagnostics to medical devices and pharmaceuticals.
Avidin's affinity for biotin is exploited in wide-ranging biochemical assays, including western blot, ELISA, ELISPOT and pull-down assays. In some cases the use of biotinylated antibodies has allowed the replacement of radioiodine labeled antibodies in radioimmunoassay systems, to give an assay system which is not radioactive.
Avidin immobilized onto solid supports is also used as purification media to capture biotin-labelled protein or nucleic acid molecules. For example, cell surface proteins can be specifically labelled with membrane impermeable biotin reagent, then specifically captured using an avidin-based support.
 Modified forms of avidin
As a basically charged glycoprotein, avidin exhibits non-specific binding in some applications. Neutravidin, a deglycosylated avidin with modified arginines, exhibits a more neutral pI and is available as an alternative to native avidin, whenever problems of non-specific binding arise. Deglycosylated, neutral forms of avidin are available through Sigma-Aldrich (Extravidin), Thermo Scientific (NeutrAvidin), Invitrogen (NeutrAvidin), and Belovo (NeutraLite).
Given the strength of the avidin-biotin bond, dissociation of the avidin-biotin complex requires extreme conditions that cause protein denaturation. The non-reversible nature of the avidin-biotin complex can limit avidinâs application in affinity chromatography applications where release of the captured ligand is desirable. Researchers have created an avidin with reversible binding characteristics through nitration or iodination of the binding site tyrosine. The modified avidin exhibits strong biotin binding characteristics at pH 4 and releases biotin at a pH of 10 or higher. A monomeric form of avidin with a reduced affinity for biotin is also employed in many commercially available affinity resins. The monomeric avidin is created by treatment of immobilized native avidin with urea or guanidine HCl (6â8 M), giving it a lower dissociation KD â 10â7M. This allows elution from the avidin matrix to occur under milder, non-denaturing conditions, using low concentrations of biotin or low pH conditions.
 Inactivation of biotin binding activity
The thermal stability and biotin binding activity of avidin are of both practical and theoretical interest to researchers, as avidin's stability is unusually high and avidin is an antinutrient in human food. A 1966 study published in Biochemical and Biophysical Research Communications found that the structure of avidin remains stable at temperatures below 70 Â°C (158 Â°F). Above 70 Â°C (158 Â°F), avidin's structure is rapidly disrupted and by 85 Â°C (185 Â°F), extensive loss of structure and ability to bind biotin is found. A 1991 assay for the Journal of Food Science detected substantial avidin activity in cooked egg white: "mean residual avidin activity in fried, poached and boiled (2 min) egg white was 33, 71 and 40% of the activity in raw egg white." The assay surmised that cooking times were not sufficient to adequately heat all cold spot areas within the egg white. Complete inactivation of avidin's biotin binding capacity required boiling for over 4 minutes.
A 1992 study found that thermal inactivation of the biotin binding activity of avidin was described by D121Â°C = 25 min and z = 33Â°C. The study disagreed with prior assumptions "that the binding site of avidin is destroyed on heat denaturation".
The biotin-binding properties of avidin were exploited during the development of idrabiotaparinux, a long-acting low molecular weight heparin used in the treatment of venous thrombosis. Due to the long-acting nature of idraparinux, concerns were made about the clinical management of bleeding complications. By adding a biotin moiety to the idraparinux molecule, idrabiotaparinux was formed; its anticoagulant activity in the setting of a bleeding event can be reversed through an intravenous infusion of avidin.
 See also
- Nurminen et al. 2007
- Green 1963
- Korpela 1984
- Green 1975
- Bruch & White 1982
- Hendrickson et al. 1989
- Hiller et al. 1987
- Eakin, McKinley & Williams 1940
- Snell, Eakin & Williams 1940
- Gyorgy 1941
- Kresge, Simoni & Hill 2004
- Hofmann & Kiso 1976
- Bayer et al. 1976
- Angerer et al. 1976
- Heffegeness & Ash 1977
- Bayer, Zalis & Wilchek 1985
- Wilchek, Ben-Hur & Bayer 1986
- Morag, Bayer & Wilchek 1996
- Kohanski & Lane 1990
- Durance & Wong 1992
- Pritchard, McCormick & Wright 1966
- Durance 1991
- BÃ¼ller 2012
- Angerer, Lynne; Davidson, Norman; Murphy, William; Lynch, Dennis; Attardi, Giuseppe (1976). "An electron microscope study of the relative positions of the 4S and ribosomal RNA genes in HeLa cell mitochondrial DNA". Cell 9 (1): 81â90. doi:10.1016/0092-8674(76)90054-4. PMID 975242.
- BÃ¼ller, Harry; Gallus, Alex; Pillion, Gerard; Prins, Martin; Raskob, Gary (2012). "Enoxaparin followed by once-weekly idrabiotaparinux versus enoxaparin plus warfarin for patients with acute symptomatic pulmonary embolism: a randomised, double-blind, double-dummy, non-inferiority trial". Lancet 379 (9811): 123â129. doi:10.1016/S0140-6736(11)61505-5. PMID 22130488.
- Bayer, Edward A.; Zalis, Mariano G.; Wilchek, Meir (1985). "3-(N-maleimido-propionyl) biocytin: A versatile thiol-specific biotinylating reagent". Analytical Biochemistry 149 (2): 529â36. doi:10.1016/0003-2697(85)90609-8. PMID 3935007.
- Bayer, E. A.; Skutelsky, E.; Wynne, D.; Wilchek, M. (1976). "Preparation of ferritin-avidin conjugates by reductive alkylation for use in electron microscopic cytochemistry". Journal of Histochemistry & Cytochemistry 24 (8): 933â9. doi:10.1177/24.8.182877. PMID 182877.
- Bruch, Richard C.; White, Harold B. (1982). "Compositional and structural heterogeneity of avidin glycopeptides". Biochemistry 21 (21): 5334â41. doi:10.1021/bi00264a033. PMID 6816268.
- Durance, T. D. (1991). "Residual Avid in Activity in Cooked Egg White Assayed with Improved Sensitivity". Journal of Food Science 56 (3): 707â9. doi:10.1111/j.1365-2621.1991.tb05361.x.
- Durance, T.D.; Wong, N.S. (1992). "Kinetics of thermal inactivation of avidin". Food Research International 25 (2): 89â92. doi:10.1016/0963-9969(92)90148-X.
- Eakin, R. E.; McKinley, W. A.; Williams, R. J. (1940). "Egg-White Injury in Chicks and Its Relationship to a Deficiency of Vitamin H (Biotin)". Science 92 (2384): 224â5. Bibcode:1940Sci....92..224E. doi:10.1126/science.92.2384.224. PMID 17743857.
- Green, NM (1963). "Avidin. 1. The Use of (14-C)Biotin for Kinetic Studies and for Assay". The Biochemical Journal 89: 585â91. PMC 1202466. PMID 14101979.
- Green, N. Michael (1975). "Avidin". In Anfinsen, Christian B.; Edsall, John Tileston; Richards, Frederic Middlebrook. Advances in Protein Chemistry Volume 29. pp. 85â133. doi:10.1016/S0065-3233(08)60411-8. ISBN 978-0-12-034229-7.
- Gyorgy, P.; Rose, C. S.; Eakin, R. E.; Snell, E. E.; Williams, R. J. (1941). "Egg-White Injury As the Result of Nonabsorption or Inactivation of Biotin". Science 93 (2420): 477â8. Bibcode:1941Sci....93..477G. doi:10.1126/science.93.2420.477. PMID 17757050.
- Heggeness, Michael H.; Ash, John F. (1977). "Use of the avidin-biotin complex for the localization of actin and myosin with fluorescence microscopy". The Journal of Cell Biology 73 (3): 783â8. doi:10.1083/jcb.73.3.783. PMC 2111432. PMID 326797.
- Nurminen, Kirsi P.; Helppolainen, Satu H.; MÃ¤Ã¤ttÃ¤, Juha A. E.; Halling, Katrin K.; Slotte, J. Peter; Huhtala, Tuulia; Liimatainen, Timo; YlÃ¤-Herttuala, Seppo et al. (2007). "Rhizavidin from Rhizobium etli: The first natural dimer in the avidin protein family". Biochemical Journal 405 (3): 397â405. doi:10.1042/BJ20070076. PMC 2267316. PMID 17447892. Citation uses old-style implicit et al. for authors
- Hendrickson, Wayne A.; Pahler, Arno; Smith, Janet L.; Satow, Yoshinori; Merritt, Ethan A.; Phizackerley, R. Paul (1989). "Crystal Structure of Core Streptavidin Determined from Multiwavelength Anomalous Diffraction of Synchrotron Radiation". Proceedings of the National Academy of Sciences 86 (7): 2190â4. Bibcode:1989PNAS...86.2190H. doi:10.1073/pnas.86.7.2190. JSTOR 33443. PMC 286877. PMID 2928324.
- Hiller, Y; Gershoni, JM; Bayer, EA; Wilchek, M (1987). "Biotin binding to avidin. Oligosaccharide side chain not required for ligand association". The Biochemical Journal 248 (1): 167â71. PMC 1148514. PMID 3435435.
- Hofmann, Klaus; Kiso, Yoshiaki; Kiso, Y (1976). "An Approach to the Targeted Attachment of Peptides and Proteins to Solid Supports". Proceedings of the National Academy of Sciences 73 (10): 1784â5. Bibcode:1976PNAS...73.3516H. doi:10.1073/pnas.73.10.3516. JSTOR 66631. PMID 18051425.
- Kohanski, Ronald A.; Daniel Lane, M. (1990). "Monovalent avidin affinity columns". Avidin-Biotin Technology. Methods in Enzymology 184. pp. 194â200. doi:10.1016/0076-6879(90)84274-K. ISBN 978-0-12-182085-5. PMID 2388570.
- Korpela, J (1984). "Avidin, a high affinity biotin-binding protein, as a tool and subject of biological research". Medical Biology 62 (1): 5â26. PMID 6379329.
- Kresge, Nicole; Simoni, Robert D.; Hill, Robert L. (2004). "The Discovery of Avidin by Esmond E. Snell". The Journal of Biological Chemistry 279 (41): e5.
- Morag, Ely; Bayer, Edward A.; Wilchek, Meir (1996). "Reversibility of biotin-binding by selective modification of tyrosine in avidin". The Biochemical Journal 316 (1): 193â9. PMC 1217322. PMID 8645205.
- Pritchard, Alan B.; McCormick, Donald B.; Wright, Lemuel D. (1966). "Optical rotatory dispersion studies of the heat denaturation of avidin and the avidin-biotin complex". Biochemical and Biophysical Research Communications 25 (5): 524â8. doi:10.1016/0006-291X(66)90623-1.
- Snell, Esmond E.; Eakin, Robert E.; Williams, Roger J. (1940). "A Quantitative Test for Biotin and Observations Regarding its Occurrence and Properties". Journal of the American Chemical Society 62: 175â8. doi:10.1021/ja01858a052.
- Wilchek, Meir; Ben-Hur, Haya; Bayer, Edward A. (1986). "P-Diazobenzoyl biocytin â A new biotinylating reagent for the labeling of tyrosines and histidines in proteins". Biochemical and Biophysical Research Communications 138 (2): 872â9. doi:10.1016/S0006-291X(86)80577-0. PMID 3741438.
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.
Avidin family Provide feedback
No Pfam abstract.
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005468Avidin [PUBMED:2388586] is a minor constituent of egg white in several groups of oviparous vertebrates. Avidin, which was discovered in the 1920's, takes its name from the avidity with which it binds biotin. These two molecules bind so strongly that is extremely difficult to separate them. Streptavidin is a protein produced by Streptomyces avidinii which also binds biotin and whose sequence is evolutionary related to that of avidin.
Avidin and streptavidin both form homotetrameric complexes of noncovalently associated chains. Each chain forms a very strong and specific non-covalent complex with one molecule of biotin.
The three-dimensional structures of both streptavidin [PUBMED:2928324, PUBMED:8515446] and avidin [PUBMED:2784773] have been determined and revealed them to share a common fold: an eight stranded anti-parallel beta-barrel with a repeated +1 topology enclosing an internal ligand binding site.
Fibropellins I and III [PUBMED:8500658] are proteins that form the apical lamina of the sea urchin embryo, a component of the extracellular matrix. These two proteins have a modular structure composed of a CUB domain (seePROSITEDOC), followed by a variable number of EGF repeats and a C-terminal avidin-like domain.
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:||15|
|Number in full:||142|
|Average length of the domain:||107.70 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||48.71 %|
|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:||12|
|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 Avidin domain has been found. There are 454 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...