Summary: Glutathione S-transferase N-terminal domain
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Glutathione S-transferase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
Glutathione S-transferases (GSTs), previously known as ligandins, comprise a family of eukaryotic and prokaryotic phase II metabolic isozymes best known for their ability to catalyze the conjugation of the reduced form of glutathione (GSH) to xenobiotic substrates for the purpose of detoxification. The GST family consists of three superfamilies: the cytosolic, mitochondrial, and microsomal—also known as MAPEG—proteins. Members of the GST superfamily are extremely diverse in amino acid sequence, and a large fraction of the sequences deposited in public databases are of unknown function. The Enzyme Function Initiative (EFI) is using GSTs as a model superfamily to identify new GST functions.
GSTs can constitute up to 10% of cytosolic protein in some mammalian organs. GSTs catalyse the conjugation of GSH—via a sulfhydryl group—to electrophilic centers on a wide variety of substrates in order to make the compounds more water-soluble. This activity detoxifies endogenous compounds such as peroxidised lipids and enables the breakdown of xenobiotics. GSTs may also bind toxins and function as transport proteins, which gave rise to the early term for GSTs, ligandin.
Protein sequence and structure are important additional classification criteria for the three superfamilies (cytosolic, mitochondrial, and MAPEG) of GSTs: while classes from the cytosolic superfamily of GSTs possess more than 40% sequence homology, those from other classes may have less than 25%. Cytosolic GSTs are divided into 13 classes based upon their structure: alpha, beta, delta, epsilon, zeta, theta, mu, nu, pi, sigma, tau, phi, and omega. Mitochondrial GSTs are in class kappa. The MAPEG superfamily of microsomal GSTs consists of subgroups designated I-IV, between which amino acid sequences share less than 20% identity. Human cytosolic GSTs belong to the alpha, zeta, theta, mu, pi, sigma, and omega classes, while six isozymes belonging to classes I, II, and IV of the MAPEG superfamily are known to exist.
Standardized GST nomenclature first proposed in 1992 identifies the species to which the isozyme of interest belongs with a lower-case initial (e.g., "h" for human), which precedes the abbreviation GST. The isozyme class is subsequently identified with an upper-case letter (e.g., "A" for alpha), followed by an Arabic numeral representing the class subfamily (or subunit). Because both mitochondrial and cytosolic GSTs exist as dimers, and only heterodimers form between members of the same class, the second subfamily component of the enzyme dimer is denoted with a hyphen, followed by an additional Arabic numeral. Therefore, if a human glutathione S-transferase is a homodimer in the pi-class subfamily 1, its name will be written as "hGSTP1-1."
The early nomenclature for GSTs referred to them as “Y” proteins, referring to their separation in the “Y” fraction (as opposed to the “X and Z” fractions) using Sephadex G75 chromatography. As GST sub-units were identified they were referred to as Ya, Yp, etc. with if necessary, a number identifying the monomer isoform (e.g. Yb1). Litwack et al proposed the term “Ligandin” to cover the proteins previously known as “Y” proteins.
In clinical chemistry and toxicology, the terms alpha GST, mu GST, and pi GST are most commonly used.
|Glutathione S-transferase, C-terminal domain|
The glutathione binding site, or "G-site," is located in the thioredoxin-like domain of both cytosolic and mitochondrial GSTs. The region containing the greatest amount of variability between the assorted classes is that of helix α2, where one of three different amino acid residues interacts with the glycine residue of glutathione. Two subgroups of cytosolic GSTs have been characterized based upon their interaction with glutathione: the Y-GST group, which uses a tyrosine residue to activate glutathione, and the S/C-GST, which instead uses serine or cysteine residues.
"GST proteins are globular proteins with an N-terminal mixed helical and beta-strand domain and an all-helical C-terminal domain . "
The porcine pi-class enzyme pGTSP1-1 was the first GST to have its structure determined, and it is representative of other members of the cytosolic GST superfamily, which contain a thioredoxin-like N-terminal domain as well as a C-terminal domain consisting of alpha helices.
Mammalian cytosolic GSTs are dimeric, with both subunits being from the same class of GSTs, although not necessarily identical. The monomers are approximately 25 kDa in size. They are active over a wide variety of substrates with considerable overlap. The following table lists all GST enzymes of each class known to exist in Homo sapiens, as found in the UniProtKB/Swiss-Prot database.
|GST Class||Homo sapiens GST Class Members (22)|
|Alpha||GSTA1, GSTA2, GSTA3, GSTA4, GSTA5|
|Mu||GSTM1, GSTM1L (RNAi), GSTM2, GSTM3, GSTM4, GSTM5|
|Theta||GSTT1, GSTT2, GSTT4|
|Zeta||GSTZ1 (aka GSTZ1 MAAI-Maleylacetoacetate isomerase)|
|Microsomal||MGST1, MGST2, MGST3|
The activity of GSTs is dependent upon a steady supply of GSH from the synthetic enzymes gamma-glutamylcysteine synthetase and glutathione synthetase, as well as the action of specific transporters to remove conjugates of GSH from the cell. The primary role of GSTs is to detoxify xenobiotics by catalyzing the nucleophilic attack by GSH on electrophilic carbon, sulfur, or nitrogen atoms of said nonpolar xenobiotic substrates, thereby preventing their interaction with crucial cellular proteins and nucleic acids. Specifically, the function of GSTs in this role is twofold: to bind both the substrate at the enzyme's hydrophobic H-site and GSH at the adjacent, hydrophilic G-site, which together form the active site of the enzyme; and subsequently to activate the thiol group of GSH, enabling the nucleophilic attack upon the substrate. The glutathione molecule binds in a cleft between N and C-terminal domains - the catalytically important residues are proposed to reside in the N-terminal domain. Both subunits of the GST dimer, whether hetero- or homodimeric in nature, contain a single nonsubstrate binding site, as well as a GSH-binding site. In heterodimeric GST complexes such as those formed by the cytosolic mu and alpha classes, however, the cleft between the two subunits is home to an additional high-affinity nonsubstrate xenobiotic binding site, which may account for the enzymes' ability to form heterodimers.
The compounds targeted in this manner by GSTs encompass a diverse range of environmental or otherwise exogenous toxins, including chemotherapeutic agents and other drugs, pesticides, herbicides, carcinogens, and variably-derived epoxides; indeed, GSTs are responsible for the conjugation of β1-8,9-epoxide, a reactive intermediate formed from aflatoxin B1, which is a crucial means of protection against the toxin in rodents. The detoxification reactions comprise the first four steps of mercapturic acid synthesis, with the conjugation to GSH serving to make the substrates more soluble and allowing them to be removed from the cell by transporters such as multidrug resistance-associated protein 1 (MRP1). After export, the conjugation products are converted into mercapturic acids and excreted via the urine or bile.
Most mammalian isoenzymes have affinity for the substrate 1-chloro-2,4-dinitrobenzene, and spectrophotometric assays utilising this substrate are commonly used to report GST activity. However, some endogenous compounds, e.g., bilirubin, can inhibit the activity of GSTs. In mammals, GST isoforms have cell specific distributions (e.g., alpha GST in hepatocytes and pi GST in the biliary tract of the human liver).
Role in cell signaling
Although best known for their ability to conjugate xenobiotics to GSH and thereby detoxify cellular environments, GSTs are also capable of binding nonsubstrate ligands, with important cell signaling implications. Several GST isozymes from various classes have been shown to inhibit the function of a kinase involved in the MAPK pathway that regulates cell proliferation and death, preventing the kinase from carrying out its role in facilitating the signaling cascade.
Cytosolic GSTP1-1, a well-characterized isozyme of the mammalian GST family, is expressed primarily in heart, lung, and brain tissues; in fact, it is the most common GST expressed outside the liver. Based on its overexpression in a majority of human tumor cell lines and prevalence in chemotherapeutic-resistant tumors, GSTP1-1 is thought to play a role in the development of cancer and its potential resistance to drug treatment. Further evidence for this comes from the knowledge that GSTP can selectively inhibit C-jun phosphorylation by JNK, preventing apoptosis. During times of low cellular stress, a complex forms through direct protein–protein interactions between GSTP and the C-terminus of JNK, effectively preventing the action of JNK and thus its induction of the JNK pathway. Cellular oxidative stress causes the dissociation of the complex, oligomerization of GSTP, and induction of the JNK pathway, resulting in apoptosis. The connection between GSTP inhibition of the pro-apoptotic JNK pathway and the isozyme's overexpression in drug-resistant tumor cells may itself account for the tumor cells' ability to escape apoptosis mediated by drugs that are not substrates of GSTP.
Like GSTP, GSTM1 is involved in regulating apoptotic pathways through direct protein–protein interactions, although it acts on ASK1, which is upstream of JNK. The mechanism and result are similar to that of GSTP and JNK, in that GSTM1 sequesters ASK1 through complex formation and prevents its induction of the pro-apoptotic p38 and JNK portions of the MAPK signaling cascade. Like GSTP, GSTM1 interacts with its partner in the absence of oxidative stress, although ASK1 is also involved in heat shock response, which is likewise prevented during ASK1 sequestration. The fact that high levels of GST are associated with resistance to apoptosis induced by a range of substances, including chemotherapeutic agents, supports its putative role in MAPK signaling prevention.
Implications in cancer development
There is a growing body of evidence supporting the role of GST, particularly GSTP, in cancer development and chemotherapeutic resistance. The link between GSTP and cancer is most obvious in the overexpression of GSTP in many cancers, but it is also supported by the fact that the transformed phenotype of tumor cells is associated with aberrantly regulated kinase signaling pathways and cellular addiction to overexpressed proteins. That most anti-cancer drugs are poor substrates for GSTP indicates that the role of elevated GSTP in many tumor cell lines is not to detoxify the compounds, but must have another purpose; this hypothesis is also given credence by the common finding of GSTP overexpression in tumor cell lines that are not drug resistant.
In addition to their roles in cancer development and chemotherapeutic drug resistance, GSTs are implicated in a variety of diseases by virtue of their involvement with GSH. Although the evidence is minimal for the influence of GST polymorphisms of the alpha, mu, pi, and theta classes on susceptibility to various types of cancer, numerous studies have implicated such genotypic variations in asthma, atherosclerosis, allergies, and other inflammatory diseases.
Because diabetes is a disease that involves oxidative damage, and GSH metabolism is dysfunctional in diabetic patients, GSTs may represent a potential target for diabetic drug treatment. In addition, insulin administration is known to result in increased GST gene expression through the PI3K/AKT/mTOR pathway and reduced intracellular oxidative stress, while glucagon decreases such gene expression.
Omega-class GST (GSTO) genes, in particular, are associated with neurological diseases such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis; again, oxidative stress is believed to be the culprit, with decreased GSTO gene expression resulting in a lowered age of onset for the diseases.
Release of GSTs as an indication of organ damage
The high intracellular concentrations of GSTs coupled with their cell-specific cellular distribution allows them to function as biomarkers for localising and monitoring injury to defined cell types. For example, hepatocytes contain high levels of alpha GST and serum alpha GST has been found to be an indicator of hepatocyte injury in transplantation, toxicity and viral infections.
Similarly, in humans, renal proximal tubular cells contain high concentrations of alpha GST, while distal tubular cells contain pi GST. This specific distribution enables the measurement of urinary GSTs to be used to quantify and localise renal tubular injury in transplantation, nephrotoxicity and ischaemic injury.
GST can be added to a protein of interest to purify it from solution in a process known as a pull-down assay. This is accomplished by inserting the GST DNA coding sequence next to that which codes for the protein of interest. Thus, after transcription and translation, the GST protein and the protein of interest will be expressed together as a fusion protein. Because the GST protein has a strong binding affinity for GSH, beads coated with the compound can be added to the protein mixture; as a result, the protein of interest attached to the GST will stick to the beads, isolating the protein from the rest of those in solution. The beads are recovered and washed with free GSH to detach the protein of interest from the beads, resulting in a purified protein. This technique can be used to elucidate direct protein–protein interactions. A drawback of this assay is that the protein of interest is attached to GST, altering its native state.
A GST-tag is often used to separate and purify proteins that contain the GST-fusion protein. The tag is 220 amino acids (roughly 26 KDa) in size, which, compared to tags such as the Myc-tag or the FLAG-tag, is quite large. It can be fused to either the N-terminus or C-terminus of a protein. However, many commercially available sources of GST-tagged plasmids include a thrombin domain for cleavage of the GST tag during protein purification.
- Affinity chromatography
- Bacterial glutathione transferase
- Glutathione S-transferase Mu 1
- Glutathione S-transferase, C-terminal domain
- Maltose-binding protein
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- Park AK, Moon JH, Jang EH, Park H, Ahn IY, Lee KS, et al. (2013). "The structure of a shellfish specific GST class glutathione S-transferase from antarctic bivalve Laternula elliptica reveals novel active site architecture.". Proteins. 81 (3): 531–7. PMID 23152139. doi:10.1002/prot.24208.
- Landi S (October 2000). "Mammalian class theta GST and differential susceptibility to carcinogens: a review". Mutat. Res. 463 (3): 247–83. PMID 11018744. doi:10.1016/s1383-5742(00)00050-8.
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- Hayes JD, Flanagan JU, Jowsey IR (2005). "Glutathione transferases". Annu. Rev. Pharmacol. Toxicol. 45: 51–88. PMID 15822171. doi:10.1146/annurev.pharmtox.45.120403.095857.
- Nishida M, Harada S, Noguchi S, Satow Y, Inoue H, Takahashi K (1998). "Three-dimensional structure of Escherichia coli glutathione S-transferase complexed with glutathione sulfonate: catalytic roles of Cys10 and His106.". J Mol Biol. 281 (1): 135–47. PMID 9680481. doi:10.1006/jmbi.1998.1927.
- Vargo MA, Colman RF (January 2001). "Affinity labeling of rat glutathione S-transferase isozyme 1-1 by 17beta -iodoacetoxy-estradiol-3-sulfate". J. Biol. Chem. 276 (3): 2031–6. PMID 11031273. doi:10.1074/jbc.M008212200.
- Habig WH, Pabst MJ, Fleischner G, Gatmaitan Z, Arias IM, Jakoby WB (October 1974). "The Identity of Glutathione S-Transferase B with Ligandin, a Major Binding Protein of Liver". Proc. Natl. Acad. Sci. U.S.A. 71 (10): 3879–82. PMC . PMID 4139704. doi:10.1073/pnas.71.10.3879.
- Beckett GJ, Hayes JD (1987). "Glutathione S-transferase measurements and liver disease in man". Journal of Clinical Biochemistry and Nutrition. 2: 1–24. doi:10.3164/jcbn.2.1.
- Laborde E (September 2010). "Glutathione transferases as mediators of signaling pathways involved in cell proliferation and cell death". Cell Death Differ. 17 (9): 1373–80. PMID 20596078. doi:10.1038/cdd.2010.80.
- Adler V, Yin Z, Fuchs SY, et al. (March 1999). "Regulation of JNK signaling by GSTp". EMBO J. 18 (5): 1321–34. PMC . PMID 10064598. doi:10.1093/emboj/18.5.1321.
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- Franco R, Schoneveld OJ, Pappa A, Panayiotidis MI (2007). "The central role of glutathione in the pathophysiology of human diseases". Arch. Physiol. Biochem. 113 (4–5): 234–58. PMID 18158646. doi:10.1080/13813450701661198.
- Board PG (May 2011). "The omega-class glutathione transferases: structure, function, and genetics". Drug Metab. Rev. 43 (2): 226–35. PMID 21495794. doi:10.3109/03602532.2011.561353.
- Beckett GJ, Chapman BJ, Dyson EH, Hayes JD (January 1985). "Plasma glutathione S-transferase measurements after paracetamol overdose: evidence for early hepatocellular damage". Gut. 26 (1): 26–31. PMC . PMID 3965363. doi:10.1136/gut.26.1.26.
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- Sundberg AG, Appelkvist EL, Bäckman L, Dallner G (1994). "Urinary pi-class glutathione transferase as an indicator of tubular damage in the human kidney". Nephron. 67 (3): 308–16. PMID 7936021. doi:10.1159/000187985.
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- Overview of Glutathione-S-Transferases
- UMich Orientation of Proteins in Membranes families/superfamily-199 - MAPEG (Eicosanoid and Glutathione metabolism proteins) family
- Glutathione S-Transferase at the US National Library of Medicine Medical Subject Headings (MeSH)
- EC 184.108.40.206
- Preparation of GST Fusion Proteins
- GST Gene Fusion System Handbook
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.
Glutathione S-transferase N-terminal domain Provide feedback
This domain is homologous to PF02798.
Internal database links
|SCOOP:||Glutaredoxin GST_C GST_C_2 GST_N GST_N_2 GST_N_3 Tom37|
|Similarity to PfamA using HHSearch:||GST_N Tom37 GST_N_2 GST_N_3|
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:
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This example describes an architecture with one
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EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
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- 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 54 members:2Fe-2S_thioredx AhpC-TSA AhpC-TSA_2 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 MRP-S23 MRP-S25 OST3_OST6 Phe_hydrox_dim 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
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:||166|
|Number in full:||1132|
|Average length of the domain:||96.60 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||32.99 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||3|
|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.