Summary: Transcription factor TFIID (or TATA-binding protein, TBP)
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 "TATA-binding protein". 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.
TATA-binding protein Edit Wikipedia article
crystal structure of a yeast brf1-tbp-dna ternary complex
|TATA box binding protein|
PDB rendering based on 1c9b.
|Symbols||; GTF2D; GTF2D1; HDL4; SCA17; TFIID|
|RNA expression pattern|
The TATA-binding protein (TBP) is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters. TBP, along with a variety of TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex. As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. However, it is estimated that only 10-20% of human promoters have TATA boxes. Therefore, TBP is probably not the only protein involved in positioning RNA polymerase II.
TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β sheet.
Another distinctive feature of TBP is a long string of glutamines in the N-terminus of the protein. This region modulates the DNA binding activity of the C-terminus, and modulation of DNA-binding affects the rate of transcription complex formation and initiation of transcription. Mutations that expand the number of CAG repeats encoding this polyglutamine tract, and thus increase the length of the polyglutamine string, are associated with spinocerebellar ataxia 17, a neurodegenerative disorder classified as a polyglutamine disease.
Role as Transcription Factor Subunit
TBP is a subunit of the eukaryotic transcription factor TFIID. TFIID is the first protein to bind to DNA during the formation of the pre-initiation transcription complex of RNA polymerase II (RNA Pol II). Binding of TFIID to the TATA box in the promoter region of the gene initiates the recruitment of other factors required for RNA Pol II to begin transcription. Some of the other recruited transcription factors include TFIIA, TFIIB, and TFIIF. Each of these transcription factors is formed from the interaction of many protein subunits, indicating that transcription is a heavily regulated process.
When TBP binds to a TATA box within the DNA, it distorts the DNA by inserting amino acid side-chains between base pairs, partially unwinding the helix, and doubly kinking it. The distortion is accomplished through a great amount of surface contact between the protein and DNA. TBP binds with the negatively charged phosphates in the DNA backbone through positively charged lysine and arginine amino acid residues. The sharp bend in the DNA is produced through projection of four bulky phenylalanine residues into the minor groove. As the DNA bends, its contact with TBP increases, thus enhancing the DNA-protein interaction.
The strain imposed on the DNA through this interaction initiates melting, or separation, of the strands. Because this region of DNA is rich in adenine and thymine residues, which base-pair through only two hydrogen bonds, the DNA strands are more easily separated. Separation of the two strands exposes the bases and allows RNA polymerase II to begin transcription of the gene.
TBP's C-terminus composes of a helicoidal shape that (incompletely) complements the T-A-T-A region of DNA. It is interesting to note that this incompleteness allows DNA to be passively bent on binding.
TATA-binding protein has been shown to interact with:
- GTF2B (TFIIB),
- GTF2A1 (TFIIA subunit 1),
- GTF2F1 (TFIIF subunit 1)
- GTF2H4 (TFIIH subunit 4),
- TAF13, and
The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins.
The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins . By contrast, the N-terminal region varies in both length and sequence.
- Kornberg RD (2007). "The molecular basis of eukaryotic transcription". Proc. Natl. Acad. Sci. U.S.A. 104 (32): 12955–61. doi:10.1073/pnas.0704138104. PMC 1941834. PMID 17670940.
- Lee TI, Young RA (2000). "Transcription of eukaryotic protein-coding genes". Annu. Rev. Genet. 34: 77–137. doi:10.1146/annurev.genet.34.1.77. PMID 11092823.
- "Entrez Gene: TBP TATA box binding protein".
- McCulloch V, Hardin P, Peng W, Ruppert JM, Lobo-Ruppert SM (August 2000). "Alternatively spliced hBRF variants function at different RNA polymerase III promoters". EMBO J. 19 (15): 4134–43. doi:10.1093/emboj/19.15.4134. PMC 306597. PMID 10921893.
- Wang Z, Roeder RG (July 1995). "Structure and function of a human transcription factor TFIIIB subunit that is evolutionarily conserved and contains both TFIIB- and high-mobility-group protein 2-related domains". Proc. Natl. Acad. Sci. U.S.A. 92 (15): 7026–30. doi:10.1073/pnas.92.15.7026. PMC 41464. PMID 7624363.
- Scully R, Anderson SF, Chao DM, Wei W, Ye L, Young RA, Livingston DM, Parvin JD (May 1997). "BRCA1 is a component of the RNA polymerase II holoenzyme". Proc. Natl. Acad. Sci. U.S.A. 94 (11): 5605–10. doi:10.1073/pnas.94.11.5605. PMC 20825. PMID 9159119.
- Chicca JJ, Auble DT, Pugh BF (March 1998). "Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1". Mol. Cell. Biol. 18 (3): 1701–10. PMC 108885. PMID 9488487.
- Metz R, Bannister AJ, Sutherland JA, Hagemeier C, O'Rourke EC, Cook A, Bravo R, Kouzarides T (September 1994). "c-Fos-induced activation of a TATA-box-containing promoter involves direct contact with TATA-box-binding protein". Mol. Cell. Biol. 14 (9): 6021–9. doi:10.1128/MCB.14.9.6021. PMC 359128. PMID 8065335.
- Franklin CC, McCulloch AV, Kraft AS (February 1995). "In vitro association between the Jun protein family and the general transcription factors, TBP and TFIIB". Biochem. J. 305 (3): 967–74. PMC 1136352. PMID 7848298.
- Brendel C, Gelman L, Auwerx J (June 2002). "Multiprotein bridging factor-1 (MBF-1) is a cofactor for nuclear receptors that regulate lipid metabolism". Mol. Endocrinol. 16 (6): 1367–77. doi:10.1210/me.16.6.1367. PMID 12040021.
- Mariotti M, De Benedictis L, Avon E, Maier JA (August 2000). "Interaction between endothelial differentiation-related factor-1 and calmodulin in vitro and in vivo". J. Biol. Chem. 275 (31): 24047–51. doi:10.1074/jbc.M001928200. PMID 10816571.
- Kabe Y, Goto M, Shima D, Imai T, Wada T, Morohashi K, Shirakawa M, Hirose S, Handa H (November 1999). "The role of human MBF1 as a transcriptional coactivator". J. Biol. Chem. 274 (48): 34196–202. doi:10.1074/jbc.274.48.34196. PMID 10567391.
- Tang H, Sun X, Reinberg D, Ebright RH (February 1996). "Protein-protein interactions in eukaryotic transcription initiation: structure of the preinitiation complex". Proc. Natl. Acad. Sci. U.S.A. 93 (3): 1119–24. doi:10.1073/pnas.93.3.1119. PMC 40041. PMID 8577725.
- Bushnell DA, Westover KD, Davis RE, Kornberg RD (February 2004). "Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms". Science 303 (5660): 983–8. doi:10.1126/science.1090838. PMID 14963322.
- DeJong J, Bernstein R, Roeder RG (April 1995). "Human general transcription factor TFIIA: characterization of a cDNA encoding the small subunit and requirement for basal and activated transcription". Proc. Natl. Acad. Sci. U.S.A. 92 (8): 3313–7. doi:10.1073/pnas.92.8.3313. PMC 42156. PMID 7724559.
- Ozer J, Mitsouras K, Zerby D, Carey M, Lieberman PM (June 1998). "Transcription factor IIA derepresses TATA-binding protein (TBP)-associated factor inhibition of TBP-DNA binding". J. Biol. Chem. 273 (23): 14293–300. doi:10.1074/jbc.273.23.14293. PMID 9603936.
- Sun X, Ma D, Sheldon M, Yeung K, Reinberg D (October 1994). "Reconstitution of human TFIIA activity from recombinant polypeptides: a role in TFIID-mediated transcription". Genes Dev. 8 (19): 2336–48. doi:10.1101/gad.8.19.2336. PMID 7958900.
- Ruppert S, Tjian R (November 1995). "Human TAFII250 interacts with RAP74: implications for RNA polymerase II initiation". Genes Dev. 9 (22): 2747–55. doi:10.1101/gad.9.22.2747. PMID 7590250.
- Malik S, Guermah M, Roeder RG (March 1998). "A dynamic model for PC4 coactivator function in RNA polymerase II transcription". Proc. Natl. Acad. Sci. U.S.A. 95 (5): 2192–7. doi:10.1073/pnas.95.5.2192. PMC 19292. PMID 9482861.
- Thut CJ, Goodrich JA, Tjian R (August 1997). "Repression of p53-mediated transcription by MDM2: a dual mechanism". Genes Dev. 11 (15): 1974–86. doi:10.1101/gad.11.15.1974. PMC 316412. PMID 9271120.
- Léveillard T, Wasylyk B (December 1997). "The MDM2 C-terminal region binds to TAFII250 and is required for MDM2 regulation of the cyclin A promoter". J. Biol. Chem. 272 (49): 30651–61. doi:10.1074/jbc.272.49.30651. PMID 9388200.
- Shetty S, Takahashi T, Matsui H, Ayengar R, Raghow R (May 1999). "Transcriptional autorepression of Msx1 gene is mediated by interactions of Msx1 protein with a multi-protein transcriptional complex containing TATA-binding protein, Sp1 and cAMP-response-element-binding protein-binding protein (CBP/p300)". Biochem. J. 339 (3): 751–8. doi:10.1042/0264-6021:3390751. PMC 1220213. PMID 10215616.
- Zhang H, Hu G, Wang H, Sciavolino P, Iler N, Shen MM, Abate-Shen C (May 1997). "Heterodimerization of Msx and Dlx homeoproteins results in functional antagonism". Mol. Cell. Biol. 17 (5): 2920–32. PMC 232144. PMID 9111364.
- Zhang H, Catron KM, Abate-Shen C (March 1996). "A role for the Msx-1 homeodomain in transcriptional regulation: residues in the N-terminal arm mediate TATA binding protein interaction and transcriptional repression". Proc. Natl. Acad. Sci. U.S.A. 93 (5): 1764–9. doi:10.1073/pnas.93.5.1764. PMC 39855. PMID 8700832.
- Bellorini M, Lee DK, Dantonel JC, Zemzoumi K, Roeder RG, Tora L, Mantovani R (June 1997). "CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues". Nucleic Acids Res. 25 (11): 2174–81. doi:10.1093/nar/25.11.2174. PMC 146709. PMID 9153318.
- Seto E, Usheva A, Zambetti GP, Momand J, Horikoshi N, Weinmann R, Levine AJ, Shenk T (December 1992). "Wild-type p53 binds to the TATA-binding protein and represses transcription". Proc. Natl. Acad. Sci. U.S.A. 89 (24): 12028–32. doi:10.1073/pnas.89.24.12028. PMC 50691. PMID 1465435.
- Cvekl A, Kashanchi F, Brady JN, Piatigorsky J (June 1999). "Pax-6 interactions with TATA-box-binding protein and retinoblastoma protein". Invest. Ophthalmol. Vis. Sci. 40 (7): 1343–50. PMID 10359315.
- Zwilling S, Annweiler A, Wirth T (May 1994). "The POU domains of the Oct1 and Oct2 transcription factors mediate specific interaction with TBP". Nucleic Acids Res. 22 (9): 1655–62. doi:10.1093/nar/22.9.1655. PMC 308045. PMID 8202368.
- Guermah M, Malik S, Roeder RG (June 1998). "Involvement of TFIID and USA components in transcriptional activation of the human immunodeficiency virus promoter by NF-kappaB and Sp1". Mol. Cell. Biol. 18 (6): 3234–44. PMC 108905. PMID 9584164.
- Schmitz ML, Stelzer G, Altmann H, Meisterernst M, Baeuerle PA (March 1995). "Interaction of the COOH-terminal transactivation domain of p65 NF-kappa B with TATA-binding protein, transcription factor IIB, and coactivators". J. Biol. Chem. 270 (13): 7219–26. doi:10.1074/jbc.270.13.7219. PMID 7706261.
- Schulman IG, Chakravarti D, Juguilon H, Romo A, Evans RM (August 1995). "Interactions between the retinoid X receptor and a conserved region of the TATA-binding protein mediate hormone-dependent transactivation". Proc. Natl. Acad. Sci. U.S.A. 92 (18): 8288–92. doi:10.1073/pnas.92.18.8288. PMC 41142. PMID 7667283.
- Siegert JL, Robbins PD (January 1999). "Rb inhibits the intrinsic kinase activity of TATA-binding protein-associated factor TAFII250". Mol. Cell. Biol. 19 (1): 846–54. PMC 83941. PMID 9858607.
- Ruppert S, Wang EH, Tjian R (March 1993). "Cloning and expression of human TAFII250: a TBP-associated factor implicated in cell-cycle regulation". Nature 362 (6416): 175–9. doi:10.1038/362175a0. PMID 7680771.
- O'Brien T, Tjian R (May 1998). "Functional analysis of the human TAFII250 N-terminal kinase domain". Mol. Cell 1 (6): 905–11. doi:10.1016/S1097-2765(00)80089-1. PMID 9660973.
- Pointud JC, Mengus G, Brancorsini S, Monaco L, Parvinen M, Sassone-Corsi P, Davidson I (May 2003). "The intracellular localisation of TAF7L, a paralogue of transcription factor TFIID subunit TAF7, is developmentally regulated during male germ-cell differentiation". J. Cell. Sci. 116 (Pt 9): 1847–58. doi:10.1242/jcs.00391. PMID 12665565.
- Tao Y, Guermah M, Martinez E, Oelgeschläger T, Hasegawa S, Takada R, Yamamoto T, Horikoshi M, Roeder RG (March 1997). "Specific interactions and potential functions of human TAFII100". J. Biol. Chem. 272 (10): 6714–21. doi:10.1074/jbc.272.10.6714. PMID 9045704.
- Martinez E, Palhan VB, Tjernberg A, Lymar ES, Gamper AM, Kundu TK, Chait BT, Roeder RG (October 2001). "Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo". Mol. Cell. Biol. 21 (20): 6782–95. doi:10.1128/MCB.21.20.6782-6795.2001. PMC 99856. PMID 11564863.
- Mengus G, May M, Jacq X, Staub A, Tora L, Chambon P, Davidson I (April 1995). "Cloning and characterization of hTAFII18, hTAFII20 and hTAFII28: three subunits of the human transcription factor TFIID". EMBO J. 14 (7): 1520–31. PMC 398239. PMID 7729427.
- May M, Mengus G, Lavigne AC, Chambon P, Davidson I (June 1996). "Human TAF(II28) promotes transcriptional stimulation by activation function 2 of the retinoid X receptors". EMBO J. 15 (12): 3093–104. PMC 450252. PMID 8670810.
- Hoffmann A, Roeder RG (July 1996). "Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation". J. Biol. Chem. 271 (30): 18194–202. doi:10.1074/jbc.271.30.18194. PMID 8663456.
- Hochheimer A, Tjian R (June 2003). "Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression". Genes Dev. 17 (11): 1309–20. doi:10.1101/gad.1099903. PMID 12782648.
- Pugh BF (September 2000). "Control of gene expression through regulation of the TATA-binding protein". Gene 255 (1): 1–14. doi:10.1016/s0378-1119(00)00288-2. PMID 10974559.
- Davidson I (July 2003). "The genetics of TBP and TBP-related factors". Trends Biochem. Sci. 28 (7): 391–8. doi:10.1016/S0968-0004(03)00117-8. PMID 12878007.
- Nikolov DB, Hu SH, Lin J, Gasch A, Hoffmann A, Horikoshi M, Chua NH, Roeder RG, Burley SK (November 1992). "Crystal structure of TFIID TATA-box binding protein". Nature 360 (6399): 40–6. doi:10.1038/360040a0. PMID 1436073.
- GeneReviews/NCBI/NIH/UW entry on Spinocerebellar Ataxia Type 17
- Interactive TBP Structure at massey.ac.nz
- PDB Molecule of the Month pdb67_1
- TATA-Box Binding Protein at the US National Library of Medicine Medical Subject Headings (MeSH)
- FactorBook TBP
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.
Transcription factor TFIID (or TATA-binding protein, TBP) Provide feedback
No Pfam abstract.
Hoffman A, Sinn E, Yamamoto T, Wang J, Roy A, Horikoshi M, Roeder RG; , Nature 1990;346:387-390.: Highly conserved core domain and unique N terminus with presumptive regulatory motifs in a human TATA factor (TFIID). PUBMED:2374612 EPMC:2374612
Internal database links
|SCOOP:||DUF3252 DUF3378 T4bSS_IcmS DUF4295|
|Similarity to PfamA using HHSearch:||DUF3378|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000814
The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [PUBMED:12782648, PUBMED:10974559]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins [PUBMED:12878007].
The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins [PUBMED:1436073]. By contrast, the N-terminal region varies in both length and sequence.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA binding (GO:0003677)|
|Biological process||DNA-templated transcription, initiation (GO:0006352)|
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...
TBP is a transcription factor whose DNA binding fold is composed of a curved antiparallel beta-sheet . This fold is also found in the N terminal region of DNA repair glycosylases. The N terminal domain of DNA glycosylase has only a single copy of the fold, whereas TBP contains a duplication of this fold [2-3].
The clan contains the following 4 members:AlkA_N DUF3378 OGG_N TBP
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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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 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.
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
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.
MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
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.
|Number in seed:||331|
|Number in full:||3882|
|Average length of the domain:||81.00 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||63.07 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 8 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the TBP domain has been found. There are 134 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
Loading structure mapping...