Summary: Dynactin p62 family
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "Dynactin". 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.
Dynactin Edit Wikipedia article
Dynactin was identified as an activity that allowed purified cytoplasmic dynein to move membrane vesicles along microtubules in vitro. It was shown to be a multiprotein complex and named "dynactin" because of its role in dynein activation.
The main features of dynactin were visualized by quick-freeze, deep-etch, rotary shadow electron microscopy. It appears as a short filament, 37-nm in length, which resembles F-actin, plus a thinner, laterally oriented arm. Antibody labelling was used to map the location of the dynactin subunits.
Dynactin consists of three major structural domains: (1) sidearm-shoulder: DCTN1/p150Glued, DCTN2/p50/dynamitin, DCTN3/p24/p22;(2)the Arp1 filament: ACTR1A/Arp1/centractin, actin, CapZ; and (3) the pointed end complex: Actr10/Arp11, DCTN4/p62, DCTN5/p25, and DCTN6/p27.
A 4Ã… cryo-EM structure of dynactin  revealed that its filament contains eight Arp1 molecules, one Î²-actin and one Arp11. In the pointed end complex p62/DCTN4 binds to Arp11 and Î²-actin and p25 and p27 bind both p62 and Arp11. At the barbed end the capping protein (CapZÎ±Î²) binds the Arp1 filament in the same way that it binds actin, although with more charge complementarity, explaining why it binds dynactin more tightly than actin.
The shoulder contains two copies of p150Glued/DCTN1, four copies of p50/DCTN2 and two copies of p24/DCTN3. These proteins form long bundles of alpha helices, which wrap over each other and contact the Arp1 filament. The N-termini of p50/DCTN2 emerge from the shoulder and coat the filament, providing a mechanism for controlling the filament length. The C-termini of the p150Glued/DCTN1 dimer are embedded in the shoulder, whereas the N-terminal 1227 amino acids form the projecting arm. The arm consists of an N-terminal CAPGly domain which can bind the C-terminal tails of microtubules and the microtubule plus end binding protein EB1. This is followed by a basic region, also involved in microtubule binding, a folded-back coiled coil (CC1), the intercoiled domain (ICD) and a second coiled coil domain (CC2). The p150Glued arm can dock into against the side of the Arp1 filament and pointed end complex.
DCTN2 (dynamitin) is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development. Arp1 has been suggested as the domain for dynactin binding to membrane vesicles (such as Golgi or late endosome) through its association with Î²-spectrin. The pointed end complex (PEC) has been shown to be involved in selective cargo binding. PEC subunits p62/DCTN4 and Arp11/Actr10 are essential for dynactin complex integrity and dynactin/dynein targeting to the nuclear envelope before mitosis. Actr10 along with Drp1 (Dynamin related protein 1) have been documented as vital to the attachment of mitochondria to the dynactin complex. Dynactin p25/DCTN5 and p27/DCTN6 are not essential for dynactin complex integrity, but are required for early and recycling endosome transport during the interphase and regulation of the spindle assembly checkpoint in mitosis.
Interaction with dynein
Dynein and dynactin were reported to interact directly by the binding of dynein intermediate chains with p150Glued. The affinity of this interaction is around 3.5Î¼M. Dynein and dynactin do not run together in a sucrose gradient, but can be induced to form a tight complex in the presence of the N-terminal 400 amino acids of Bicaudal D2 (BICD2), a cargo adaptor that links dynein and dynactin to Golgi derived vesicles. In the presence of BICD2, dynactin binds to dynein and activates it to move for long distances along microtubules.
A cryo-EM structure of dynein, dynactin and BICD2  showed that the BICD2 coiled coil runs along the dynactin filament. The tail of dynein also binds to the Arp1 filament, sitting in the equivalent site that myosin uses to bind actin. The contacts between the dynein tail and dynactin all involve BICD, explaining why it is needed to bring them together. The dynein/dynactin/BICD2 (DDB) complex has also been observed, by negative stain EM, on microtubules. This shows that the cargo (Rab6) binding end of BICD2 extends out through the pointed end complex at the opposite end away from the dynein motor domains.
Dynactin is often essential for dynein activity and can be thought of as a "dynein receptor" that modulates binding of dynein to cell organelles which are to be transported along microtubules. Dynactin also enhances the processivity of cytoplasmic dynein and kinesin-2 motors. Dynactin is involved in various processes like chromosome alignment and spindle organization in cell division. Dynactin contributes to mitotic spindle pole focusing through its binding to nuclear mitotic apparatus protein (NuMA). Dynactin also targets to the kinetochore through binding between DCTN2/dynamitin and zw10 and has a role in mitotic spindle checkpoint inactivation. During prometaphase, dynactin also helps target polo-like kinase 1 (Plk1) to kinetochores through cyclin dependent kinase 1 (Cdk1)-phosphorylated DCTN6/p27, which is involved in proper microtubule-kinetochore attachment and recruitment of spindle assembly checkpoint protein Mad1. In addition, dynactin has been shown to play an essential role in maintaining nuclear position in Drosophila, zebrafish or in different fungi. Dynein and dynactin concentrate on the nuclear envelope during the prophase and facilitate nuclear envelope breakdown via its DCTN4/p62 and Arp11 subunits. Dynactin is also required for microtubule anchoring at centrosomes and centrosome integrity. Destabilization of the centrosomal pool of dynactin also causes abnormal G1 centriole separation and delayed entry into S phase, suggesting that dynactin contributes to the recruitment of important cell cycle regulators to centrosomes. In addition to transport of various organelles in the cytoplasm, dynactin also links kinesin II to organelles.
- Schroer TA (November 2004). "Dynactin". Annual Review of Cell and Developmental Biology. 20: 759â€“79. doi:10.1146/annurev.cellbio.20.012103.094623. PMID 15473859.
- Carter AP, Diamant AG, Urnavicius L (April 2016). "How dynein and dynactin transport cargos: a structural perspective". Current Opinion in Structural Biology. 37: 62â€“70. doi:10.1016/j.sbi.2015.12.003. PMID 26773477.
- Schroer TA, Sheetz MP (December 1991). "Two activators of microtubule-based vesicle transport". The Journal of Cell Biology. 115 (5): 1309â€“18. doi:10.1083/jcb.115.5.1309. PMC 2289226. PMID 1835460.
- Gill SR, Schroer TA, Szilak I, Steuer ER, Sheetz MP, Cleveland DW (December 1991). "Dynactin, a conserved, ubiquitously expressed component of an activator of vesicle motility mediated by cytoplasmic dynein". The Journal of Cell Biology. 115 (6): 1639â€“50. doi:10.1083/jcb.115.6.1639. PMC 2289205. PMID 1836789.
- Schafer DA, Gill SR, Cooper JA, Heuser JE, Schroer TA (July 1994). "Ultrastructural analysis of the dynactin complex: an actin-related protein is a component of a filament that resembles F-actin". The Journal of Cell Biology. 126 (2): 403â€“12. doi:10.1083/jcb.126.2.403. PMC 2200042. PMID 7518465.
- Eckley DM, Gill SR, Melkonian KA, Bingham JB, Goodson HV, Heuser JE, Schroer TA (October 1999). "Analysis of dynactin subcomplexes reveals a novel actin-related protein associated with the arp1 minifilament pointed end". The Journal of Cell Biology. 147 (2): 307â€“20. doi:10.1083/jcb.147.2.307. PMC 2174220. PMID 10525537.
- Cheong FK, Feng L, Sarkeshik A, Yates JR, Schroer TA (July 2014). "Dynactin integrity depends upon direct binding of dynamitin to Arp1". Molecular Biology of the Cell. 25 (14): 2171â€“80. doi:10.1091/mbc.E14-03-0842. PMC 4091830. PMID 24829381.
- Uetake Y, Terada Y, Matuliene J, Kuriyama R (May 2004). "Interaction of Cep135 with a p50 dynactin subunit in mammalian centrosomes". Cell Motility and the Cytoskeleton. 58 (1): 53â€“66. doi:10.1002/cm.10175. PMID 14983524.
- Holleran EA, Tokito MK, Karki S, Holzbaur EL (December 1996). "Centractin (ARP1) associates with spectrin revealing a potential mechanism to link dynactin to intracellular organelles". The Journal of Cell Biology. 135 (6 Pt 2): 1815â€“29. doi:10.1083/jcb.135.6.1815. PMC 2133946. PMID 8991093.
- Holleran EA, Ligon LA, Tokito M, Stankewich MC, Morrow JS, Holzbaur EL (September 2001). "beta III spectrin binds to the Arp1 subunit of dynactin". The Journal of Biological Chemistry. 276 (39): 36598â€“605. doi:10.1074/jbc.M104838200. PMID 11461920.
- Muresan V, Stankewich MC, Steffen W, Morrow JS, Holzbaur EL, Schnapp BJ (January 2001). "Dynactin-dependent, dynein-driven vesicle transport in the absence of membrane proteins: a role for spectrin and acidic phospholipids". Molecular Cell. 7 (1): 173â€“83. doi:10.1016/S1097-2765(01)00165-4. PMID 11172722.
- Johansson M, Rocha N, Zwart W, Jordens I, Janssen L, Kuijl C, Olkkonen VM, Neefjes J (February 2007). "Activation of endosomal dynein motors by stepwise assembly of Rab7-RILP-p150Glued, ORP1L, and the receptor betalll spectrin". The Journal of Cell Biology. 176 (4): 459â€“71. doi:10.1083/jcb.200606077. PMC 2063981. PMID 17283181.
- Salina D, Bodoor K, Eckley DM, Schroer TA, Rattner JB, Burke B (January 2002). "Cytoplasmic dynein as a facilitator of nuclear envelope breakdown". Cell. 108 (1): 97â€“107. doi:10.1016/S0092-8674(01)00628-6. PMID 11792324.
- Zhang J, Wang L, Zhuang L, Huo L, Musa S, Li S, Xiang X (July 2008). "Arp11 affects dynein-dynactin interaction and is essential for dynein function in Aspergillus nidulans". Traffic. 9 (7): 1073â€“87. doi:10.1111/j.1600-0854.2008.00748.x. PMC 2586032. PMID 18410488.
- Yeh TY, Quintyne NJ, Scipioni BR, Eckley DM, Schroer TA (October 2012). "Dynactin's pointed-end complex is a cargo-targeting module". Molecular Biology of the Cell. 23 (19): 3827â€“37. doi:10.1091/mbc.E12-07-0496. PMC 3459859. PMID 22918948.
- Catherine Drerup, Amy Herbert, Kelly Monk, Alex Nechiporuk, "Regulation of mitochondria-dynactin interaction and mitochondrial retrograde transport in axons"
- Zhang J, Yao X, Fischer L, Abenza JF, PeÃ±alva MA, Xiang X (June 2011). "The p25 subunit of the dynactin complex is required for dynein-early endosome interaction". The Journal of Cell Biology. 193 (7): 1245â€“55. doi:10.1083/jcb.201011022. PMC 3216330. PMID 21708978.
- Yeh TY, Kowalska AK, Scipioni BR, Cheong FK, Zheng M, Derewenda U, Derewenda ZS, Schroer TA (April 2013). "Dynactin helps target Polo-like kinase 1 to kinetochores via its left-handed beta-helical p27 subunit". The EMBO Journal. 32 (7): 1023â€“35. doi:10.1038/emboj.2013.30. PMC 3616283. PMID 23455152.
- Vaughan KT, Vallee RB (December 1995). "Cytoplasmic dynein binds dynactin through a direct interaction between the intermediate chains and p150Glued". The Journal of Cell Biology. 131 (6 Pt 1): 1507â€“16. doi:10.1083/jcb.131.6.1507. PMC 2120689. PMID 8522607.
- Morgan JL, Song Y, Barbar E (November 2011). "Structural dynamics and multiregion interactions in dynein-dynactin recognition". The Journal of Biological Chemistry. 286 (45): 39349â€“59. doi:10.1074/jbc.M111.296277. PMC 3234759. PMID 21931160.
- Splinter D, Razafsky DS, Schlager MA, Serra-Marques A, Grigoriev I, Demmers J, Keijzer N, Jiang K, Poser I, Hyman AA, Hoogenraad CC, King SJ, Akhmanova A (November 2012). "BICD2, dynactin, and LIS1 cooperate in regulating dynein recruitment to cellular structures". Molecular Biology of the Cell. 23 (21): 4226â€“41. doi:10.1091/mbc.E12-03-0210. PMC 3484101. PMID 22956769.
- Schlager MA, Hoang HT, Urnavicius L, Bullock SL, Carter AP (September 2014). "In vitro reconstitution of a highly processive recombinant human dynein complex". The EMBO Journal. 33 (17): 1855â€“68. doi:10.15252/embj.201488792. PMC 4158905. PMID 24986880.
- McKenney RJ, Huynh W, Tanenbaum ME, Bhabha G, Vale RD (July 2014). "Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes". Science. 345 (6194): 337â€“41. doi:10.1126/science.1254198. PMC 4224444. PMID 25035494.
- Chowdhury S, Ketcham SA, Schroer TA, Lander GC (April 2015). "Structural organization of the dynein-dynactin complex bound to microtubules". Nature Structural & Molecular Biology. 22 (4): 345â€“7. doi:10.1038/nsmb.2996. PMC 4385409. PMID 25751425.
- Schroer TA, Sheetz MP (December 1991). "Two activators of microtubule-based vesicle transport". The Journal of Cell Biology. 115 (5): 1309â€“18. doi:10.1083/jcb.115.5.1309. PMC 2289226. PMID 1835460.
- Waterman-Storer CM, Karki SB, Kuznetsov SA, Tabb JS, Weiss DG, Langford GM, Holzbaur EL (October 1997). "The interaction between cytoplasmic dynein and dynactin is required for fast axonal transport". Proceedings of the National Academy of Sciences of the United States of America. 94 (22): 12180â€“5. doi:10.1073/pnas.94.22.12180. PMC 23743. PMID 9342383.
- McGrail M, Gepner J, Silvanovich A, Ludmann S, Serr M, Hays TS (October 1995). "Regulation of cytoplasmic dynein function in vivo by the Drosophila Glued complex". The Journal of Cell Biology. 131 (2): 411â€“25. doi:10.1083/jcb.131.2.411. PMC 2199972. PMID 7593168.
- King SJ, Schroer TA (January 2000). "Dynactin increases the processivity of the cytoplasmic dynein motor". Nature Cell Biology. 2 (1): 20â€“4. doi:10.1038/71338. PMID 10620802.
- Berezuk MA, Schroer TA (February 2007). "Dynactin enhances the processivity of kinesin-2". Traffic. 8 (2): 124â€“9. doi:10.1111/j.1600-0854.2006.00517.x. PMID 17181772.
- Echeverri CJ, Paschal BM, Vaughan KT, Vallee RB (February 1996). "Molecular characterization of the 50-kD subunit of dynactin reveals function for the complex in chromosome alignment and spindle organization during mitosis". The Journal of Cell Biology. 132 (4): 617â€“33. doi:10.1083/jcb.132.4.617. PMC 2199864. PMID 8647893.
- Karki S, Holzbaur EL (February 1999). "Cytoplasmic dynein and dynactin in cell division and intracellular transport". Current Opinion in Cell Biology. 11 (1): 45â€“53. doi:10.1016/S0955-0674(99)80006-4. PMID 10047518.
- Gaglio T, Saredi A, Bingham JB, Hasbani MJ, Gill SR, Schroer TA, Compton DA (October 1996). "Opposing motor activities are required for the organization of the mammalian mitotic spindle pole". The Journal of Cell Biology. 135 (2): 399â€“414. doi:10.1083/jcb.135.2.399. PMC 2121053. PMID 8896597.
- Merdes A, Heald R, Samejima K, Earnshaw WC, Cleveland DW (May 2000). "Formation of spindle poles by dynein/dynactin-dependent transport of NuMA". The Journal of Cell Biology. 149 (4): 851â€“62. doi:10.1083/jcb.149.4.851. PMC 2174573. PMID 10811826.
- Howell BJ, McEwen BF, Canman JC, Hoffman DB, Farrar EM, Rieder CL, Salmon ED (December 2001). "Cytoplasmic dynein/dynactin drives kinetochore protein transport to the spindle poles and has a role in mitotic spindle checkpoint inactivation". The Journal of Cell Biology. 155 (7): 1159â€“72. doi:10.1083/jcb.200105093. PMC 2199338. PMID 11756470.
- Starr DA, Williams BC, Hays TS, Goldberg ML (August 1998). "ZW10 helps recruit dynactin and dynein to the kinetochore". The Journal of Cell Biology. 142 (3): 763â€“74. doi:10.1083/jcb.142.3.763. PMC 2148168. PMID 9700164.
- Whited JL, Cassell A, Brouillette M, Garrity PA (October 2004). "Dynactin is required to maintain nuclear position within postmitotic Drosophila photoreceptor neurons". Development. 131 (19): 4677â€“86. doi:10.1242/dev.01366. PMC 2714772. PMID 15329347.
- Tsujikawa M, Omori Y, Biyanwila J, Malicki J (September 2007). "Mechanism of positioning the cell nucleus in vertebrate photoreceptors". Proceedings of the National Academy of Sciences of the United States of America. 104 (37): 14819â€“24. doi:10.1073/pnas.0700178104. PMC 1976238. PMID 17785424.
- Xiang X, Han G, Winkelmann DA, Zuo W, Morris NR (May 2000). "Dynamics of cytoplasmic dynein in living cells and the effect of a mutation in the dynactin complex actin-related protein Arp1". Current Biology. 10 (10): 603â€“6. doi:10.1016/S0960-9822(00)00488-7. PMID 10837229.
- Bruno KS, Tinsley JH, Minke PF, Plamann M (May 1996). "Genetic interactions among cytoplasmic dynein, dynactin, and nuclear distribution mutants of Neurospora crassa". Proceedings of the National Academy of Sciences of the United States of America. 93 (10): 4775â€“80. doi:10.1073/pnas.93.10.4775. PMC 39355. PMID 8643479.
- Quintyne NJ, Gill SR, Eckley DM, Crego CL, Compton DA, Schroer TA (October 1999). "Dynactin is required for microtubule anchoring at centrosomes". The Journal of Cell Biology. 147 (2): 321â€“34. doi:10.1083/jcb.147.2.321. PMC 2174233. PMID 10525538.
- Quintyne NJ, Schroer TA (October 2002). "Distinct cell cycle-dependent roles for dynactin and dynein at centrosomes". The Journal of Cell Biology. 159 (2): 245â€“54. doi:10.1083/jcb.200203089. PMC 2173046. PMID 12391026.
- Deacon SW, Serpinskaya AS, Vaughan PS, Lopez Fanarraga M, Vernos I, Vaughan KT, Gelfand VI (February 2003). "Dynactin is required for bidirectional organelle transport". The Journal of Cell Biology. 160 (3): 297â€“301. doi:10.1083/jcb.200210066. PMC 2172679. PMID 12551954.
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.
Dynactin p62 family Provide feedback
Dynactin is a multi-subunit complex and a required cofactor for most, or all, of the cellular processes powered by the microtubule-based motor cytoplasmic dynein. p62 binds directly to the Arp1 subunit of dynactin [1,2].
Internal database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR008603
DCTN4 (also known as dynactin subunit p62) is a subunit of the dynactin that may have a dual role in dynein targeting and in ACTR1A/Arp1 subunit of dynactin pointed-end capping. It could be involved in ACTR1A pointed-end binding and in additional roles in linking dynein and dynactin to the cortical cytoskeleton [ PUBMED:10607597 ]. It also interacts with the N terminus of P-type ATPase ATP7B [ PUBMED:16554302 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||dynactin complex (GO:0005869)|
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 and the UniProtKB 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
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_4912 (release 8.0)|
|Number in seed:||25|
|Number in full:||2061|
|Average length of the domain:||230.70 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||69.16 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|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.
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 Dynactin_p62 domain has been found. There are 10 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...