Summary: DHHC palmitoyltransferase
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 "DHHC domain". 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.
DHHC domain Edit Wikipedia article
A depiction of the topology of DHHC family palmitoyltransferases. Transmembrane alpha helices are represented as black tubes. The DHHC domain is shown as a light orange oval.
In molecular biology the DHHC domain is a protein domain that acts as an enzyme, which adds a palmitoyl chemical group to proteins in order to anchor them to cell membranes. The DHHC domain was discovered in 1999 and named after a conserved sequence motif found in its protein sequence. Roth and colleagues showed that the yeast Akr1p protein could palmitoylate Yck2p in vitro and inferred that the DHHC domain defined a large family of palmitoyltransferases. In mammals twenty three members of this family have been identified and their substrate specificities investigated. Some members of the family such as ZDHHC3 and ZDHHC7 enhance palmitoylation of proteins such as PSD-95, SNAP-25, GAP43, Gαs. Others such as ZDHHC9 showed specificity only toward the H-Ras protein. However, a recent study questions the involvement of classical enzyme-substrate recognition and specificity in the palmitoylation reaction. Several members of the family have been implicated in human diseases.
Conserved motifs within protein sequences point towards the most important amino acid residues for function. In the DHHC domain there is a tetrapeptide motif composed of aspartate-histidine-histidine-cysteine. However this short sequence is embedded in a larger region of about fifty amino acids in length that shares many more conserved amino acids. The canonical DHHC domain can be described with the following sequence motif:
However many examples of DHHC domains are known that do not contain all these conserved residues. In addition to the central DHHC domain three further sequence motifs have been identified in members of the DHHC family. A DPG (aspartate-proline-glycine) motif has been identified just to the C-terminus of the second transmembrane region. A TTxE (threonine-threonine-any-glutamate) motif has also been identified after the fourth transmembrane helix. A third motif towards the C-terminus of many proteins has been identified that contains a conserved aromatic amino acid, a glycine and an asparagine called the PaCCT motif (PAlmitoiltransferase Conserved C-Terminus motif).
In 2006, five chemical classes of small molecules were discovered which were shown to act against palmitoyltransferases. Further studies in 2009 showed that of the 5 classes studied, 2-(2-hydroxy-5-nitro-benzylidene)-benzo[b]thiophen-3-one was shown to behave similarly to 2-Bromopalmitate and were identified as able to inhibit the palmitoylation reaction of a range of DHHC domain containing proteins. Inhibition with 2-Bromopalmitate was found to be irreversible, the other however was found to be mostly reversible. Because of the roles of DHHC domain proteins in human diseases it has been suggested that chemical inhibitors of specific DHHC proteins may be a potential route to treatment of disease.
In human disease
Several proteins containing DHHC domains have been implicated in human disease. Two missense mutations within the DHHC domain of ZDHHC9 were identified in X-linked mental retardation associated with a Marfanoid Habitus. A potential link of ZDHHC11 with bladder cancer has been suggested by the discovery that 5 out of 9 high-grade bladder cancer samples surveyed contained a duplication of the 5p15.33 genomic region. However, this region contains another gene TPPP which may be the causative gene. The HIP14 palmitoyltransferase is responsible for palmitoylating the Huntingtin protein. Expansions of the triplet repeat in the huntington's gene leads to loss of interaction with HIP14 which Yanai and colleagues speculate is involved in the pathology of Huntington's disease. A gene knockout experiment of the mouse homologue of ZDHHC13 showed hair loss, severe osteoporosis, and systemic amyloidosis, both of AL and AA depositions.
Human proteins containing this domain
ZDHHC1; ZDHHC2; ZDHHC3; ZDHHC4; ZDHHC5; ZDHHC6; ZDHHC7; ZDHHC8; ZDHHC9; ZDHHC11; ZDHHC11B; ZDHHC12; ZDHHC13; ZDHHC14; ZDHHC15; ZDHHC16; ZDHHC17; ZDHHC18; ZDHHC19; ZDHHC20; ZDHHC21; ZDHHC22; ZDHHC23; ZDHHC24;
- Putilina T, Wong P, Gentleman S (May 1999). "The DHHC domain: a new highly conserved cysteine-rich motif". Mol. Cell. Biochem. 195 (1–2): 219–26. PMID 10395086. doi:10.1023/A:1006932522197.
- Roth AF, Feng Y, Chen L, Davis NG (October 2002). "The yeast DHHC cysteine-rich domain protein Akr1p is a palmitoyl transferase". J. Cell Biol. 159 (1): 23–8. PMC . PMID 12370247. doi:10.1083/jcb.200206120.
- Fukata Y, Iwanaga T, Fukata M (October 2006). "Systematic screening for palmitoyl transferase activity of the DHHC protein family in mammalian cells". Methods. 40 (2): 177–82. PMID 17012030. doi:10.1016/j.ymeth.2006.05.015.
- Rocks O, Gerauer M, Vartak N, et al. (April 2010). "The palmitoylation machinery is a spatially organizing system for peripheral membrane proteins". Cell. 141 (3): 458–71. PMID 20416930. doi:10.1016/j.cell.2010.04.007.
- Mitchell DA, Vasudevan A, Linder ME, Deschenes RJ (June 2006). "Protein palmitoylation by a family of DHHC protein S-acyltransferases". J. Lipid Res. 47 (6): 1118–27. PMID 16582420. doi:10.1194/jlr.R600007-JLR200.
- González Montoro A, Quiroga R, Maccioni HJ, Valdez Taubas J (April 2009). "A novel motif at the C-terminus of palmitoyltransferases is essential for Swf1 and Pfa3 function in vivo". Biochem. J. 419 (2): 301–8. PMID 19138168. doi:10.1042/BJ20080921.
- Stober R (June 1987). "[Total or subtotal amputation of a long finger with destruction of the metacarpophalangeal joint--regaining function by replantation?]". Aktuelle Traumatol (in German). 17 (3): 100–4. PMID 2888271.
- Jennings BC, Nadolski MJ, Ling Y, et al. (February 2009). "2-Bromopalmitate and 2-(2-hydroxy-5-nitro-benzylidene)-benzobthiophen-3-one inhibit DHHC-mediated palmitoylation in vitro". J. Lipid Res. 50 (2): 233–42. PMC . PMID 18827284. doi:10.1194/jlr.M800270-JLR200.
- Raymond FL, Tarpey PS, Edkins S, et al. (May 2007). "Mutations in ZDHHC9, Which Encodes a Palmitoyltransferase of NRAS and HRAS, Cause X-Linked Mental Retardation Associated with a Marfanoid Habitus". Am. J. Hum. Genet. 80 (5): 982–7. PMC . PMID 17436253. doi:10.1086/513609.
- Yamamoto Y, Chochi Y, Matsuyama H, et al. (2007). "Gain of 5p15.33 is associated with progression of bladder cancer". Oncology. 72 (1–2): 132–8. PMID 18025801. doi:10.1159/111132.
- Yanai A, Huang K, Kang R, et al. (June 2006). "Palmitoylation of huntingtin by HIP14 is essential for its trafficking and function". Nat. Neurosci. 9 (6): 824–31. PMC . PMID 16699508. doi:10.1038/nn1702.
- Saleem AN, Chen YH, Baek HJ, et al. (2010). MacDonald ME, ed. "Mice with Alopecia, Osteoporosis, and Systemic Amyloidosis Due to Mutation in Zdhhc13, a Gene Coding for Palmitoyl Acyltransferase". PLoS Genet. 6 (6): e1000985. PMC . PMID 20548961. doi:10.1371/journal.pgen.1000985.
- Greaves J, Gorleku OA, Salaun C, Chamberlain LH (August 2010). "Palmitoylation of the SNAP25 Protein Family: SPECIFICITY AND REGULATION BY DHHC PALMITOYL TRANSFERASES". J. Biol. Chem. 285 (32): 24629–38. PMC . PMID 20519516. doi:10.1074/jbc.M110.119289.
- Greaves J, Chamberlain LH (April 2010). "S-acylation by the DHHC protein family". Biochem. Soc. Trans. 38 (2): 522–4. PMID 20298214. doi:10.1042/BST0380522.
- Hines RM, Kang R, Goytain A, Quamme GA (February 2010). "Golgi-specific DHHC Zinc Finger Protein GODZ Mediates Membrane Ca2+ Transport". J. Biol. Chem. 285 (7): 4621–8. PMC . PMID 19955568. doi:10.1074/jbc.M109.069849.
- Mizumaru C, Saito Y, Ishikawa T, et al. (December 2009). "Suppression of APP-containing vesicle trafficking and production of beta-amyloid by AID/DHHC-12 protein". J. Neurochem. 111 (5): 1213–24. PMID 19780898. doi:10.1111/j.1471-4159.2009.06399.x.
- Noritake J, Fukata Y, Iwanaga T, et al. (July 2009). "Mobile DHHC palmitoylating enzyme mediates activity-sensitive synaptic targeting of PSD-95". J. Cell Biol. 186 (1): 147–60. PMC . PMID 19596852. doi:10.1083/jcb.200903101.
- Hou H, John Peter AT, Meiringer C, Subramanian K, Ungermann C (August 2009). "Analysis of DHHC acyltransferases implies overlapping substrate specificity and a two-step reaction mechanism". Traffic. 10 (8): 1061–73. PMID 19453970. doi:10.1111/j.1600-0854.2009.00925.x.
- Greaves J, Prescott GR, Fukata Y, Fukata M, Salaun C, Chamberlain LH (March 2009). "The Hydrophobic Cysteine-rich Domain of SNAP25 Couples with Downstream Residues to Mediate Membrane Interactions and Recognition by DHHC Palmitoyl Transferases". Mol. Biol. Cell. 20 (6): 1845–54. PMC . PMID 19158383. doi:10.1091/mbc.E08-09-0944.
- Johswich A, Kraft B, Wuhrer M, et al. (January 2009). "Golgi targeting of Drosophila melanogaster β4GalNAcTB requires a DHHC protein family–related protein as a pilot". J. Cell Biol. 184 (1): 173–83. PMC . PMID 19139268. doi:10.1083/jcb.200801071.
- Matakatsu H, Blair SS (September 2008). "approximated encodes a DHHC palmitoyltransferase that regulates Fat signaling and the subcellular localization and activity of Dachs". Curr. Biol. 18 (18): 1390–5. PMC . PMID 18804377. doi:10.1016/j.cub.2008.07.067.
- Bannan BA, Van Etten J, Kholer JA, et al. (2008). "The Drosophila protein palmitoylome: Characterizing palmitoyl-thioesterases and DHHC palmitoyl-transferases". Fly (Austin). 2 (4): 198–214. PMC . PMID 18719403. doi:10.4161/fly.6621.
- Dighe SA, Kozminski KG (October 2008). "Swf1p, a Member of the DHHC-CRD Family of Palmitoyltransferases, Regulates the Actin Cytoskeleton and Polarized Secretion Independently of Its DHHC Motif". Mol. Biol. Cell. 19 (10): 4454–68. PMC . PMID 18701706. doi:10.1091/mbc.E08-03-0252.
- Lam KK, Davey M, Sun B, Roth AF, Davis NG, Conibear E (July 2006). "Palmitoylation by the DHHC protein Pfa4 regulates the ER exit of Chs3". J. Cell Biol. 174 (1): 19–25. PMC . PMID 16818716. doi:10.1083/jcb.200602049.
- Ohno Y, Kihara A, Sano T, Igarashi Y (April 2006). "Intracellular localization and tissue-specific distribution of human and yeast DHHC cysteine-rich domain-containing proteins". Biochim. Biophys. Acta. 1761 (4): 474–83. PMID 16647879. doi:10.1016/j.bbalip.2006.03.010.
- Mitchell DA, Vasudevan A, Linder ME, Deschenes RJ (June 2006). "Protein palmitoylation by a family of DHHC protein S-acyltransferases". J. Lipid Res. 47 (6): 1118–27. PMID 16582420. doi:10.1194/jlr.R600007-JLR200.
- Hou H, Subramanian K, LaGrassa TJ, et al. (November 2005). "The DHHC protein Pfa3 affects vacuole-associated palmitoylation of the fusion factor Vac8". Proc. Natl. Acad. Sci. U.S.A. 102 (48): 17366–71. PMC . PMID 16301533. doi:10.1073/pnas.0508885102.
- Smotrys JE, Schoenfish MJ, Stutz MA, Linder ME (September 2005). "The vacuolar DHHC-CRD protein Pfa3p is a protein acyltransferase for Vac8p". J. Cell Biol. 170 (7): 1091–9. PMC . PMID 16186255. doi:10.1083/jcb.200507048.
- Gleason EJ, Lindsey WC, Kroft TL, Singson AW, L'hernault SW (January 2006). "spe-10 Encodes a DHHC–CRD Zinc-Finger Membrane Protein Required for Endoplasmic Reticulum/Golgi Membrane Morphogenesis During Caenorhabditis elegans Spermatogenesis". Genetics. 172 (1): 145–58. PMC . PMID 16143610. doi:10.1534/genetics.105.047340.
- Seydel KB, Gaur D, Aravind L, Subramanian G, Miller LH (August 2005). "Plasmodium falciparum: characterization of a late asexual stage golgi protein containing both ankyrin and DHHC domains". Exp. Parasitol. 110 (4): 389–93. PMID 15882865. doi:10.1016/j.exppara.2005.03.030.
- Saitoh F, Tian QB, Okano A, Sakagami H, Kondo H, Suzuki T (July 2004). "NIDD, a novel DHHC-containing protein, targets neuronal nitric-oxide synthase (nNOS) to the synaptic membrane through a PDZ-dependent interaction and regulates nNOS activity". J. Biol. Chem. 279 (28): 29461–8. PMID 15105416. doi:10.1074/jbc.M401471200.
- Nagaya M, Inohaya K, Imai Y, Kudo A (December 2002). "Expression of zisp, a DHHC zinc finger gene, in somites and lens during zebrafish embryogenesis". Gene Expr. Patterns. 2 (3–4): 355–8. PMID 12617825. doi:10.1016/S1567-133X(02)00021-2.
- Uemura T, Mori H, Mishina M (August 2002). "Isolation and characterization of Golgi apparatus-specific GODZ with the DHHC zinc finger domain". Biochem. Biophys. Res. Commun. 296 (2): 492–6. PMID 12163046. doi:10.1016/S0006-291X(02)00900-2.
- Li B, Cong F, Tan CP, Wang SX, Goff SP (August 2002). "Aph2, a protein with a zf-DHHC motif, interacts with c-Abl and has pro-apoptotic activity". J. Biol. Chem. 277 (32): 28870–6. PMID 12021275. doi:10.1074/jbc.M202388200.
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.
DHHC palmitoyltransferase Provide feedback
This entry refers to the DHHC domain, found in DHHC proteins which are palmitoyltransferases . Palmitoylation or, more specifically S-acylation, plays important roles in the regulation of protein localization, stability, and activity. It is a post-translational protein modification that involves the attachment of palmitic acid to Cys residues through a thioester linkage. Protein acyltransferases (PATs), also known as palmitoyltransferases, catalyze this reaction by transferring the palmitoyl group from palmitoyl-CoA to the thiol group of Cys residues. They are characterized by the presence of a 50-residue-long domain called the DHHC domain, which in most but not all cases is also cysteine-rich and gets its name from a highly conserved DHHC signature tetrapeptide (Asp-His-His-Cys). The Cys residue within the DHHC domain forms a stable acyl intermediate and transfers the acyl chain to the Cys residues of a target protein . Some proteins containing a DHHC domain include Drosophila DNZ1 protein  Mouse Abl-philin 2 (Aph2) protein  Mammalian ZDHHC9  Yeast ankyrin repeat-containing protein AKR1  Yeast Erf2 protein  and Arabidopsis thaliana tip growth defective 1 .
Ohno Y, Kashio A, Ogata R, Ishitomi A, Yamazaki Y, Kihara A;, Mol Biol Cell. 2012;23:4543-4551.: Analysis of substrate specificity of human DHHC protein acyltransferases using a yeast expression system. PUBMED:23034182 EPMC:23034182
Gonzalez Montoro A, Chumpen Ramirez S, Valdez Taubas J;, J Biol Chem. 2015;290:22448-22459.: The canonical DHHC motif is not absolutely required for the activity of the yeast S-acyltransferases Swf1 and Pfa4. PUBMED:26224664 EPMC:26224664
Mesilaty-Gross S, Reich A, Motro B, Wides R; , Gene 1999;231:173-186.: The drosophila STAM gene homolog is in a tight gene cluster, and its expression correlates to that of the adjacent gene ial. PUBMED:10231582 EPMC:10231582
Swarthout JT, Lobo S, Farh L, Croke MR, Greentree WK, Deschenes RJ, Linder ME;, J Biol Chem. 2005;280:31141-31148.: DHHC9 and GCP16 constitute a human protein fatty acyltransferase with specificity for H- and N-Ras. PUBMED:16000296 EPMC:16000296
Bartels DJ, Mitchell DA, Dong X, Deschenes RJ; , Mol Cell Biol 1999;19:6775-6787.: Erf2, a Novel Gene Product That Affects the Localization and Palmitoylation of Ras2 in Saccharomyces cerevisiae. PUBMED:10490616 EPMC:10490616
This tab holds annotation information from the InterPro database.
InterPro entry IPR001594
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [PUBMED:10529348, PUBMED:15963892, PUBMED:15718139, PUBMED:17210253, PUBMED:12665246]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [PUBMED:11179890]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 [PUBMED:10231582]. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif [PUBMED:10231582]. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues [PUBMED:17051234]. This domain is found in the DHHC proteins which are palmitoyl transferases [PUBMED:15603741]; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||zinc ion binding (GO:0008270)|
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_945 (release 4.0)|
|Number in seed:||74|
|Number in full:||9980|
|Average length of the domain:||129.10 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||30.39 %|
|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:||19|
|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.