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This is the Wikipedia entry entitled "Thioredoxin". More...
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Thioredoxin Edit Wikipedia article
|, TRDX, TRX, TRX1, thioredoxin|
|RNA expression pattern|
|View/Edit Human||View/Edit Mouse|
Thioredoxin is a class of small redox proteins known to be present in all organisms. It plays a role in many important biological processes, including redox signaling. In humans, it is encoded by the TXN gene. Loss-of-function mutation of either of the two human thioredoxin genes is lethal at the four-cell stage of the developing embryo. Although not entirely understood, thioredoxin plays a central role in humans and is increasingly linked to medicine through their response to reactive oxygen species (ROS). In plants, thioredoxins regulate a spectrum of critical functions, ranging from photosynthesis to growth, flowering and the development and germination of seeds. It has also recently been found to play a role in cell-to-cell communication.
Thioredoxins are proteins that act as antioxidants by facilitating the reduction of other proteins by cysteine thiol-disulfide exchange. Thioredoxins are found in nearly all known organisms and are essential for life in mammals.
Thioredoxin is a 12-kD oxidoreductase enzyme containing a dithiol-disulfide active site. It is ubiquitous and found in many organisms from plants and bacteria to mammals. Multiple in vitro substrates for thioredoxin have been identified, including ribonuclease, choriogonadotropins, coagulation factors, glucocorticoid receptor, and insulin. Reduction of insulin is classically used as an activity test.
Thioredoxins are characterized at the level of their amino acid sequence by the presence of two vicinal cysteines in a CXXC motif. These two cysteines are the key to the ability of thioredoxin to reduce other proteins. Thioredoxin proteins also have a characteristic tertiary structure termed the thioredoxin fold.
The thioredoxins are kept in the reduced state by the flavoenzyme thioredoxin reductase, in a NADPH-dependent reaction. Thioredoxins act as electron donors to peroxidases and ribonucleotide reductase. The related glutaredoxins share many of the functions of thioredoxins, but are reduced by glutathione rather than a specific reductase.
The benefit of thioredoxins to reduce oxidative stress is shown by transgenic mice that overexpress thioredoxin, are more resistant to inflammation, and live 35% longer — supporting the free radical theory of aging. However, the controls of this study were short lived, which may have contributed to the apparent increase in longevity.
Plants have an unusually complex complement of Trxs composed of six well-defined types (Trxs f, m, x, y, h, and o) that reside in different cell compartments and function in an array of processes. In 2010 it was discovered for the first time that thioredoxin proteins are able to move from cell to cell, representing a novel form of cellular communication in plants.
Thioredoxin has been shown to interact with:
- Collagen, type I, alpha 1,
- Glucocorticoid receptor,
- SENP1, and
- RuBisCO - enzyme activity regulated by thioredoxin
- Peroxiredoxin - enzyme activity regulated by thioredoxin
- Thioredoxin fold
- Wollman EE, d'Auriol L, Rimsky L, Shaw A, Jacquot JP, Wingfield P, Graber P, Dessarps F, Robin P, Galibert F (October 1988). "Cloning and expression of a cDNA for human thioredoxin". J. Biol. Chem. 263 (30): 15506–12. PMID 3170595.
- Meng L, Wong JH, Feldman LJ, Lemaux PG, Buchanan BB (2010). "A membrane-associated thioredoxin required for plant growth moves from cell to cell, suggestive of a role in intercellular communication". Proceedings of the National Academy of Sciences of the USA 107 (8): 3900–5. doi:10.1073/pnas.0913759107. PMC 2840455. PMID 20133584.
- Holmgren A (1989). "Thioredoxin and glutaredoxin systems" (PDF). J Biol Chem 264 (24): 13963–6. PMID 2668278.
- Nordberg J, Arnér ES (2001). "Reactive oxygen species, antioxidants, and the mammalian thioredoxin system". Free Radic Biol Med 31 (11): 1287–312. doi:10.1016/S0891-5849(01)00724-9. PMID 11728801.
- "Entrez Gene: TXN thioredoxin".
- Mustacich D, Powis G (February 2000). "Thioredoxin reductase". Biochem J 346 (Pt 1): 1–8. doi:10.1042/0264-6021:3460001. PMC 1220815. PMID 10657232.
- Arnér ES, Holmgren A (2000). "Physiological functions of thioredoxin and thioredoxin reductase". Eur J Biochem 267 (20): 6102–9. doi:10.1046/j.1432-1327.2000.01701.x. PMID 11012661.
- Yoshida T, Nakamura H, Masutani H, Yodoi J (2005). "The involvement of thioredoxin and thioredoxin binding protein-2 on cellular proliferation and aging process". Annals of the New York Academy of Sciences 1055: 1–12. doi:10.1196/annals.1323.002. PMID 16387713.
- Muller, F.L., Lustgarten, M.S., Jang, Y., Richardson, A. & Van Remmen, H. Trends in oxidative aging theories. Free Radic Biol Med 43, 477-503 (2007).
- Liu Y, Min W (June 2002). "Thioredoxin promotes ASK1 ubiquitination and degradation to inhibit ASK1-mediated apoptosis in a redox activity-independent manner". Circ. Res. 90 (12): 1259–66. doi:10.1161/01.res.0000022160.64355.62. PMID 12089063.
- Morita K, Saitoh M, Tobiume K, Matsuura H, Enomoto S, Nishitoh H, Ichijo H (November 2001). "Negative feedback regulation of ASK1 by protein phosphatase 5 (PP5) in response to oxidative stress". EMBO J. 20 (21): 6028–36. doi:10.1093/emboj/20.21.6028. PMC 125685. PMID 11689443.
- Saitoh M, Nishitoh H, Fujii M, Takeda K, Tobiume K, Sawada Y, Kawabata M, Miyazono K, Ichijo H (May 1998). "Mammalian thioredoxin is a direct inhibitor of apoptosis signal-regulating kinase (ASK) 1". EMBO J. 17 (9): 2596–606. doi:10.1093/emboj/17.9.2596. PMC 1170601. PMID 9564042.
- Matsumoto K, Masutani H, Nishiyama A, Hashimoto S, Gon Y, Horie T, Yodoi J (July 2002). "C-propeptide region of human pro alpha 1 type 1 collagen interacts with thioredoxin". Biochem. Biophys. Res. Commun. 295 (3): 663–7. doi:10.1016/s0006-291x(02)00727-1. PMID 12099690.
- Makino Y, Yoshikawa N, Okamoto K, Hirota K, Yodoi J, Makino I, Tanaka H (January 1999). "Direct association with thioredoxin allows redox regulation of glucocorticoid receptor function". J. Biol. Chem. 274 (5): 3182–8. doi:10.1074/jbc.274.5.3182. PMID 9915858.
- Li X, Luo Y, Yu L, Lin Y, Luo D, Zhang H, He Y, Kim YO, Kim Y, Tang S, Min W (April 2008). "SENP1 mediates TNF-induced desumoylation and cytoplasmic translocation of HIPK1 to enhance ASK1-dependent apoptosis". Cell Death Differ. 15 (4): 739–50. doi:10.1038/sj.cdd.4402303. PMID 18219322.
- Nishiyama A, Matsui M, Iwata S, Hirota K, Masutani H, Nakamura H, Takagi Y, Sono H, Gon Y, Yodoi J (July 1999). "Identification of thioredoxin-binding protein-2/vitamin D(3) up-regulated protein 1 as a negative regulator of thioredoxin function and expression". J. Biol. Chem. 274 (31): 21645–50. doi:10.1074/jbc.274.31.21645. PMID 10419473.
- Arnér ES, Holmgren A (2000). "Physiological functions of thioredoxin and thioredoxin reductase". Eur. J. Biochem. 267 (20): 6102–9. doi:10.1046/j.1432-1327.2000.01701.x. PMID 11012661.
- Nishinaka Y, Masutani H, Nakamura H, Yodoi J (2002). "Regulatory roles of thioredoxin in oxidative stress-induced cellular responses". Redox Rep. 6 (5): 289–95. doi:10.1179/135100001101536427. PMID 11778846.
- Ago T, Sadoshima J (2007). "Thioredoxin and Ventricular Remodeling". J. Mol. Cell. Cardiol. 41 (5): 762–73. doi:10.1016/j.yjmcc.2006.08.006. PMC 1852508. PMID 17007870.
- Tonissen KF, Wells JR (1991). "Isolation and characterization of human thioredoxin-encoding genes". Gene 102 (2): 221–8. doi:10.1016/0378-1119(91)90081-L. PMID 1874447.
- Martin H, Dean M (1991). "Identification of a thioredoxin-related protein associated with plasma membranes". Biochem. Biophys. Res. Commun. 175 (1): 123–8. doi:10.1016/S0006-291X(05)81209-4. PMID 1998498.
- Forman-Kay JD, Clore GM, Wingfield PT, Gronenborn AM (1991). "High-resolution three-dimensional structure of reduced recombinant human thioredoxin in solution". Biochemistry 30 (10): 2685–98. doi:10.1021/bi00224a017. PMID 2001356.
- Jacquot JP, de Lamotte F, Fontecave M, Schürmann P, Decottignies P, Miginiac-Maslow M, Wollman E (1991). "Human thioredoxin reactivity-structure/function relationship". Biochem. Biophys. Res. Commun. 173 (3): 1375–81. doi:10.1016/S0006-291X(05)80940-4. PMID 2176490.
- Forman-Kay JD, Clore GM, Driscoll PC, Wingfield P, Richards FM, Gronenborn AM (1990). "A proton nuclear magnetic resonance assignment and secondary structure determination of recombinant human thioredoxin". Biochemistry 28 (17): 7088–97. doi:10.1021/bi00443a045. PMID 2684271.
- Tagaya Y, Maeda Y, Mitsui A, Kondo N, Matsui H, Hamuro J, Brown N, Arai K, Yokota T, Wakasugi H (1989). "ATL-derived factor (ADF), an IL-2 receptor/Tac inducer homologous to thioredoxin; possible involvement of dithiol-reduction in the IL-2 receptor induction". EMBO J. 8 (3): 757–64. PMC 400872. PMID 2785919.
- Wollman EE, d'Auriol L, Rimsky L, Shaw A, Jacquot JP, Wingfield P, Graber P, Dessarps F, Robin P, Galibert F (1988). "Cloning and expression of a cDNA for human thioredoxin". J. Biol. Chem. 263 (30): 15506–12. PMID 3170595.
- Heppell-Parton A, Cahn A, Bench A, Lowe N, Lehrach H, Zehetner G, Rabbitts P (1995). "Thioredoxin, a mediator of growth inhibition, maps to 9q31". Genomics 26 (2): 379–81. doi:10.1016/0888-7543(95)80223-9. PMID 7601465.
- Qin J, Clore GM, Kennedy WM, Huth JR, Gronenborn AM (1995). "Solution structure of human thioredoxin in a mixed disulfide intermediate complex with its target peptide from the transcription factor NF kappa B". Structure 3 (3): 289–97. doi:10.1016/S0969-2126(01)00159-9. PMID 7788295.
- Kato S, Sekine S, Oh SW, Kim NS, Umezawa Y, Abe N, Yokoyama-Kobayashi M, Aoki T (1995). "Construction of a human full-length cDNA bank". Gene 150 (2): 243–50. doi:10.1016/0378-1119(94)90433-2. PMID 7821789.
- Qin J, Clore GM, Gronenborn AM (1994). "The high-resolution three-dimensional solution structures of the oxidized and reduced states of human thioredoxin". Structure 2 (6): 503–22. doi:10.1016/S0969-2126(00)00051-4. PMID 7922028.
- Gasdaska PY, Oblong JE, Cotgreave IA, Powis G (1994). "The predicted amino acid sequence of human thioredoxin is identical to that of the autocrine growth factor human adult T-cell derived factor (ADF): thioredoxin mRNA is elevated in some human tumors". Biochim. Biophys. Acta 1218 (3): 292–6. doi:10.1016/0167-4781(94)90180-5. PMID 8049254.
- Qin J, Clore GM, Kennedy WP, Kuszewski J, Gronenborn AM (1996). "The solution structure of human thioredoxin complexed with its target from Ref-1 reveals peptide chain reversal". Structure 4 (5): 613–20. doi:10.1016/S0969-2126(96)00065-2. PMID 8736558.
- Weichsel A, Gasdaska JR, Powis G, Montfort WR (1996). "Crystal structures of reduced, oxidized, and mutated human thioredoxins: evidence for a regulatory homodimer". Structure 4 (6): 735–51. doi:10.1016/S0969-2126(96)00079-2. PMID 8805557.
- Andersen JF, Sanders DA, Gasdaska JR, Weichsel A, Powis G, Montfort WR (1997). "Human thioredoxin homodimers: regulation by pH, role of aspartate 60, and crystal structure of the aspartate 60 --> asparagine mutant". Biochemistry 36 (46): 13979–88. doi:10.1021/bi971004s. PMID 9369469.
- Maruyama T, Kitaoka Y, Sachi Y, Nakanoin K, Hirota K, Shiozawa T, Yoshimura Y, Fujii S, Yodoi J (1998). "Thioredoxin expression in the human endometrium during the menstrual cycle". Mol. Hum. Reprod. 3 (11): 989–93. doi:10.1093/molehr/3.11.989. PMID 9433926.
- Sahlin L, Stjernholm Y, Holmgren A, Ekman G, Eriksson H (1998). "The expression of thioredoxin mRNA is increased in the human cervix during pregnancy". Mol. Hum. Reprod. 3 (12): 1113–7. doi:10.1093/molehr/3.12.1113. PMID 9464857.
- Maeda K, Hägglund P, Finnie C, Svensson B, Henriksen A (2006). "Structural basis for target protein recognition by the protein disulfide reductase thioredoxin". Structure 14 (11): 1701–10. doi:10.1016/j.str.2006.09.012. PMID 17098195.
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.
Thioredoxin-like Provide feedback
Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond.
Internal database links
|Similarity to PfamA using HHSearch:||Thioredoxin AhpC-TSA SCO1-SenC Redoxin Thioredoxin_2 TraF Thioredoxin_7 Thioredoxin_9|
This tab holds annotation information from the InterPro database.
InterPro entry IPR012336
Several biological processes regulate the activity of target proteins through changes in the redox state of thiol groups (S2 to SH2), where a hydrogen donor is linked to an intermediary disulphide protein. Such processes include the ferredoxin/thioredoxin system, the NADP/thioredoxin system, and the glutathione/glutaredoxin system [PUBMED:15862094]. Several of these disulphide proteins share a common structure, consisting of a three-layer alpha/beta/alpha core. Proteins that contain domains with a thioredoxin-like fold include:
- Arsenate reductase (ArsC) [PUBMED:11709171]
- Calsequestrin (contains three tandem repeats of this fold) [PUBMED:9628486]
- Circadian oscillation regulator KaiB [PUBMED:15071498]
- Disulphide bond isomerase DsbC and DsbG (C-terminal domain) [PUBMED:10700276, PUBMED:15184683]
- Disulphide bond facilitator DsbA (contains an alpha-helical insertion) [PUBMED:9300489]
- Endoplasmic reticulum protein ERP29 (N-terminal domain) [PUBMED:11435111]
- Glutathione S-transferase (GST) (N-terminal domain) [PUBMED:16597834]
- Mitochondrial ribosomal protein L51/S25/CI-B8 domain (variable positions for Cys residues in active site) [PUBMED:15341729]
- Phosducin [PUBMED:8898209]
- Protein disulphide isomerase (PDI) (contains two tandem repeats of this fold) [PUBMED:10383197]
- Glutathione peroxidase-like enzymes [PUBMED:6852035]
- Selenoprotein W-related [PUBMED:16319061]
- SH3-binding glutamic acid-rich protein like (SH3BGR) (lacks both conserved Cys residues) [PUBMED:15120624]
- Spliceosomal protein U5-15Kd [PUBMED:10610776]
- Thioltransferases, including thioredoxin [PUBMED:2181145], glutaredoxon [PUBMED:1304339], hybrid peroxiredoxin hyPrx5 [PUBMED:12529327]
- Thioredoxin-like 2Fe-2S ferredoxin [PUBMED:12089152]
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.
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This clan contains families related to the thioredoxin family. Thioredoxins are small enzymes that are involved in redox reactions via the reversible oxidation of an active centre disulfide bond. The thioredoxin fold consists of a 3 layer alpha/beta/alpha sandwich and a central beta sheet.
The clan contains the following 57 members:2Fe-2S_thioredx AhpC-TSA AhpC-TSA_2 Aminopep ArsC ArsD Calsequestrin DIM1 DSBA DUF1223 DUF1462 DUF1525 DUF1687 DUF2703 DUF2847 DUF4174 DUF836 DUF899 DUF953 ERp29_N GILT Glutaredoxin GSHPx GST_N GST_N_2 GST_N_3 GST_N_4 HyaE KaiB L51_S25_CI-B8 Metallopep MRP-S23 MRP-S25 OST3_OST6 Peptidase_M76 Phosducin Rdx Redoxin SCO1-SenC SelP_N Sep15_SelM SH3BGR T4_deiodinase Thioredox_DsbH Thioredoxin Thioredoxin_2 Thioredoxin_3 Thioredoxin_4 Thioredoxin_5 Thioredoxin_6 Thioredoxin_7 Thioredoxin_8 Thioredoxin_9 Tom37 TraF YtfJ_HI0045 Zincin_1
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.
|Number in seed:||58|
|Number in full:||2489|
|Average length of the domain:||94.70 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||26.54 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||4|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
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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:
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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 Thioredoxin_8 domain has been found. There are 37 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.
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