Summary: Fungal hydrophobin
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 "Hydrophobin". 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.
Hydrophobin Edit Wikipedia article
Structure of hydrophobin HFBI from Trichoderma reesei
Hydrophobins are a group of small (~100 amino acids) cysteine-rich proteins that are expressed only by filamentous fungi. They are known for their ability to form a hydrophobic (water-repellent) coating on the surface of an object. They were first discovered and separated in Schizophyllum commune in 1991. Based on differences in hydropathy patterns and biophysical properties, they can be divided into two categories: class I and class II. Hydrophobins can self-assemble into a monolayer on hydrophobic:hydrophilic interfaces such as a water:air interface. Class I monolayer contains the same core structure as amyloid fibrils, and is positive to Congo red and thioflavin T. The monolayer formed by class I hydrophobins has a highly ordered structure, and can only be dissociated by concentrated trifluoroacetate or formic acid. Monolayer assembly involves large structural rearrangements with respect to the monomer.
Hydrophobins have been identified in ascomycetes and basidiomycetes; whether they exist in other groups is not known. Hydrophobins are generally found on the outer surface of conidia and of the hyphal wall, and may be involved in mediating contact and communication between the fungus and its environment. Some family members contain multiple copies of the domain.
This family of proteins includes the rodlet proteins of Neurospora crassa (gene eas) and Emericella nidulans (gene rodA), these proteins are the main component of the hydrophobic sheath covering the surface of many fungal spores.
Genomic sequencing of two fungi from dry or salty environments (Wallemia sebi and W. ichthyophaga) revealed that these species contain predicted hydrophobins with unusually high proportion of acidic amino acids and therefore with potentially novel characteristics. High proportion of acidic amino acids is thought to be an adaptation of proteins to high concentrations of salt.
Hydrophobins are characterised by the presence of 8 conserved cysteine residues that form 4 disulphide bonds. They are able to reverse the wettability of surfaces by spontaneous self-assembly of the monomeric proteins into amphipathic monolayers at hydrophobic:hydrophilic surfaces. Despite this common feature, hydrophobins are subdivided into two classes based on differences on their monomeric structure, such as the spacing between the cysteine residues, and based on the different physicochemical properties of the amphipatic monolayers they form  Extensive structural analyses of individual hydrophobins from the two classes have elucidated that the morphological and physical differences between the class I and class II polymer forms are the results of significant structural differences at the monomer-assembly level.
Class I hydrophobins are characterised by having a quite diverse amino acid sequence between different types (with exception of the conserved cysteine residues), and compared to class II, they have long, varied inter-cysteine spacing. They form rodlets which have been identified as functional amyloids due to their amyloid-like characteristics as seen in X-ray diffraction studies and confirmed by their capacity to bind to amyloid-specific dyes such as Congo red and Thioflavin T. The formation of rodlets involves conformational changes  that lead to formation of an extremely robust β-sheet structure  that can only be depolymerised by treatment with strong acids. The rodlets can spontaneously form ordered monolayers by lateral assembly, displaying a regular fibrillary morphology on hydrophobic:hydrophilic interfaces. The most well characterised class I hydrophobin is EAS, which coats the spores of the fungus Neurospora crassa, followed by characterisation of DewA from Aspergillus nidulans.
Class II hydrophobins have overall a more conserved amino acid sequence between the different types and, contrary to class, I they have short, regular inter-cysteine spacing. Opposite to class I, the class II hydrophobins monolayer formed at hydrophobic:hydrophilic interfaces is not fibrillar and it is not associated with formation of amyloid-structures, nor with large conformational changes. Nonetheless, high resolution atomic-force microscopy studies revealed the formation of a notable hexagonal repeating pattern over surfaces coated with the class II hydrophobin HBFI, meaning that these proteins are also able to form an ordered network in surface films.
The crystal structures or HFBI and HFBII from Trichoderma reesei were the first class II hydrophobins to be determined.
Rodlet self-assembly of class I hydrophobins
There is special interest in understanding the mechanism underlying class I monomers self-assembly that leads to formation of tough, ordered amphipathic rodlet monolayers, due to their intrinsic properties and due to substantial information available from several characterisation studies of the class I hydrophobins EAS and DewA. These mechanisms have been greatly studied by targeted mutagenesis in an effort to identify the key amino acid sequence regions driving rodlet self-assembly. A model for the monomeric form of EAS was proposed by Kwan et al. (2006) from structural data obtained from NMR spectroscopy and X-ray diffraction experiments that indicated the presence of four-stranded, antiparallel β-barrel core structure in EAS that allows monomer linking through backbone H-bonding. There are secondary elements around this β-barrel core like the Cys3-Cys4 and Cys7-Cys8 loops. This model is consistent with the amyloid-like structure that class I rodlets form, in which the β-strands are oriented perpendicular to the cross-β scaffold axis of the fibre.
Site-directed mutagenesis of EAS has given insights into the specific structural changes responsible for self-assembly of monomers into rodlets and subsequent formation of amphipathic monolayer in hydrophobic:hydrophilic interfaces. Kwan et al. (2008) reported that the long hydrophobic Cys3-Cys4 loop is not required for rodlet assembly because its deletion does not affect the folding and physical properties of the monomeric protein, neither the morphology of the polymeric rodlet form. Instead, a region of the short Cys7-Cys8 loop, containing mainly uncharged polar residues, has been found to be critical for rodlet assembly.
Characterization of EAS secondary elements involved in rodlet assembly have given insights into the mechanism behind class I hydrophobins self-assembly, but important structural differences with DewA, another class I hydrophobin, suggest that the mechanisms driving rodlet assembly vary among different types of hydrophobins. Like EAS, DewA also has a β-barrel core structure, but it differs significantly from it because of its considerable content of helical secondary elements. A unique feature of DewA is its capacity to exist as two types of conformers in solution, both able to form rodlet assemblies but at different rates. Despite these differences in structural and self-assembly mechanisms, both EAS and DewA form robust fibrillar monolayers, meaning that there must exist several pathways, protein sequences and tertiary conformations able to self-assemble into amphipathic monolayers. Further characterisation of both EAS and DewA and their rodlet self-assembly mechanisms will open up opportunities for rational design of hydrophobins with novel biotechnological applications.
Potentiality for use
Since the very first studies that gave insights into the properties of hydrophobins, these small proteins have been regarded as great candidates for technological use. The detailed understanding of the molecular mechanisms underlying hydrophobin self-assembly into amphipathic monolayer in hydrophobic:hydrophilic interfaces is of great academic interest but mainly of commercial interest. This is because a deep understanding of the elements driving these mechanisms would allow engineering of hydrophobins (or other biomolecules) for nano and biotechnological applications. An example is that the hydrophobin-coating of carbon nanotubes was found to increase their solubility and reduce their toxicity, a finding that increases the prospects of carbon nanotubes to be used as vehicles for drug delivery. Other areas of potential use of hydrophobins include:
- Fabrication and coating of nanodevices and medical implants to increase biocompatibility.
- Emulsifiers in food industry and personal care products.
- Class I high stability can be very useful in the coating of surfaces of prolonged use or under harsh conditions.
- The easy dissociation of a class II hydrophobin monolayer might be desirable and this can easily be achieved by the use of detergents and alcohols.
- The use of hydrophobins in protein purification, drug delivery  and cell attachment has been reported.
- Sunde M, Kwan AH, Templeton MD, Beever RE, Mackay JP (October 2008). "Structural analysis of hydrophobins". Micron. 39 (7): 773–84. doi:10.1016/j.micron.2007.08.003. PMID 17875392.
- Wessels J, De Vries O, Asgeirsdottir SA, Schuren F (1991). "Hydrophobin Genes Involved in Formation of Aerial Hyphae and Fruit Bodies in Schizophyllum". Plant Cell. 3 (8): 793–799. doi:10.1105/tpc.3.8.793. PMC . PMID 12324614.
- Morris V. K.; Linser R.; Wilde K. L.; Duff A. P.; Sunde M.; Kwan A. H. (2012). "Solid-State NMR Spectroscopy of Functional Amyloid from a Fungal Hydrophobin: A Well-Ordered β-Sheet Core Amidst Structural Heterogeneity". Angew. Chem. Int. Ed. 51: 12621–12625. doi:10.1002/anie.201205625.
- Wösten (2001). "Hydrophobins: multipurpose proteins". Annual Review of Microbiology. 55: 625–646. doi:10.1146/annurev.micro.55.1.625. PMID 11544369.
- Whiteford JR, Spanu PD (2001). "The hydrophobin HCf-1 of Cladosporium fulvum is required for efficient water-mediated dispersal of conidia". Fungal Genet. Biol. 32 (3): 159–168. doi:10.1006/fgbi.2001.1263. PMID 11343402.
- Stringer MA, Dean RA, Sewall TC, Timberlake WE (July 1991). "Rodletless, a new Aspergillus developmental mutant induced by directed gene inactivation". Genes Dev. 5 (7): 1161–71. doi:10.1101/gad.5.7.1161. PMID 2065971.
- Lauter FR, Russo VE, Yanofsky C (December 1992). "Developmental and light regulation of eas, the structural gene for the rodlet protein of Neurospora". Genes Dev. 6 (12A): 2373–81. doi:10.1101/gad.6.12a.2373. PMID 1459459.
- Zajc, J.; Liu, Y.; Dai, W.; Yang, Z.; Hu, J.; Gostin Ar, C.; Gunde-Cimerman, N. (2013). "Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: Haloadaptations present and absent". BMC Genomics. 14: 617. doi:10.1186/1471-2164-14-617. PMC . PMID 24034603.
- Madern, D.; Ebel, C.; Zaccai, G. (2000). "Halophilic adaptation of enzymes". Extremophiles : life under extreme conditions. 4 (2): 91–98. doi:10.1007/s007920050142. PMID 10805563.
- Macindoe, I. et al., 2012. Self-assembly of functional, amphipathic amyloid monolayers by the fungal hydrophobin EAS. Proceedings of the National Academy of Sciences, 109(14), pp. E804-E811
- Wessels, J., 1994. Developmental Regulation of Fungal Cell Wall Formation. Annual Review Phytopathology, 32(1), pp. 413-437
- Wessels, J., 1996. Hydrophobins: proteins that change the nature of the fungal surface. Advances in microbial physiology, Volume 38, pp. 1-45
- Kwan, A. et al., 2006. Structural basis for rodlet assembly in fungal hydrophobins. Proceedings of the National Academy of Sciences, 103(10), pp. 3621-3626
- Eichner, T. & Radford, S. E., 2011. A diversity of assembly mechanisms of a generic amyloid fold. Molecular Cell, Volume 43, pp. 8-18
- Wösten, H. & Wessels, J., 1979. Purification and chemical characterization of the rodlet layer of Neurospora crassa conidia. Journal of Bacteriology, Volume 140, pp. 1063-1070
- de Vries, O. M., Fekkes, M. P., Wösten, H. A. & Wessels, J. G., 1993. Insoluble hydrophobin complexes in the walls of Schizophyllum commune and other filamentous fungi. Archives of Microbiology, 159(4), pp. 330-335
- Ren, Q., Kwan, A. & Sunde, M., 2013. Two forms and two faces, multiple states and multiple uses: Properties and applications of the self-assembling fungal hydrophobins. Biopolymers, 100(6), pp. 601-612
- Morris, V., Kwan, A. & Sunde, M., 2012. Analysis of the Structure and Conformational States of DewA Gives Insight into the Assembly of the Fungal Hydrophobins. Journal of Molecular Biology, Volume 452, pp. 245-256
- Szilvay, G. et al., 2007. Self-Assembled Hydrophobin Protein Films at the Air−Water Interface: Structural Analysis and Molecular Engineering. Biochemistry, 46(9), pp. 2345-2354
- Sunde, M. et al., 1997. Common core structure of amyloid fibrils by synchrotron X-ray diffraction. Journal of Molecular Biology, 273(3), pp. 729-739
- Kwan, A. et al., 2008. The Cys3–Cys4 loop of the hydrophobin EAS is not required for rodlet formation and surface activity. Journal of Molecular Biology, 382(3), pp. 708-720
- Morris, V., Kwan, A., Mackay, J. & Sunde, M., 2011. Backbone and sidechain 1H, 13C and 15N chemical shift assignments of the hydrophobin DewA from Aspergillus nidulans. Biomolecular NMR assignments, 6(1), pp. 83-86
- Wessels, J., 1994. Developmental Regulation of Fungal Cell Wall Formation.. Annual Review Phytopathology, 32(1), pp. 413-437
- Yang, W. et al., 2012. Surface functionalization of carbon nanomaterials by self-assembling hydrophobin proteins. Biopolymers, 99(1), pp. 84-94
- Lnder, M. et al., 2004. Efficient Purification of Recombinant Proteins Using Hydrophobins as Tags in Surfactant-Based Two-Phase Systems. Biochemistry, 43(37), pp. 11873-11882
- Collén, A. et al., 2002. Extraction of endoglucanase I (Cel7B) fusion proteins from Trichoderma reesei culture filtrate in a poly(ethylene glycol)–phosphate aqueous two-phase system. Journal of Chromatography A, 943(1), pp. 55-62
- Joensuu, J. et al., 2009. Hydrophobin Fusions for High-Level Transient Protein Expression and Purification in Nicotiana benthamiana. Plant Physiology, 152(2), pp. 622-633
- Akanbi, M. et al., 2010. Use of hydrophobins in formulation of water insoluble drugs for oral administration. Colloids and Surfaces B: Biointerfaces, 75(2), pp. 526-531
- Bimbo, L. et al., 2012. Cellular interactions of surface modified nanoporous silicon particles. Nanoscale, 4(10), pp. 3184-3192
- Sarparanta, M. et al., 2012. Intravenous Delivery of Hydrophobin-Functionalized Porous Silicon Nanoparticles: Stability, Plasma Protein Adsorption and Biodistribution. Mol. Pharmaceutics, 9(3), pp. 654-663
- Nakari-Setala, T. et al., 2002. Expression of a Fungal Hydrophobin in the Saccharomyces cerevisiae Cell Wall: Effect on Cell Surface Properties and Immobilization. Applied and Environmental Microbiology, 68(7), pp. 3385-3391
- Niu, B. et al., 2012. Expression and characterization of hydrophobin HGFI fused with the cell-specific peptide TPS in Pichia pastoris. Protein Expression and Purification, 83(1), pp. 92-97
- Boeuf, S. et al., 2012. Engineering hydrophobin DewA to generate surfaces that enhance adhesion of human but not bacterial cells. Acta Biomaterialia, 8(3), pp. 1037-1047
- Hektor, H. & Scholtmeijer, K., 2005. Hydrophobins: proteins with potential. Current Opinion in Biotechnology, 16(4), pp. 434-439
- Cox, P. & Hooley, P., 2009. Hydrophobins: New prospects for biotechnology. Fungal Biology Reviews, 23(1), pp. 40-47
- Scholtmeijer K (2000). Expression and engineering of hydrophobin genes (Ph.D. thesis). University of Groningen.
- Hakanpää J, Paananen A, Askolin S, Nakari-Setälä T, Parkkinen T, Penttilä M, Linder MB, Rouvinen J (January 2004). "Atomic resolution structure of the HFBII hydrophobin, a self-assembling amphiphile". J. Biol. Chem. 279 (1): 534–9. doi:10.1074/jbc.M309650200. PMID 14555650.
- Wösten HA, de Vocht ML (September 2000). "Hydrophobins, the fungal coat unravelled". Biochim. Biophys. Acta. 1469 (2): 79–86. doi:10.1016/S0304-4157(00)00002-2. PMID 10998570.
- Aimanianda V, Bayry J, Bozza S, Kniemeyer O, Perruccio K, Elluru SR, Clavaud C, Paris S, Brakhage AA, Kaveri SV, Romani L, Latgé JP (August 2009). "Surface hydrophobin prevents immune recognition of airborne fungal spores". Nature. 460 (7259): 1117–21. Bibcode:2009Natur.460.1117A. doi:10.1038/nature08264. PMID 19713928.
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.
Fungal hydrophobin Provide feedback
This is a family of fungal hydrophobins that seems to be restricted to ascomycetes. These are small, moderately hydrophobic extracellular proteins that have eight cysteine residues arranged in a strictly conserved motif. Hydrophobins are generally found on the outer surface of conidia and of the hyphal wall, and may be involved in mediating contact and communication between the fungus and its environment . Note that some family members contain multiple copies.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR010636
This is a family of fungal hydrophobins that seems to be restricted to ascomycetes. Hydrophobins are small, moderately hydrophobic extracellular proteins that have eight cysteine residues arranged in a strictly conserved motif. Hydrophobins are generally found on the outer surface of conidia and of the hyphal wall, and may be involved in mediating contact and communication between the fungus and its environment [PUBMED:11343402]. The family includes cryparin, which is a cell-surface-associated hydrophobin secreted by filamentous fungi [PUBMED:10584000], and cerato-ulmin, a secreted toxin hydrophobin involved in Dutch Elm disease [PUBMED:9344630].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||extracellular region (GO:0005576)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Seed source:||Pfam-B_3587 (release 10.0)|
|Author:||Vella Briffa B|
|Number in seed:||87|
|Number in full:||483|
|Average length of the domain:||63.70 aa|
|Average identity of full alignment:||42 %|
|Average coverage of the sequence by the domain:||44.87 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|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 Hydrophobin_2 domain has been found. There are 26 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...