Summary: Putative auto-transporter adhesin, head GIN domain
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "Bacterial adhesin". 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.
Bacterial adhesin Edit Wikipedia article
Adhesins are cell-surface components or appendages of bacteria that facilitate adhesion or adherence to other cells or to surfaces, usually the host they are infecting or living in. Adhesins are a type of virulence factor.
Adherence is an essential step in bacterial pathogenesis or infection, required for colonizing a new host. Adhesion and bacterial adhesins are also a potential target for prophylaxis or treatment of bacterial infections.
Bacteria are typically found attached to and living in close association with surfaces. During the bacterial lifespan, a bacterium is subjected to frequent shear-forces. In the crudest sense, bacterial adhesins serve as anchors allowing bacteria to overcome these environmental shear forces, thus remaining in their desired environment. However, bacterial adhesins do not serve as a sort of universal bacterial Velcro. Rather, they act as specific surface recognition molecules, allowing the targeting of a particular bacterium to a particular surface such as root tissue in plants, lacrimal duct tissues in mammals, or even tooth enamel.
Most fimbria of gram-negative bacteria function as adhesins, but in many cases it is a minor subunit protein at the tip of the fimbriae that is the actual adhesin. In gram-positive bacteria, a protein or polysaccharide surface layer serves as the specific adhesin. To effectively achieve adherence to host surfaces, many bacteria produce multiple adherence factors called adhesins.
Bacterial adhesins provide species and tissue tropism. Adhesins are expressed by both pathogenic bacteria and saprophytic bacteria. This prevalence marks them as key microbial virulence factors in addition to a bacteriumâ€™s ability to produce toxins and resist the immune defenses of the host.
Through the mechanisms of evolution, different species of bacteria have developed different solutions to the problem of attaching receptor specific proteins to the bacteria surface. Today many different types and subclasses of bacterial adhesins may be observed in the literature.
The typical structure of a bacterial adhesion is that of a fimbria or pilus. The bacterial adhesion consists primarily of an intramembranous structural protein which provides a scaffold upon which several extracellular adhesins may be attached. However, as in the case of the CFA1 fimbriae, the structural protein itself can sometimes act as an adhesion if a portion of the protein extends into the ECM.
The best characterized bacterial adhesin is the type 1 fimbrial FimH adhesin. This adhesin is responsible for D-mannose sensitive adhesion. The bacterium synthesizes a precursor protein consisting of 300 amino acids then processes the protein by removing several signal peptides ultimately leaving a 279 amino acid protein. Mature FimH is displayed on the bacterial surface as a component of the type 1 fimbrial organelle.
In 1999, the structure of FimH was resolved via x-ray crystallography. FimH is folded into two domains. The N terminal adhesive domain plays the main role in surface recognition while the C-terminal domain is responsible for organelle integration. A tetra-peptide loop links the two domains. Additionally, a carbohydrate-binding pocket has been identified at the tip of the N-terminal adhesive domain. This basic structure is conserved across type 1 fimbrial adhesins though recent studies have shown that in vitro induced mutations can lead to the addition of C-terminal domain specificity resulting in a bacterial adhesion with dual bending sites and related binding phenotypes.
As virulence factors
The majority of bacterial pathogens exploit specific adhesion to host cells as their main virulence factor. "A large number of bacterial adhesins with individual receptor specificities have been identified." Many bacterial pathogens are able to express an array of different adhesins. Expression of these adhesins at different phases during infection play the most important role in adhesion based virulence. Numerous studies have shown that inhibiting a single adhesin in this coordinated effort can often be enough to make a pathogenic bacterium non-virulent. This has led to the exploration of adhesin activity interruption as a method of bacterial infection treatment.
Vaccines based on adhesins
The study of adhesins as a point of exploitation for vaccines comes from early studies which indicated that an important component of protective immunity against certain bacteria came from an ability to prevent adhesin binding. Additionally, Adhesins are attractive vaccine candidates because they are often essential to infection and are surface-located, making them readily accessible to antibodies.
The effectiveness of anti-adhesin antibodies is illustrated by studies with FimH, the adhesin of uropathogenic Escherichia coli (UPEC). Work with E. coli stems from observations of human acquired immunity. Children in third world countries may suffer from several episodes of E. coli associated diarrhea during the first three years of life. If the child survives this initial period of susceptibility, infection rates typically drop substantially. Field studies show that this acquired immunity is directed primarily against bacterial adhesins.
Recent studies from Worcester Polytechnic Institute show that the consumption of cranberry juice may inhibit the action of UPEC adhesins. Using atomic force microscopy researchers have shown that adhesion forces decrease with time following cranberry juice consumption. This research has opened the door to further exploration of orally administered vaccines which exploit bacterial adhesins.
A number of problems create challenges for the researcher exploring the anti-adhesin immunity concept. First, a large number of different bacterial adhesins target the same human tissues. Further, an individual bacterium can produce multiple different types of adhesin, at different times, in different places, and in response to different environmental triggers. Finally, many adhesins present as different immunologically distinct antigenic varieties, even within the same clone (as is the case in Neisseria gonorrhoeae).
Despite these challenges, progress is being made in the creation of anti-adhesion vaccines. In animal models, passive immunization with anti FimH-antibodies and vaccination with the protein significantly reduced colonization by UPEC. Moreover, the Bordetella pertussis adhesins FHA and pertactin are components of three of the four acellular pertussis vaccines currently licensed for use in the U.S. Additionally, anti-adhesion vaccines are being explored as a solution to urinary tract infection (UTIs). The use of synthetic FimH adhesion peptides was shown to prevent urogenital mucosal infection by E. coli in mice.
drae adhesin from escherichia coli
The Dr family of adhesins bind to the Dr blood group antigen component of decay-accelerating factor (DAF). These proteins contain both fimbriated and afimbriated adherence structures and mediate adherence of uropathogenic Escherichia coli to the urinary tract. They do so by inducing the development of long cellular extensions that wrap around the bacteria. They also confer the mannose-resistant hemaglutination phenotype, which can be inhibited by chloramphenicol. The N-terminal portion of the mature protein is thought to be responsible for chloramphenicol sensitivity. Also, they induce activation of several signal transduction cascades, including activation of PI-3 kinase.
Multivalent Adhesion Molecules
Multivalent Adhesion Molecules (MAMs) are a widespread family of adhesins found in Gram negative bacteria, including E. coli, Vibrio, Yersinia, and Pseudomonas aeruginosa. MAMs contain tandem repeats of mammalian cell entry (MCE) domains which specifically bind to extracellular matrix proteins and anionic lipids on host tissues. Since they are abundant in many pathogens of clinical importance, Multivalent Adhesion Molecules are a potential target for prophylactic or therapeutic anti-infectives. The use of a MAM targeting adhesion inhibitor was shown to significantly decrease the colonization of burn wounds by multidrug resistant Pseudomonas aeruginosa in rats.
N. gonorrhoeae is host restricted almost entirely to humans. "Extensive studies have established type 4 fimbrial adhesins of N. gonorrhoeae virulence factors." These studies have shown that only strains capable of expressing fimbriae are pathogenic. High survival of polymorphonuclear neutrophils (PMNs) characterizes Neisseria gonorrhoeae infections. Additionally, recent studies out of Stockholm have shown that Neisseria can hitchhike on PMNs using their adhesin pili thus hiding them from neutrophil phagocytic activity. This action facilitates the spread of the pathogen throughout the epithelial cell layer.
Escherichia coli strains most known for causing diarrhea can be found in the intestinal tissue of pigs and humans where they express the K88 and CFA1. to attach to the intestinal lining. Additionally, UPEC causes about 90% of urinary tract infections. Of those E. coli which cause UTIs, 95% express type 1 fimbriae. FimH in E. coli overcomes the antibody based immune response by natural conversion from the high to the low affinity state. Through this conversion, FimH adhesion may shed the antibodies bound to it. Escherichia coli FimH provides an example of conformation specific immune response which enhances impact on the protein. By studying this particular adhesion, researchers hope to develop adhesion-specific vaccines which may serve as a model for antibody-mediation of pathogen adhesion.
- Coutte L, Alonso S, Reveneau N, Willery E, Quatannens B, Locht C, Jacob-Dubuisson F (2003). "Role of adhesin release for mucosal colonization by a bacterial pathogen". J Exp Med. 197 (6): 735â€“42. doi:10.1084/jem.20021153. PMC 2193847. PMID 12629063.
- Krachler, AM; Orth, K (2014). "Targeting the bacteria-host interface: strategies in anti-adhesion therapy". Virulence. 4 (4): 284â€“94. doi:10.4161/viru.24606. PMC 3710331. PMID 23799663.
- Klemm P, Schembri MA (March 2000). "Bacterial adhesins: function and structure". Int. J. Med. Microbiol. 290 (1): 27â€“35. doi:10.1016/S1438-4221(00)80102-2. PMID 11043979.
- Kline, Kimberly A.; FÃ¤lker, Stefan; Dahlberg, Sofia; Normark, Staffan; Henriques-Normark, Birgitta (2009). "Bacterial Adhesins in Host-Microbe Interactions". Cell Host & Microbe. 5 (6): 580â€“592. doi:10.1016/j.chom.2009.05.011. PMID 19527885.
- Choudhury D, Thompson A, Stojanoff V, et al. (August 1999). "X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli". Science. 285 (5430): 1061â€“6. doi:10.1126/science.285.5430.1061. PMID 10446051.
- Schembri MA, Klemm P (May 1998). "Heterobinary adhesins based on the Escherichia coli FimH fimbrial protein". Appl. Environ. Microbiol. 64 (5): 1628â€“33. PMC 106206. PMID 9572927.
- Levine, M. M.; Giron, J. A.; Noriega, E. R. (1994). "Fimbrial vaccines". In Klemm, Per (ed.). Fimbriae : adhesion, genetics, biogenesis, and vaccines. Boca Raton: CRC Press. pp. 255â€“270. ISBN 978-0849348945.
- Tao Y, PinzÃ³n-Arango PA, Howell AB, Camesano TA (2011). "Oral consumption of cranberry juice cocktail inhibits molecular-scale adhesion of clinical uropathogenic Escherichia coli". J Med Food. 14 (7â€“8): 739â€“45. doi:10.1089/jmf.2010.0154. PMC 3133681. PMID 21480803.
- Davies, J. K.; Koomey, J. M.; Seifert, H. S. (1994). "Pili (fimbriae) of Neisseria gonorrhoeae". In Klemm, Per (ed.). Fimbriae : adhesion, genetics, biogenesis, and vaccines. Boca Raton: CRC Press. pp. 147â€“155. ISBN 978-0849348945.
- Langermann S, MÃ¶llby R, Burlein J, Palaszynski S, Auguste C, DeFusco A, Strouse R, Schenerman M, Hultgren S, Pinkner J, Winberg J, Guldevall L, SÃ¶derhÃ¤ll M, Ishikawa K, Normark S, Koenig S (2000). "Vaccination with FimH adhesin protects cynomolgus monkeys from colonization and infection by uropathogenic Escherichia coli". J Infect Dis. 181 (2): 774â€“8. doi:10.1086/315258. PMID 10669375.
- Langermann S, Palaszynski S, Barnhart M, et al. (April 1997). "Prevention of mucosal Escherichia coli infection by FimH-adhesin-based systemic vaccination". Science. 276 (5312): 607â€“11. doi:10.1126/science.276.5312.607. PMID 9110982.
- Identified Virulence Factors of UPEC : Adherence, State Key Laboratory for Moleclular Virology and Genetic Engineering, Beijing. Retrieved July 2011
- Zhang L, Foxman B, Tallman P, Cladera E, Le Bouguenec C, Marrs CF (June 1997). "Distribution of drb genes coding for Dr binding adhesins among uropathogenic and fecal Escherichia coli isolates and identification of new subtypes". Infection and Immunity. 65 (6): 2011â€“8. PMC 175278. PMID 9169726.
- Swanson TN, Bilge SS, Nowicki B, Moseley SL (January 1991). "Molecular structure of the Dr adhesin: nucleotide sequence and mapping of receptor-binding domain by use of fusion constructs". Infection and Immunity. 59 (1): 261â€“8. PMC 257736. PMID 1670929.
- Krachler, Anne Marie; Ham, Hyeilin; Orth, Kim (2011-07-12). "Outer membrane adhesion factor multivalent adhesion molecule 7 initiates host cell binding during infection by gram-negative pathogens". Proceedings of the National Academy of Sciences of the United States of America. 108 (28): 11614â€“11619. doi:10.1073/pnas.1102360108. ISSN 1091-6490. PMC 3136308. PMID 21709226.
- Huebinger, Ryan M.; Stones, Daniel H.; de Souza Santos, Marcela; Carlson, Deborah L.; Song, Juquan; Vaz, Diana Pereira; Keen, Emma; Wolf, Steven E.; Orth, Kim (2016-12-20). "Targeting bacterial adherence inhibits multidrug-resistant Pseudomonas aeruginosa infection following burn injury". Scientific Reports. 6: 39341. doi:10.1038/srep39341. ISSN 2045-2322. PMC 5171828. PMID 27996032.
- SÃ¶derholm N, Vielfort K, Hultenby K, Aro H (2011). "Pathogenic Neisseria hitchhike on the uropod of human neutrophils". PLoS ONE. 6 (9): e24353. doi:10.1371/journal.pone.0024353. PMC 3174955. PMID 21949708.
- Gaastra W, de Graaf FK (June 1982). "Host-specific fimbrial adhesins of noninvasive enterotoxigenic Escherichia coli strains". Microbiol. Rev. 46 (2): 129â€“61. PMC 281536. PMID 6126799.
- Tchesnokova V, Aprikian P, Kisiela D, et al. (October 2011). "Type 1 fimbrial adhesin FimH elicits an immune response that enhances cell adhesion of Escherichia coli". Infect. Immun. 79 (10): 3895â€“904. doi:10.1128/IAI.05169-11. PMC 3187269. PMID 21768279.
Adhesins are also used in cell communication, and bind to surface communicators. Can also be used to bind to other bacteria.
"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.
Putative auto-transporter adhesin, head GIN domain Provide feedback
This bacterial family of proteins shows structural similarity to other pectin lyase families. Although structures from this family align with acetyl-transferases, there is no conservation of catalytic residues found. It is likely that the function is one of cell-adhesion. In PDB:3jx8 it is interesting to note that the sequence of contains several well defined sequence repeats, centred around GSG motifs defining the tight beta turn between the two sheets of the super-helix; there are 8 such repeats in the C-terminal half of the protein, which could be grouped into 4 repeats of two. It seems likely that this family belongs to the superfamily of trimeric auto-transporter adhesins (TAAs), which are important virulence factors in Gram-negative pathogens  . In the case of Parabacteroides distasonis, which is a component of the normal distal human gut microbiota, TAA-like complexes probably modulate adherence to the host (information derived from TOPSAN).
Nummelin H, Merckel MC, Leo JC, Lankinen H, Skurnik M, Goldman A;, EMBO J. 2004;23:701-711.: The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll. PUBMED:14765110 EPMC:14765110
Szczesny P, Linke D, Ursinus A, Bar K, Schwarz H, Riess TM, Kempf VA, Lupas AN, Martin J, Zeth K;, PLoS Pathog. 2008;4:e1000119.: Structure of the head of the Bartonella adhesin BadA. PUBMED:18688279 EPMC:18688279
Internal database links
|Similarity to PfamA using HHSearch:||DUF4097|
This tab holds annotation information from the InterPro database.
InterPro entry IPR021255
Proteins containing this domain show structural similarity to other pectin lyase families. Although these proteins align with acetyl-transferases, there is no conservation of catalytic residues found. It is likely that the function is one of cell-adhesion. In PDB:3jx8, it is interesting to note that the sequence of contains several well defined sequence repeats, centred around GSG motifs defining the tight beta turn between the two sheets of the super-helix; there are 8 such repeats in the C-terminal half of the protein, which could be grouped into 4 repeats of two. It seems likely that proteins in this entry belongs to the superfamily of trimeric auto-transporter adhesins (TAAs), which are important virulence factors in Gram-negative pathogens [PUBMED:14765110, PUBMED:18688279]. In the case of Parabacteroides distasonis, which is a component of the normal distal human gut microbiota, TAA-like complexes probably modulate adherence to the host (information derived from TOPSAN).
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...
This superfamily all contain a right handed beta helix similar to that first found in pectate lyase .
The clan contains the following 29 members:Adeno_E1B_55K AIDA Beta_helix Chlam_PMP Chondroitinas_B Cthe_2159 Disaggr_assoc DUF1565 DUF2154 DUF2807 DUF3737 DUF4097 DUF4957 End_N_terminal Fil_haemagg Fil_haemagg_2 Glyco_hydro_28 Glyco_hydro_49 Glyco_hydro_92 Haemagg_act NosD Pec_lyase_C Pectate_lyase Pectate_lyase_3 Pectinesterase Pertactin PhageP22-tail Toast_rack_N VacA
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Seed source:||Pfam-B_001516 (release 23.0)|
|Author:||Pollington J , Finn RD|
|Number in seed:||51|
|Number in full:||4123|
|Average length of the domain:||168.10 aa|
|Average identity of full alignment:||19 %|
|Average coverage of the sequence by the domain:||70.56 %|
|HMM build commands:||
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|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 DUF2807 domain has been found. There are 39 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
Loading structure mapping...