Summary: Hemocyanin, copper containing 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 "Hemocyanin". 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.
Hemocyanin Edit Wikipedia article
|Hemocyanin, copper containing domain|
Single Oxygenated Functional Unit from the hemocyanin of an octopus
|Hemocyanin, all-alpha domain|
Crystal structure of hexameric haemocyanin from Panulirus interruptus refined at 3.2 angstroms resolution
|Hemocyanin, ig-like domain|
crystallographic analysis of oxygenated and deoxygenated states of arthropod hemocyanin shows unusual differences
Hemocyanins (also spelled haemocyanins and abbreviated Hc) are proteins that transport oxygen throughout the bodies of some invertebrate animals. These metalloproteins contain two copper atoms that reversibly bind a single oxygen molecule (O2). They are second only to hemoglobin in frequency of use as an oxygen transport molecule. Unlike the hemoglobin in red blood cells found in vertebrates, hemocyanins are not bound to blood cells but are instead suspended directly in the hemolymph. Oxygenation causes a color change between the colorless Cu(I) deoxygenated form and the blue Cu(II) oxygenated form.
Hemocyanins are found only in the Mollusca and Arthropoda: the earliest discoveries of hemocyanins were in the snail Helix pomatia (a mollusc) and in the horseshoe crab (an arthropod). They were subsequently found to be common among crustaceans and are utilized by some land arthropods such as the tarantula Eurypelma californicum, the emperor scorpion, and the centipede Scutigera coleoptrata. Also, larval storage proteins in many insects appear to be derived from hemocyanins .
The hemocyanin superfamily
Phenoloxidase are copper containing tyrosinases. These proteins are involved in the process of sclerotization of arthropod cuticle, in wound healing, and humoral immune defense. Phenoloxidase is synthesized by zymogens and are activated by cleaving a N-terminal peptide.
Hexamerins are storage proteins commonly found in insects. These proteins are synthesized by the larval fat body and are associated with molting cycles or nutritional conditions.
Pseudohemocyanin and cryptocyanins genetic sequences are closely related to hemocyanins in crustaceans. These proteins have a similar structure and function, but lack the copper binding sites.
The evolutionary changes within the phylogeny of the hemocyanin superfamily are closely related to the emergence of these different proteins in various species. The understanding of proteins within this superfamily would not be well understood without the extensive studies of hemocyanin in arthropods.
Structure and mechanism
Although the respiratory function of hemocyanin is similar to that of hemoglobin, there are a significant number of differences in its molecular structure and mechanism. Whereas hemoglobin carries its iron atoms in porphyrin rings (heme groups), the copper atoms of hemocyanin are bound as prosthetic groups coordinated by histidine residues. The active site of hemocyanin is composed of a pair of copper(I) cations which are directly coordinated to the protein through the driving force of imidazolic rings of six histidine residues. It has been noted that species using hemocyanin for oxygen transportation include crustaceans living in cold environments with low oxygen pressure. Under these circumstances hemoglobin oxygen transportation is less efficient than hemocyanin oxygen transportation. Nevertheless, there are also terrestrial arthropods using hemocyanin, notably spiders and scorpions, that live in warm climates.
Most hemocyanins bind with oxygen non-cooperatively and are roughly one-fourth as efficient as hemoglobin at transporting oxygen per amount of blood. Hemoglobin binds oxygen cooperatively due to steric conformation changes in the protein complex, which increases hemoglobin's affinity for oxygen when partially oxygenated. In some hemocyanins of horseshoe crabs and some other species of arthropods, cooperative binding is observed, with Hill coefficients of 1.6 - 3.0. Hill coefficients vary depending on species and laboratory measurement settings. Hemoglobin, for comparison, has a Hill coefficient of usually 2.8 - 3.0. In these cases of cooperative binding hemocyanin was arranged in protein sub-complexes of 6 subunits (hexamer) each with one oxygen binding site; binding of oxygen on one unit in the complex would increase the affinity of the neighboring units. Each hexamer complex was arranged together to form a larger complex of dozens of hexamers. In one study, cooperative binding was found to be dependent on hexamers being arranged together in the larger complex, suggesting cooperative binding between hexamers. Hemocyanin oxygen-binding profile is also affected by dissolved salt ion levels and pH.
Hemocyanin is made of many individual subunit proteins, each of which contains two copper atoms and can bind one oxygen molecule (O2). Each subunit weighs about 75 kilodaltons (kDa). Subunits may be arranged in dimers or hexamers depending on species; the dimer or hexamer complex is likewise arranged in chains or clusters with weights exceeding 1500 kDa. The subunits are usually homogeneous, or heterogeneous with two variant subunit types. Because of the large size of hemocyanin, it is usually found free-floating in the blood, unlike hemoglobin.
Hexamers are characteristic of arthropod hemocyanins. A hemocyanin of the tarantula Eurypelma californicum is made up of 4 hexamers or 24 pepide chains. A hemocyanin from the house centipede Scutigera coleoptrata is made up of 6 hexamers or 36 chains. Horseshoe crabs have an 8-hexamer (i. e. 48-chain) hemocyanin. Simple hexamers are found in the spiny lobster Panulirus interruptus and the isopod Bathynomus giganteus. Peptide chains in crustaceans are about 660 amino acid residues long, and in chelicerates they are about 625. In the large complexes there is a variety of variant chains, all about the same length; pure components do not usually self-assemble.
Hemocyanin is homologous to the phenol oxidases (e.g. tyrosinase) since both enzymes share type 3 Cu active site coordination. In both cases inactive proenzymes such as hemocyanin, tyrosinase, and catcholoxidase must be activated first. This is done by removing the amino acid that blocks the entrance channel to the active site when the proenzyme is not active. There is currently no other known modifications necessary to activate the proenzyme and enable catalytic activity. Conformational differences determine the type of catalytic activity that the hemocyanin is able to perform. Hemocyanin also exhibits phenol oxidase activity, but with slowed kinetics from greater steric bulk at the active site. Partial denaturation actually improves hemocyanin’s phenol oxidase activity by providing greater access to the active site.
Spectroscopy of oxyhemocyanin shows several salient features:
- Resonance Raman spectroscopy shows symmetric binding
- UV-Vis spectroscopy shows strong absorbances at 350 (20000) and 580 (1000) nm
- OxyHc is EPR-silent indicating the absence of unpaired electrons
- Infrared spectroscopy shows ν(O-O) of 755 cm−1
(1) rules out a mononuclear peroxo complex (2) does not match with the UV-Vis spectra of mononuclear peroxo and Kenneth D. Karlin's dinuclear end-on coordinated trans-peroxo model complexes. (4) shows a considerably weaker O-O bond compared with Karlin's trans-peroxo model.
On the other hand, Nobumasa Kitajima's dinuclear side-on coordinated peroxo model complexes shows ν(O-O) of 741 cm−1 and UV-Vis absorbances at 349 and 551 nm, which agree with the experimental observations for oxyHc. The Cu-Cu separation in the model complex is 3.56 Å, that of oxyhemocyanin is ca. 3.6 Å (deoxyHc: ca. 4.6 Å).
The hemocyanin found in the blood of the Chilean abalone, Concholepas concholepas, has immunotherapeutic effects against bladder cancer in murine models. Mice primed with C. concholepas before implantation of bladder tumor (MBT-2) cells. Mice treated with C. concholepas hemocyanin showed antitumor effects: prolonged survival, decreased tumor growth and incidence, and lack of toxic effects and may have a potential use in future immunotherapy for superficial bladder cancer.
Keyhole limpet hemocyanin (KLH) is an immune stimulant derived from circulating glycoproteins of the marine mollusk Megathura crenulata. KLH has been shown to be a significant treatment against the proliferations of breast cancer, pancreas cancer, and prostate cancer cells when delivered in vitro. Keyhole limpet hemocyanin inhibits growth of human Barrett's esophageal cancer through both apoptic and nonapoptic mechanisms of cell death.
Case studies: environmental impact on hemocyanin levels
A 2003 study of the effect of culture conditions of blood metabolites and hemocyanin of the white shrimp Litopenaeus vannamei found that the levels of hemocyanin, oxyhemocyanin in particular, are affected by the diet. The study compared oxyhemocyanin levels in the blood of white shrimp housed in an indoor pond with a commercial diet with that of white shrimp housed in an outdoor pond with a more readily available protein source (natural live food) as well. Oxyhemocyanin and blood glucose levels were higher in shrimp housed in outdoor ponds. It was also found that blood metabolite levels tended to be lower in low activity level species, such as crabs, lobsters, and the indoor shrimp when compared to the outdoor shrimp. This correlation is possibly indicative of the morphological and physiological evolution of crustaceans. The levels of these blood proteins and metabolites appear to be dependent on energetic demands and availability of those energy sources.
|Wikimedia Commons has media related to Hemocyanin.|
- Coates CJ, Nairn J (July 2014). "Diverse immune functions of hemocyanins". Developmental and Comparative Immunology. 45 (1): 43–55. PMID 24486681. doi:10.1016/j.dci.2014.01.021.
- Voit R, Feldmaier-Fuchs G, Schweikardt T, Decker H, Burmester T (December 2000). "Complete sequence of the 24-mer hemocyanin of the tarantula Eurypelma californicum. Structure and intramolecular evolution of the subunits". The Journal of Biological Chemistry. 275 (50): 39339–44. PMID 10961996. doi:10.1074/jbc.M005442200.
- Jaenicke E, Pairet B, Hartmann H, Decker H (2012). "Crystallization and preliminary analysis of crystals of the 24-meric hemocyanin of the emperor scorpion (Pandinus imperator)". PloS One. 7 (3): e32548. Bibcode:2012PLoSO...732548J. PMC . PMID 22403673. doi:10.1371/journal.pone.0032548. Lay summary – Johannes Gutenberg-Universität Mainz (June 22, 2012).
- Beintema JJ, Stam WT, Hazes B, Smidt MP (1994). "Evolution of arthropod hemocyanins and insect storage proteins (hexamerins)". Mol Biol Evol. 11 (3): 493–503. doi:10.1093/oxfordjournals.molbev.a040129.
- Burmester T (February 2001). "Molecular evolution of the arthropod hemocyanin superfamily". Molecular Biology and Evolution. 18 (2): 184–95. PMID 11158377. doi:10.1093/oxfordjournals.molbev.a003792.
- Rannulu NS, Rodgers MT (March 2005). "Solvation of copper ions by imidazole: structures and sequential binding energies of Cu+(imidazole)x, x = 1-4. Competition between ion solvation and hydrogen bonding". Physical Chemistry Chemical Physics. 7 (5): 1014–25. Bibcode:2005PCCP....7.1014R. PMID 19791394. doi:10.1039/b418141g.
- Strobel A, Hu MY, Gutowska MA, Lieb B, Lucassen M, Melzner F, Pörtner HO, Mark FC (December 2012). "Influence of temperature, hypercapnia, and development on the relative expression of different hemocyanin isoforms in the common cuttlefish Sepia officinalis". Journal of Experimental Zoology. Part A, Ecological Genetics and Physiology. 317 (8): 511–23. PMID 22791630. doi:10.1002/jez.1743.
- Perton FG, Beintema JJ, Decker H (May 1997). "Influence of antibody binding on oxygen binding behavior of Panulirus interruptus hemocyanin". FEBS Letters. 408 (2): 124–6. PMID 9187351. doi:10.1016/S0014-5793(97)00269-X.
- Waxman L (May 1975). "The structure of arthropod and mollusc hemocyanins". The Journal of Biological Chemistry. 250 (10): 3796–806. PMID 1126935.
- van Holde KE, Miller KI (1995). Anfinsen CB, Richards FM, Edsall JT, Eisenberg DS, eds. "Hemocyanins". Advances in Protein Chemistry. 47: 1–81. ISBN 978-0-12-034247-1. PMID 8561049. doi:10.1016/S0065-3233(08)60545-8.
- Kusche K, Hembach A, Hagner-Holler S, Gebauer W, Burmester T (July 2003). "Complete subunit sequences, structure and evolution of the 6 x 6-mer hemocyanin from the common house centipede, Scutigera coleoptrata". European Journal of Biochemistry. 270 (13): 2860–8. PMID 12823556. doi:10.1046/j.1432-1033.2003.03664.x.
- Decker H, Tuczek F (August 2000). "Tyrosinase/catecholoxidase activity of hemocyanins: structural basis and molecular mechanism". Trends in Biochemical Sciences. 25 (8): 392–7. PMID 10916160. doi:10.1016/S0968-0004(00)01602-9.
- Decker H, Schweikardt T, Nillius D, Salzbrunn U, Jaenicke E, Tuczek F (August 2007). "Similar enzyme activation and catalysis in hemocyanins and tyrosinases". Gene. 398 (1-2): 183–91. PMID 17566671. doi:10.1016/j.gene.2007.02.051.
- Freedman TB, Loehr JS, Loehr TM (May 1976). "A resonance Raman study of the copper protein, hemocyanin. New evidence for the structure of the oxygen-binding site". Journal of the American Chemical Society. 98 (10): 2809–15. PMID 942598. doi:10.1021/ja00426a023.
- Karlin KD, Cruse RW, Gultneh Y, Farooq A, Hayes JC, Zubieta J (1987). "Dioxygen-copper reactivity. Reversible binding of O2 and CO to a phenoxo-bridged dicopper(I) complex". Journal of the American Chemical Society. 109 (9): 2668–79. doi:10.1021/ja00243a019.
- Kitajima N, Fujisawa K, Fujimoto C, Morooka Y, Hashimoto S, Kitagawa T, Toriumi K, Tatsumi K, Nakamura A (1992). "A new model for dioxygen binding in hemocyanin. Synthesis, characterization, and molecular structure of the μ-η2:η2 peroxo dinuclear copper(II) complexes, [Cu(BH(3,5-R2pz)3)]2(O2) (R = i-Pr and Ph)". Journal of the American Chemical Society. 114 (4): 1277–91. doi:10.1021/ja00030a025.
- Gaykema WP, Hol WG, Vereijken JM, Soeter NM, Bak HJ, Beintema JJ (1984). "3.2 Å structure of the copper-containing, oxygen-carrying protein Panulirus interruptus haemocyanin". Nature. 309 (5963): 23–9. Bibcode:1984Natur.309...23G. doi:10.1038/309023a0.
- Kodera M, Katayama K, Tachi Y, Kano K, Hirota S, Fujinami S, Suzuki M (1999). "Crystal Structure and Reversible O2-Binding of a Room Temperature Stable μ-η2:η2-Peroxodicopper(II) Complex of a Sterically Hindered Hexapyridine Dinucleating Ligand". Journal of the American Chemical Society. 121 (47): 11006–7. doi:10.1021/ja992295q.
- Atala A (2006). "This Month in Investigative Urology". The Journal of Urology. 176 (6): 2335–6. doi:10.1016/j.juro.2006.09.002.
- McFadden DW, Riggs DR, Jackson BJ, Vona-Davis L (November 2003). "Keyhole limpet hemocyanin, a novel immune stimulant with promising anticancer activity in Barrett's esophageal adenocarcinoma". American Journal of Surgery. 186 (5): 552–5. PMID 14599624. doi:10.1016/j.amjsurg.2003.08.002.
- Pascual C, Gaxiola G, Rosas C (2003). "Blood metabolites and hemocyanin of the white shrimp, Litopenaeus vannamei: The effect of culture conditions and a comparison with other crustacean species". Marine Biology. 142 (4): 735. doi:10.1007/s00227-002-0995-2.
- Rehm P, Pick C, Borner J, Markl J, Burmester T (February 2012). "The diversity and evolution of chelicerate hemocyanins". BMC Evolutionary Biology. 12: 19. PMC . PMID 22333134. doi:10.1186/1471-2148-12-19.
- Ali SA, Abbasi A (2011). Scorpion Hemocyanin: The blue blood. Saarbrücken: VDM Verlag Dr. Müller. p. 160. ISBN 978-3-639-33725-9.
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.
Hemocyanin, copper containing domain Provide feedback
This family includes arthropod hemocyanins and insect larval storage proteins.
Jones G, Brown N, Manczak M, Hiremath S, Kafatos FC; , J Biol Chem 1990;265:8596-8602.: Molecular cloning, regulation, and complete sequence of a hemocyanin-related, juvenile hormone-suppressible protein from insect hemolymph. PUBMED:2341396 EPMC:2341396
Willott E, Wang XY, Wells MA; , J Biol Chem 1989;264:19052-19059.: cDNA and gene sequence of Manduca sexta arylphorin, an aromatic amino acid-rich larval serum protein. Homology to arthropod hemocyanins. PUBMED:2808410 EPMC:2808410
Hazes B, Magnus KA, Bonaventura C, Bonaventura J, Dauter Z, Kalk KH, Hol WG; , Protein Sci 1993;2:597-619.: Crystal structure of deoxygenated Limulus polyphemus subunit II hemocyanin at 2.18 A resolution: clues for a mechanism for allosteric regulation. PUBMED:8518732 EPMC:8518732
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000896
Crustacean and cheliceratan hemocyanins (oxygen-transport proteins) and insect hexamerins (storage proteins) are homologous gene products, although the latter do not bind oxygen [PUBMED:8015442].
Haemocyanins are found in the haemolymph of many invertebrates. They are divided into 2 main groups, arthropodan and molluscan. These have structurally similar oxygen-binding centres, which are similar to the oxygen-binding centre of tyrosinases, but their quaternary structures are arranged differently. The arthropodan proteins exist as hexamers comprising 3 heterogeneous subunits (a, b and c) and possess 1 oxygen-binding centre per subunit; and the molluscan proteins exist as cylindrical oligomers of 10 to 20 subunits and possess 7 or 8 oxygen-binding centres per subunit [PUBMED:3207675]. Although the proteins have similar amino acid compositions, the only real similarity in their primary sequences is in the region corresponding to the second copper-binding domain, which also shows similarity to the copper-binding domain of tyrosinases.
Hexamerins are proteins from the hemolymph of insects, which may serve as a store of amino acids for synthesis of adult proteins. They do not possess the copper-binding histidines present in hemocyanins [PUBMED:8015442].
Homologues are also present in other kinds of organism, for example, AsqI from the yeast Emericella nidulans. This is a tyrosinase involved in biosynthesis of the aspoquinolone mycotoxins, though its exact function is unknown [PUBMED:25251934].This entry represents the middle domain of hemocyanin and hexamerin proteins, which is involved in copper binding in hemocyanins.
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.
|Author:||Finn RD, Sonnhammer ELL, Griffiths-Jones SR|
|Number in seed:||91|
|Number in full:||393|
|Average length of the domain:||256.80 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||38.24 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 5 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Hemocyanin_M domain has been found. There are 60 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...