Summary: TAL effector repeat
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 "TAL effector". 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.
TAL effector Edit Wikipedia article
TAL (transcription activator-like) effectors (often referred to as TALEs, but not to be confused with the three amino acid loop extension homeobox class of proteins) are proteins secreted by Xanthomonas bacteria via their type III secretion system when they infect various plant species. These proteins can bind promoter sequences in the host plant and activate the expression of plant genes that aid bacterial infection. They recognize plant DNA sequences through a central repeat domain consisting of a variable number of ~34 amino acid repeats. There appears to be a one-to-one correspondence between the identity of two critical amino acids in each repeat and each DNA base in the target sequence. These proteins are interesting to researchers both for their role in disease of important crop species and the relative ease of retargeting them to bind new DNA sequences. Similar proteins can be found in the pathogenic bacterium Ralstonia solanacearum and Burkholderia rhizoxinica., as well as yet unidentified marine microorganisms. The term TALE-likes is used to refer to the putative protein family encompassing the TALEs and these related proteins.
Function in plant pathogenesis
Xanthomonas are Gram-negative bacteria that can infect a wide variety of plant species including pepper, rice, citrus, cotton, tomato, and soybeans. Some types of Xanthomonas cause localized leaf spot or leaf streak while others spread systemically and cause black rot or leaf blight disease. They inject a number of effector proteins, including TAL effectors, into the plant via their type III secretion system. TAL effectors have several motifs normally associated with eukaryotes including multiple nuclear localization signals and an acidic activation domain. When injected into plants, these proteins can enter the nucleus of the plant cell, bind plant promoter sequences, and activate transcription of plant genes that aid in bacterial infection. Plants have developed a defense mechanism against type III effectors that includes R (resistance) genes triggered by these effectors. Some of these R genes appear to have evolved to contain TAL-effector binding sites similar to site in the intended target gene. This competition between pathogenic bacteria and the host plant has been hypothesized to account for the apparently malleable nature of the TAL effector DNA binding domain.
The most distinctive characteristic of TAL effectors is a central repeat domain containing between 1.5 and 33.5 repeats that are usually 34 residues in length (the C-terminal repeat is generally shorter and referred to as a “half repeat”). A typical repeat sequence is LTPEQVVAIASHDGGKQALETVQRLLPVLCQAHG, but the residues at the 12th and 13th positions are hypervariable (these two amino acids are also known as the repeat variable diresidue or RVD). Two separate groups have shown that there is a simple relationship between the identity of these two residues in sequential repeats and sequential DNA bases in the TAL effector’s target site. The first group, headed by Adam Bogdanove, broke this code computationally by searching for patterns in protein sequence alignments and DNA sequences of target promoters. The second group deduced the code through molecular analysis of the TAL effector AvrBs3 and its target DNA sequence in the promoter of a pepper gene activated by AvrBs3. The experimentally validated code between RVD sequence and target DNA base can be expressed as NI = A, HD = C, NG = T, NN = R (G or A), and NS = N (A, C, G, or T). Further studies have shown that the RVD code NG (but not HD) can target 5-methyl-C. Also, the RVD NK can target G, although TAL effector nucleases (TALEN) that exclusively use NK instead of NN to target G can be less active. The crystal structure of a TAL effector bound to DNA indicates that each repeat comprises two alpha helices and a short RVD-containing loop where the second residue of the RVD makes sequence-specific DNA contacts while the first residue of the RVD stabilizes the RVD-containing loop. Target sites of TAL effectors also tend to include a thymine flanking the 5’ base targeted by the first repeat; this appears to be due to a contact between this T and a conserved tryptophan in the region N-terminal of the central repeat domain. However, this "zero" position does not always contain a thymine, as some scaffolds are more permissive.
Engineering TAL effectors
This simple correspondence between amino acids in TAL effectors and DNA bases in their target sites makes them useful for protein engineering applications. Numerous groups have designed artificial TAL effectors capable of recognizing new DNA sequences in a variety of experimental systems. Such engineered TAL effectors have been used to create artificial transcription factors that can be used to target and activate or repress endogenous genes in tomato, Arabidopsis thaliana, and human cells.
Genetic constructs to encode TAL effector-based proteins can be made using either conventional gene synthesis or modular assembly. A plasmid kit for assembling custom TALEN® and other TAL effector constructs is available through the public, not-for-profit repository Addgene. Webpages providing access to public software, protocols, and other resources for TAL effector-DNA targeting applications include the TAL Effector-Nucleotide Targeter and taleffectors.com.
TAL effectors can induce susceptibility genes that are members of the NODULIN3 (N3) gene family. These genes are essential for the development of the disease. In rice two genes,Os-8N3 and Os-11N3, are induced by TAL effectors. Os-8N3 is induced by PthXo1 and Os-11N3 is induced by PthXo3 and AvrXa7. Two hypotheses exist about possible functions for N3 proteins:
- They are involved in copper transport, resulting in detoxification of the environment for bacteria. The reduction in copper level facilitates bacterial growth.
- They are involved in glucose transport, facilitating glucose flow. This mechanism provides nutrients to bacteria and stimulates pathogen growth and virulence
Engineered TAL effectors can also be fused to the cleavage domain of FokI to create TAL effector nucleases (TALEN) or to meganucleases (nucleases with longer recognition sites) to create "megaTALs." Such fusions share some properties with zinc finger nucleases and may be useful for genetic engineering and gene therapy applications.
TALEN-based approaches are used in the emerging fields of gene editing and genome engineering. TALEN fusions show activity in a yeast-based assay, at endogenous yeast genes, in a plant reporter assay, at an endogenous plant gene, at endogenous zebrafish genes, at an endogenous rat gene, and at endogenous human genes. The human HPRT1 gene has been targeted at detectable, but unquantified levels. In addition, TALEN constructs containing the FokI cleavage domain fused to a smaller portion of the TAL effector still containing the DNA binding domain have been used to target the endogenous NTF3 and CCR5 genes in human cells with efficiencies of up to 25%. TAL effector nucleases have also been used to engineer human embryonic stem cells and induced pluripotent stem cells (IPSCs) and to knock out the endogenous ben-1 gene in C. elegans.
- Heuer, H.; Yin, Y. -N.; Xue, Q. -Y.; Smalla, K.; Guo, J. -H. (2007). "Repeat Domain Diversity of avrBs3-Like Genes in Ralstonia solanacearum Strains and Association with Host Preferences in the Field". Applied and Environmental Microbiology. 73 (13): 4379–4384. doi:10.1128/AEM.00367-07. PMC . PMID 17468277.
- Lixin Li; Ahmed Atef; Agnieszka Piatek; Zahir Ali; Marek Piatek; Mustapha Aouida; Altanbadralt Sharakuu; Ali Mahjoub; Guangchao Wang; Suhail Khan; Nina V Fedoroff; Jian-Kang Zhu; Magdy M Mahfouz (July 2013). "Characterization and DNA-binding specificities of Ralstonia TAL-like effectors". Molecular plant. 6 (4): 1318–1330. doi:10.1093/mp/sst006. PMC . PMID 23300258.
- de Lange, Orlando; Christina Wolf; Jörn Dietze; Janett Elsaesser; Robert Morbitzer; Thomas Lahaye (2014). "Programmable DNA-binding proteins from Burkholderia provide a fresh perspective on the TALE-like repeat domain". Nucleic Acids Research. 42 (11): 7436–49. doi:10.1093/nar/gku329. PMC . PMID 24792163.
- de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas (19 October 2015). "DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats". Nucleic Acids Research. 43: gkv1053. doi:10.1093/nar/gkv1053. PMC . PMID 26481363.
- Boch J, Bonas U (September 2010). "XanthomonasAvrBs3 Family-Type III Effectors: Discovery and Function". Annual Review of Phytopathology. 48: 419–36. doi:10.1146/annurev-phyto-080508-081936. PMID 19400638.
- Voytas DF, Joung JK (December 2009). "Plant science. DNA binding made easy". Science. 326 (5959): 1491–2. Bibcode:2009Sci...326.1491V. doi:10.1126/science.1183604. PMID 20007890.
- Moscou MJ, Bogdanove AJ (December 2009). "A simple cipher governs DNA recognition by TAL effectors". Science. 326 (5959): 1501. Bibcode:2009Sci...326.1501M. doi:10.1126/science.1178817. PMID 19933106.
- Boch J, Scholze H, Schornack S, et al. (December 2009). "Breaking the code of DNA binding specificity of TAL-type III effectors". Science. 326 (5959): 1509–12. Bibcode:2009Sci...326.1509B. doi:10.1126/science.1178811. PMID 19933107.
- Deng D, Yin P, Yan C, Pan X, Gong X, Qi S, Xie T, Mahfouz M, Zhu JK, Yan N, Shi Y (Sep 4, 2012). "Recognition of methylated DNA by TAL effectors". Cell Research. 22 (10): 1502–4. doi:10.1038/cr.2012.127. PMC . PMID 22945353.
- Morbitzer, R.; Romer, P.; Boch, J.; Lahaye, T. (2010). "Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors". Proceedings of the National Academy of Sciences. 107 (50): 21617–21622. Bibcode:2010PNAS..10721617M. doi:10.1073/pnas.1013133107. PMC . PMID 21106758.
- Miller, J. C.; Tan, S.; Qiao, G.; Barlow, K. A.; Wang, J.; Xia, D. F.; Meng, X.; Paschon, D. E.; Leung, E.; Hinkley, S. J.; Dulay, G. P.; Hua, K. L.; Ankoudinova, I.; Cost, G. J.; Urnov, F. D.; Zhang, H. S.; Holmes, M. C.; Zhang, L.; Gregory, P. D.; Rebar, E. J. (2010). "A TALE nuclease architecture for efficient genome editing". Nature Biotechnology. 29 (2): 143–148. doi:10.1038/nbt.1755. PMID 21179091.
- Huang, P.; Xiao, A.; Zhou, M.; Zhu, Z.; Lin, S.; Zhang, B. (2011). "Heritable gene targeting in zebrafish using customized TALENs". Nature Biotechnology. 29 (8): 699–700. doi:10.1038/nbt.1939. PMID 21822242.
- Mak, A. N. -S.; Bradley, P.; Cernadas, R. A.; Bogdanove, A. J.; Stoddard, B. L. (2012). "The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target". Science. 335: 716–719. Bibcode:2012Sci...335..716M. doi:10.1126/science.1216211. PMC . PMID 22223736.
- Deng, D.; Yan, C.; Pan, X.; Mahfouz, M.; Wang, J.; Zhu, J. -K.; Shi, Y.; Yan, N. (2012). "Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors". Science. 335: 720–3. Bibcode:2012Sci...335..720D. doi:10.1126/science.1215670. PMC . PMID 22223738.
- Stella, Stefano; Molina, Rafael; Yefimenko, Igor; Prieto, Jesús; Silva, George; Bertonati, Claudia; Juillerat, Alexandre; Duchateau, Phillippe; Montoya, Guillermo (2013-09-01). "Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism". Acta Crystallographica Section D. 69 (Pt 9): 1707–1716. doi:10.1107/S0907444913016429. ISSN 1399-0047. PMC . PMID 23999294.
- Christian M, Cermak T, Doyle EL, et al. (July 2010). "TAL Effector Nucleases Create Targeted DNA Double-strand Breaks". Genetics. 186 (2): 757–61. doi:10.1534/genetics.110.120717. PMC . PMID 20660643.
- Zhang, F.; Cong, L.; Lodato, S.; Kosuri, S.; Church, G. M.; Arlotta, P. (2011). "Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription". Nature Biotechnology. 29 (2): 149–53. doi:10.1038/nbt.1775. PMC . PMID 21248753.
- Mahfouz, M. M.; Li, L.; Shamimuzzaman, M.; Wibowo, A.; Fang, X.; Zhu, J. -K. (2011). "De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks". Proceedings of the National Academy of Sciences. 108 (6): 2623–8. Bibcode:2011PNAS..108.2623M. doi:10.1073/pnas.1019533108. PMC . PMID 21262818.
- Cong, Le; Ruhong Zhou; Yu-chi Kuo; Margaret Cunniff; Feng Zhang (24 July 2012). "Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains". Nature Communications. 968. 3 (7): 968. Bibcode:2012NatCo...3E.968C. doi:10.1038/ncomms1962. PMC . PMID 22828628.
- Geiβler, R.; Scholze, H.; Hahn, S.; Streubel, J.; Bonas, U.; Behrens, S. E.; Boch, J. (2011). Shiu, Shin-Han, ed. "Transcriptional Activators of Human Genes with Programmable DNA-Specificity". PLoS ONE. 6 (5): e19509. Bibcode:2011PLoSO...619509G. doi:10.1371/journal.pone.0019509. PMC . PMID 21625585.
- Li, T.; Huang, S.; Zhao, X.; Wright, D. A.; Carpenter, S.; Spalding, M. H.; Weeks, D. P.; Yang, B. (2011). "Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes". Nucleic Acids Research. 39: 6315–6325. doi:10.1093/nar/gkr188. PMC . PMID 21459844.
- Cermak, T.; Doyle, E. L.; Christian, M.; Wang, L.; Zhang, Y.; Schmidt, C.; Baller, J. A.; Somia, N. V.; Bogdanove, A. J.; Voytas, D. F. (2011). "Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting". Nucleic Acids Research. 39 (12): e82. doi:10.1093/nar/gkr218. PMC . PMID 21493687.
- Morbitzer, R.; Elsaesser, J.; Hausner, J.; Lahaye, T. (2011). "Assembly of custom TALE-type DNA binding domains by modular cloning". Nucleic Acids Research. 39: 5790–5799. doi:10.1093/nar/gkr151. PMC . PMID 21421566.
- Weber, E.; Gruetzner, R.; Werner, S.; Engler, C.; Marillonnet, S. (2011). Bendahmane, Mohammed, ed. "Assembly of Designer TAL Effectors by Golden Gate Cloning". PLoS ONE. 6 (5): e19722. Bibcode:2011PLoSO...619722W. doi:10.1371/journal.pone.0019722. PMC . PMID 21625552.
- Sanjana, N. E.; Cong, L.; Zhou, Y.; Cunniff, M. M.; Feng, G.; Zhang, F. (2012). "A transcription activator-like effector toolbox for genome engineering". Nature Protocols. 7 (1): 171–192. doi:10.1038/nprot.2011.431. PMC . PMID 22222791.
- Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM (Aug 2012). "Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers". Nucleic Acids Res. 40: e117. doi:10.1093/nar/gks624. PMC . PMID 22740649.
- Boissel, Sandrine; Jarjour, Jordan; Astrakhan, Alexander; Adey, Andrew; Gouble, Agnès; Duchateau, Philippe; Shendure, Jay; Stoddard, Barry L.; Certo, Michael T. (2014-02-01). "megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering". Nucleic Acids Research. 42 (4): 2591–2601. doi:10.1093/nar/gkt1224. ISSN 1362-4962. PMC . PMID 24285304.
- Laura DeFrancesco (2011). "Move over ZFNs". Nature Biotechnology. 29 (8): 681–684. doi:10.1038/nbt.1935.
- Li T, Huang S, Jiang WZ, et al. (August 2010). "TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain". Nucleic Acids Res. 39 (1): 359–72. doi:10.1093/nar/gkq704. PMC . PMID 20699274.
- Sander, J. D.; Cade, L.; Khayter, C.; Reyon, D.; Peterson, R. T.; Joung, J. K.; Yeh, J. R. J. (2011). "Targeted gene disruption in somatic zebrafish cells using engineered TALENs". Nature Biotechnology. 29 (8): 697–698. doi:10.1038/nbt.1934. PMC . PMID 21822241.
- Tesson, L.; Usal, C.; Ménoret, S. V.; Leung, E.; Niles, B. J.; Remy, S. V.; Santiago, Y.; Vincent, A. I.; Meng, X.; Zhang, L.; Gregory, P. D.; Anegon, I.; Cost, G. J. (2011). "Knockout rats generated by embryo microinjection of TALENs". Nature Biotechnology. 29 (8): 695–696. doi:10.1038/nbt.1940. PMID 21822240.
- Hockemeyer, D.; Wang, H.; Kiani, S.; Lai, C. S.; Gao, Q.; Cassady, J. P.; Cost, G. J.; Zhang, L.; Santiago, Y.; Miller, J. C.; Zeitler, B.; Cherone, J. M.; Meng, X.; Hinkley, S. J.; Rebar, E. J.; Gregory, P. D.; Urnov, F. D.; Jaenisch, R. (2011). "Genetic engineering of human pluripotent cells using TALE nucleases". Nature Biotechnology. 29 (8): 731–734. doi:10.1038/nbt.1927. PMC . PMID 21738127.
- Wood, A. J.; Lo, T. -W.; Zeitler, B.; Pickle, C. S.; Ralston, E. J.; Lee, A. H.; Amora, R.; Miller, J. C.; Leung, E.; Meng, X.; Zhang, L.; Rebar, E. J.; Gregory, P. D.; Urnov, F. D.; Meyer, B. J. (2011). "Targeted Genome Editing Across Species Using ZFNs and TALENs". Science. 333 (6040): 307. Bibcode:2011Sci...333..307W. doi:10.1126/science.1207773. PMC . PMID 21700836.
- TALengineering.org A comprehensive, publicly available resource for engineered TAL effector technology
- TALengineering newsgroup Newsgroup for discussion of engineered TAL effector technology
- Boch & Schornack (2010). "ISMPMIReporter1001". International Society for Molecular Plant-Microbe Interactions.
- www.taleffectors.com An open resource for TAL effector constructs
- Life Technologies A TAL effector commercial supplier
- PDB Molecule of the Month An entry in the Protein Database's monthly structural highlight
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.
TAL effector repeat Provide feedback
Bai J, Choi SH, Ponciano G, Leung H, Leach JE; , Mol Plant Microbe Interact 2000;13:1322-1329.: Xanthomonas oryzae pv. oryzae avirulence genes contribute differently and specifically to pathogen aggressiveness. PUBMED:11106024 EPMC:11106024
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...
Tetratricopeptide-like repeats are found in a numerous and diverse proteins involved in such functions as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.
The clan contains the following 149 members:Adaptin_N Alkyl_sulf_dimr ANAPC3 ANAPC5 ANAPC8 API5 Arm Arm_2 Arm_3 Atx10homo_assoc B56 BAF250_C BTAD CAS_CSE1 ChAPs CHIP_TPR_N CLASP_N Clathrin Clathrin-link Clathrin_H_link Clathrin_propel Cnd1 Cnd3 Coatomer_E Cohesin_HEAT Cohesin_load ComR_TPR COPI_C CPL CRM1_C Cse1 DHR-2 DNA_alkylation Drf_FH3 Drf_GBD DUF1822 DUF2019 DUF2225 DUF3385 DUF3458_C DUF3808 DUF3856 DUF4042 DUF924 EST1 EST1_DNA_bind FAT Fis1_TPR_C Fis1_TPR_N Foie-gras_1 GUN4_N HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HemY_N HrpB1_HrpK IBB IBN_N IFRD KAP Leuk-A4-hydro_C LRV LRV_FeS MA3 MIF4G MIF4G_like MIF4G_like_2 MMS19_C Mo25 MRP-S27 NARP1 Neurochondrin Nipped-B_C Nro1 NSF Paf67 ParcG PC_rep PHAT PI3Ka PknG_TPR PPP5 PPR PPR_1 PPR_2 PPR_3 PPR_long PPTA Proteasom_PSMB PUF Rab5-bind Rapsyn_N RIX1 RPM2 RPN7 Sel1 SHNi-TPR SNAP SPO22 SRP_TPR_like ST7 Suf SusD-like SusD-like_2 SusD-like_3 SusD_RagB SYCP2_ARLD TAF6_C TAL_effector TAtT Tcf25 TIP120 TOM20_plant TPR_1 TPR_10 TPR_11 TPR_12 TPR_14 TPR_15 TPR_16 TPR_17 TPR_18 TPR_19 TPR_2 TPR_20 TPR_21 TPR_3 TPR_4 TPR_5 TPR_6 TPR_7 TPR_8 TPR_9 TPR_MalT UNC45-central Upf2 V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps39_1 W2 Wzy_C_2 Xpo1 YcaO_C YfiO Zmiz1_N
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:||Hirsh L , Tosatto S, Finn RD , Mifsud W , Bateman A|
|Number in seed:||41|
|Number in full:||578|
|Average length of the domain:||33.70 aa|
|Average identity of full alignment:||68 %|
|Average coverage of the sequence by the domain:||54.30 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the TAL_effector domain has been found. There are 545 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...