Summary: Alkaline phosphatase
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Alkaline phosphatase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
Structure of alkaline phosphatase.
Alkaline phosphatase (ALP, ALKP, ALPase, Alk Phos) (EC 22.214.171.124) is a hydrolase enzyme responsible for removing phosphate groups from many types of molecules, including nucleotides, proteins, and alkaloids. The process of removing the phosphate group is called dephosphorylation. As the name suggests, alkaline phosphatases are most effective in an alkaline environment. It is sometimes used synonymously as basic phosphatase.
Alkaline Phosphatase is a ubiquitous enzyme that is a dimer that contains Zinc. In Gram-negative bacteria, alkaline phosphatase is located in the periplasmic space, external to the cell membrane. Since this space is much more subject to environmental variation than the actual interior of the cell, bacterial alkaline phosphatase is resistant to inactivation, denaturation, and degradation, and contains a higher rate of activity. Although the purpose of the enzyme is not fully resolved, the simple hypothesis is that it serves to cleave phosphate groups from phosphorylated compounds facilitating transport across membranes and providing the cell with a source of inorganic phosphate at times of phosphate starvation.The main purpose of dephosphorylation by Alkaline Phosphatase is to increase the rate of diffusion of the molecules into the cells and inhibit them from diffusing out. However, other possibilities exist. For instance, the presence of phosphate groups usually prevents organic molecules from passing through the membrane; therefore, dephosphorylating them may be important for bacterial uptake of organic compounds.
Alkaline Phosphatase is a Zinc containing dimeric enzyme with the MW: 86,000 kDa. It is heat stable and its function is to remove phosphate groups from phosphorylated compounds facilitating transport across membranes and providing the cell with a source of inorganic phosphate. Alkaline Phosphatase in E.coli is located in the periplasmic space and we can thus, selectively release it with a technique that weakens the cell wall and releases the proteins. Due to the location of the enzyme, and the protein layout of the enzyme the enzyme is in solution with a small amount of proteins than there are in another portion of the cell.  Some complexities of bacterial regulation and metabolism suggest that other, more subtle, purposes for the enzyme may also play a role for the cell. In the laboratory, however, mutant Escherichia coli lacking alkaline phosphatase survive quite well, as do mutants unable to shut off alkaline phosphatase production.
Use in research
By changing the amino acids of the wild-type alkaline phosphatase enzyme produced by Escherichia coli, a mutant alkaline phosphatase is created which not only has a 36-fold increase in enzyme activity, but also retains thermal stability. Typical uses in the lab for alkaline phosphatases include removing phosphate monoesters to prevent self-ligation, which is undesirable during plasmid DNA cloning.
Common alkaline phosphatases used in research include:
- Shrimp alkaline phosphatase (SAP), from a species of Arctic shrimp (Pandalus borealis). This phosphatase is easily inactivated by heat, a useful feature in some applications.
- Calf-intestinal alkaline phosphatase (CIP)
- Placental alkaline phosphatase (PLAP) and its C terminally truncated version that lacks the last 24 amino acids (constituting the domain that targets for GPI membrane anchoring) - the secreted alkaline phosphatase (SEAP). It presents certain characteristics like heat stability, substrate specificity, and resistance to chemical inactivation.
- Human-intestinal alkaline phosphatase. The human body has multiple types of alkaline phosphatase present, which are determined by a minimum of three gene loci. Each one of these three loci controls a different kind of alkaline phosphatase isozyme. However, the development of this enzyme can be strictly regulated by other factors such as thermostability, electrophoresis, inhibition, or immunology.
Human-intestinal ALPase shows around 80% homology with bovine intestinal ALPase, which holds true their shared evolutionary origins. That same bovine enzyme has more than 70% homology with human placental enzyme. However, the human intestinal enzyme and the placental enzyme only share 20% homology despite their structural similarities.
Alkaline phosphatase has become a useful tool in molecular biology laboratories, since DNA normally possesses phosphate groups on the 5' end. Removing these phosphates prevents the DNA from ligating (the 5' end attaching to the 3' end), thereby keeping DNA molecules linear until the next step of the process for which they are being prepared; also, removal of the phosphate groups allows radiolabeling (replacement by radioactive phosphate groups) in order to measure the presence of the labeled DNA through further steps in the process or experiment. For these purposes, the alkaline phosphatase from shrimp is the most useful, as it is the easiest to inactivate once it has done its job.
Another important use of alkaline phosphatase is as a label for enzyme immunoassays.
Undifferentiated pluripotent stem cells have elevated levels of alkaline phosphatase on their cell membrane, therefore alkaline phosphatase staining is used to detect these cells and to test pluripotency (i.e., embryonic stem cells or embryonal carcinoma cells).
Current researchers are looking into the the increase of Tumor necrosis factor-α and its direct effect on the expression alkaline phosphatase in vascular smooth muscle cells. As well as the how Alkaline phosphatase (AP) effects the inflammatory responses and may have a directly play a role in preventing by organ damage.
- Alkaline phosphatase (AP) affect on the inflammatory responses in patients with Chronic kidney disease and is directly associated with Erythropoiesis stimulating agent resistant anemia.
- Intestinal alkaline phosphatase (IAP) and the mechanism it uses to regulate pH and ATP hydrolysis in rat dodenum.
- Testing the effectiveness of the inhibitor and its impact on IAP in acute intestinal inflammation as well as expoler the molecular mechanisms of IAP in "ameliorating intestinal permeability."
Alkaline phosphatase is commonly used in the dairy industry as an indicator of successful pasteurization. This is because the most heat stable bacterium found in milk, Mycobacterium paratuberculosis, is destroyed by temperatures lower than those required to denature ALP. Therefore ALP presence is ideal for indicating successful pasteurization.
Pasteurization verification is typically performed by measuring the fluorescence of a solution which becomes fluorescent when exposed to active ALP. Fluorimetry assays are required by milk producers in the UK to prove alkaline phosphatase has been denatured, as p-Nitrophenylphosphate tests are not considered accurate enough to meet health standards.
Alternatively the colour change of a para-Nitrophenylphosphate substrate in a buffered solution (Aschaffenburg Mullen Test) can be used. Raw milk would typically produce a yellow colouration within a couple of minutes, whereas properly pasteurised milk should show no change. There are exceptions to this, as in the case of heat-stable alkaline phophatases produced by some bacteria, but these bacteria should not be present in milk.
All mammalian alkaline phosphatase isoenzymes except placental (PALP and SEAP) are inhibited by homoarginine, and, in similar manner, all except the intestinal and placental ones are blocked by levamisole. Heating for ~2 hours at 65 °C inactivates most isoenzymes except placental isoforms (PALP and SEAP). Phosphate is another inhibitor which competitively inhibits alkaline phosphatase.
In humans, alkaline phosphatase is present in all tissues throughout the entire body, but is particularly concentrated in the liver, bile duct, kidney, bone, intestinal mucosa and placenta. In the serum, two types of alkaline phosphatase isozymes predominate: skeletal and liver. During childhood the majority of alkaline phosphatase are of skeletal origin. Humans and most other mammals contain the following alkaline phosphatase isozymes:
- ALPI – intestinal (molecular weight of 150 kDa)
- ALPL – tissue-nonspecific (liver/bone/kidney)
- ALPP – placental (Regan isozyme)
Alkaline Phosphatase in cancer cells
Studies show that the alkaline phosphatase protein found in cancer cells has similar characteristics to that found in non-malignant body tissues. Results show that the protein has originated from the same gene in both the malignant and the non-malignant cells. A study conducted by scientists Patricia J. Greene and Howard H. Sussman tested the structural comparison between the alkaline phosphatase proteins found in liver giant-cell carcinoma and non-malignant placental cells. In this study, an alkaline phosphatase that was immunochemically similar to placental alkaline phosphatase was purified from metastases of giant-cell carcinoma of the lung and its physical and chemical properties were determined. Thereafter, these were compared with purified placental alkaline phosphatase. The results showed great similarity in both based on evaluations of NH2-terminal sequence, peptide map, subunit molecular weight, and isoelectronic point. Overall, this study strongly supports the supposition that the alkaline phosphatase protein in both tumor and non-malignant placental cells are derived from the same gene.
In a different study in which scientists examined alkaline phosphatase protein presence in a human colon cancer cell line, also known as HT-29, results showed that the enzyme activity was similar to that of the non-malignant intestinal type. However, this study revealed that without the influence of sodium butyrate, alkaline phosphatase activity is fairly low in cancer cells. A study based on sodium butyrate effects on cancer cells conveys that it has an effect on androgen receptor co-regulator expression, transcription activity, and also on histone acetylation in cancer cells. This explains why the addition of sodium butyrate show increased activity of alkaline phosphatase in the cancer cells of the human colon. In addition, this further supports the theory that alkaline phosphatase enzyme activity is actually present in cancer cells.
In another study, choriocarcinoma cells were grown in the presence of 5-bromo-2’-deoxyuridine (BrdUrd) and results conveyed a 30- to 40- fold increase in alkaline phosphatase activity. This procedure of enhancing the activity of the enzyme is known as enzyme induction. The evidence shows that there is in fact activity of alkaline phosphatase in tumor cells, but it is minimal and needs to be enhanced. Results from this study further indicate that activities of this enzyme vary among the different choriocarcinoma cell lines and that the activity of the alkaline phosphatase protein in these cells is lower than in the non-malignant placenta cells.
Normal ALP levels in adults are approximately 20 to 140 IU/L, but levels are significantly higher in children and pregnant women. Blood tests should always be interpreted using the reference range from the laboratory that performed the test. High ALP levels can occur if the bile ducts are obstructed. Also, ALP increases if there is active bone formation occurring, as ALP is a byproduct of osteoblast activity (such as the case in Paget's disease of bone). Levels are also elevated in people with untreated coeliac disease. Lowered levels of ALP are less common than elevated levels. The source of elevated ALP levels can be deduced by obtaining serum levels of gamma glutamyltransferase (GGT). Concomitant increases of ALP with GGT should raise the suspicion of hepatobiliary disease.
Some diseases do not affect the levels of alkaline phosphatase, for example, hepatitis C. A high level of this enzyme does not reflect any damage in the liver, even though high alkaline phosphatase levels may result from a blockage of flow in the biliary tract or an increase in the pressure of the liver.
If it is unclear why alkaline phosphatase is elevated, isoenzyme studies using electrophoresis can confirm the source of the ALP. Heat stability also distinguishes bone and liver isoenzymes ("bone burns, liver lasts"). Serum alkaline phosphatase is acquired through several sources: liver, bone, kidney, intestine, and placenta (for women). Skeletal alkaline phosphatase (which is localized in osteoblasts and extracellular layers of newly synthesized matrix) is released into circulation by a yet unclear mechanism. Placental alkaline phosphatase is elevated in seminomas and active forms of rickets, as well as in the following diseases and conditions:
- Biliary obstruction
- Bone conditions
- Osteoblastic bone tumors
- Liver disease or hepatitis
- Paget's disease
- Myocardial infarction
The following conditions or diseases may lead to reduced levels of alkaline phosphatase:
- Hypophosphatasia, an autosomal recessive disease
- Postmenopausal women receiving estrogen therapy because of osteoporosis
- Men with recent heart surgery, malnutrition, magnesium deficiency, hypothyroidism, or severe anemia
- Children with achondroplasia and cretinism
- Children after a severe episode of enteritis
- Pernicious anemia
- Aplastic anemia
- Chronic myelogenous leukemia
- Wilson's disease
In addition, the following drugs have been demonstrated to reduce alkaline phosphatase:
- Oral contraceptives
Measuring alkaline phosphatase (along with prostate specific antigen) during, and after six months of hormone treated metastatic prostate cancer was shown to predict the survival of patients.
Leukocyte alkaline phosphatase
Leukocyte alkaline phosphatase (LAP) is found within mature white blood cells. White blood cell levels of LAP can help in the diagnosis of certain conditions.
- Higher levels are seen in polycythemia vera (PV), essential thrombocytosis (ET), primary myelofibrosis (PM), and the leukemoid reaction.
- Lower levels are found in chronic myelogenous leukemia (CML), paroxysmal nocturnal hemoglobinuria (PNH) and acute myelogenous leukaemia (AML).
- doi:10.1016/0022-2836(91)90724-K. PMID 2010919.: Kim EE, Wyckoff HW (March 1991). "Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis". J. Mol. Biol. 218 (2): 449–64.
- Tamás L, Huttová J, Mistrk I, Kogan G (2002). "Eﬀect of Carboxymethyl Chitin-Glucan on the Activity of Some Hydrolytic Enzymes in Maize Plants" (PDF). Chem. Pap. 56 (5): 326–329.
- Horiuchi T, Horiuchi S, Mizuno D (May 1959). "A possible negative feedback phenomenon controlling formation of alkaline phosphomonoesterase in Escherichia coli". Nature 183 (4674): 1529–30. doi:10.1038/1831529b0. PMID 13666805.
- Ammerman JW, Azam F (March 1985). "Bacterial 5-nucleotidase in aquatic ecosystems: a novel mechanism of phosphorus regeneration". Science 227 (4692): 1338–40. doi:10.1126/science.227.4692.1338. PMID 17793769.
- Wanner BL, Latterell P (October 1980). "Mutants affected in alkaline phosphatase, expression: evidence for multiple positive regulators of the phosphate regulon in Escherichia coli". Genetics 96 (2): 353–66. PMC 1214304. PMID 7021308.
- Garen A, Levinthal C (March 1960). "A fine-structure genetic and chemical study of the enzyme alkaline phosphatase of E. coli. I. Purification and characterization of alkaline phosphatase". Biochim. Biophys. Acta 38: 470–83. doi:10.1016/0006-3002(60)91282-8. PMID 13826559.
- Harada M, Udagawa N, Fukasawa K, Hiraoka BY, Mogi M (February 1986). "Inorganic pyrophosphatase activity of purified bovine pulp alkaline phosphatase at physiological pH". J. Dent. Res. 65 (2): 125–7. doi:10.1177/00220345860650020601. PMID 3003174.
- W, MANDECKI; J, TOMAZICALL; A, SHALLCROSS; J, TOMAZIC-ALLEN. "Mutant Escherichia coli alkaline phosphatase enzymes - having amino acid changes to increase specific activity while retaining thermal stability". Retrieved 1 May 2016.
- Maxam AM, Gilbert W (1980). "Sequencing end-labeled DNA with base-specific chemical cleavages". Meth. Enzymol. Methods in Enzymology 65 (1): 499–560. doi:10.1016/S0076-6879(80)65059-9. ISBN 978-0-12-181965-1. PMID 6246368.
- Birkett, Donald J.; Done, James; Neale, Francis C.; Posen, Solomon (1966-01-01). "Serum Alkaline Phosphatase In Pregnancy: An Immunological Study". The British Medical Journal 1 (5497): 1210–1212.
- Benham, Frances J.; Harris, Harry (1979-01-01). "Human Cell Lines Expressing Intestinal Alkaline Phosphatase". Proceedings of the National Academy of Sciences of the United States of America 76 (8): 4016–4019.
- Hua, Jia-Cheng; Berger, Joel; Pan, Yu-Ching E.; Hulmes, Jeffrey D.; Udenfriend, Sidney (1986-01-01). "Partial Sequencing of Human Adult, Human Fetal, and Bovine Intestinal Alkaline Phosphatases: Comparison with the Human Placental and Liver Isozymes". Proceedings of the National Academy of Sciences of the United States of America 83 (8): 2368–2372.
- "Appendix E: Stem Cell Markers". Stem Cell Information. National Institutes of Health, U.S. Department of Health and Human Services. Retrieved 2013-09-24.
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- Kay, H. (1935). "Some Results of the Application of a Simple Test for Efficiency of Pasteurisation". The Lancet 225 (5835): 1516–1518. doi:10.1016/S0140-6736(01)12532-8.
- Hoy, W. A.; Neave, F. K. (1937). "The Phosphatase Test for Efficient Pasteurisation". The Lancet 230 (5949): 595–598. doi:10.1016/S0140-6736(00)83378-4.
- BS EN ISO 11816-1:2013
- Aschaffenburg R, Mullen JE (1949). "A rapid and simple phosphatase test for milk". Journal of Dairy Research 16 (1): 58–67. doi:10.1017/S0022029900005288.
- from Everday Health.com. Retrieved October 15, 2012.
- Iqbal, J (2011) “An enzyme immobilized microassay in capillary electrophoresis for characterization and inhibition studies of alkaline phosphatases” J Anal. Biochem. 414, 226-231
- I, Reiss; D, Inderrieden; K, Kruse (Sep 1996). "Measurement of skeletal specific alkaline phosphatase in disorders of calcium metabolism in childhood". MONATSSCHRIFT KINDERHEILKUNDE 144 (9): 885–890. doi:10.1007/s001120050054. Retrieved 1 May 2016.
- Greene, Patricia J.; Sussman, Howard H. (1973-01-01). "Structural Comparison of Ectopic and Normal Placental Alkaline Phosphatase". Proceedings of the National Academy of Sciences of the United States of America 70 (10): 2936–2940.
- Herz, Fritz; Schermer, Alexander; Halwer, Murray; Bogart, Lee H. (1981-09-01). "Alkaline phosphatase in HT-29, a human colon cancer cell line: Influence of sodium butyrate and hyperosmolality". Archives of Biochemistry and Biophysics 210 (2): 581–591. doi:10.1016/0003-9861(81)90224-1.
- Paskova, Lenka; Smesny Trtkova, Katerina; Fialova, Barbora; Benedikova, Andrea; Langova, Katerina; Kolar, Zdenek (2013-08-01). "Different effect of sodium butyrate on cancer and normal prostate cells". Toxicology in Vitro 27 (5): 1489–1495. doi:10.1016/j.tiv.2013.03.002.
- Chou, Janice Y.; Robinson, J. C. (1977-01-01). "Induction of Placental Alkaline Phosphatase in Choriocarcinoma Cells by 5-Bromo-2'-Deoxyuridine". In Vitro 13 (7): 450–460.
- "MedlinePlus Medical Encyclopedia: ALP isoenzyme test".
- ALP: The Test
- Preussner, Harold T, HT (March 1998). "Detecting coeliac disease in your patients". American Family Physician 57 (5): 1023–1034. PMID 9518950.
- Vroon, David. "Clinical Methods: The History, Physical, and Laboratory Examinations. 3rd edition".
- "Alkaline phosphatase: Liver Function Test - Viral Hepatitis". www.hepatitis.va.gov. Retrieved 2016-05-02.
- l, Karaca (Feb 1999). "What do we know about serum alkaline phosphatase activity as a biochemical bone formation marker?". BIOCHEMICAL ARCHIVES 15 (1): 1–4. Retrieved 1 May 2016.
- Lange PH, Millan JL, Stigbrand T, Vessella RL, Ruoslahti E, Fishman WH (August 1982). "Placental alkaline phosphatase as a tumor marker for seminoma". Cancer Res. 42 (8): 3244–7. PMID 7093962.
- Dugdale, David C. "ALP-bloodtest:MedlinePlus Medical Encyclopedia". MedlinePlus. Retrieved 2014-02-26.
- P, FOUCAULT; MH, FOUCAULT; B, KUCHAREWICZ; F, BUREAU; M, ALIX; MA, DROSDOWSKY (1991). "BONE AND TOTAL ALKALINE-PHOSPHATASE MEASUREMENTS IN AN OSTEOPOROTIC POPULATION". ANNALES DE BIOLOGIE CLINIQUE 49 (9): 477–481. Retrieved 2 May 2016.
- Schiele F, Vincent-Viry M, Fournier B, Starck M, Siest G (November 1998). "Biological effects of eleven combined oral contraceptives on serum triglycerides, gamma-glutamyltransferase, alkaline phosphatase, bilirubin and other biochemical variables". Clin. Chem. Lab. Med. 36 (11): 871–8. doi:10.1515/CCLM.1998.153. PMID 9877094.
- Robinson, David; Sandblom, Gabriel; Johansson, Robert (Jan 2008). "Prediction of survival of metastatic prostate cancer based on early serial measurements of prostate specific antigen and alkaline phosphatase". JOURNAL OF UROLOGY 179 (1): 117–122. Retrieved 2 May 2016.
- Arceci RJ, Hann IM, Smith OP, eds. (2006). Pediatric hematology (3rd ed.). Wiley-Blackwell. p. 763. ISBN 978-1-4051-3400-2.
- Alkaline phosphatase at Lab Tests Online
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Internal database links
|SCOOP:||Sulfatase Phosphodiest Metalloenzyme PglZ|
|Similarity to PfamA using HHSearch:||Sulfatase Metalloenzyme|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001952
This entry represents alkaline phosphatases (EC) (ALP), which act as non-specific phosphomonoesterases to hydrolyse phosphate esters, optimally at high pH. The reaction mechanism involves the attack of a serine alkoxide on a phosphorus of the substrate to form a transient covalent enzyme-phosphate complex, followed by the hydrolysis of the serine phosphate. Alkaline phosphatases are found in all kingdoms of life, with the exception of some plants. Alkaline phosphatases are metalloenzymes that exist as a dimer, each monomer binding metal ions. The metal ions they carry can differ, although zinc and magnesium are the most common. For example, Escherichia coli alkaline phosphatase (encoded by phoA) requires the presence of two zinc ions bound at the M1 and M2 metal sites, and one magnesium ion bound at the M3 site [PUBMED:15938627]. However, alkaline phosphatases from Thermotoga maritima and Bacillus subtilis require cobalt for maximal activity [PUBMED:11910033].
In mammals, there are four alkaline phosphatase isozymes: placental, placental-like (germ cell), intestinal and tissue-nonspecific (liver/bone/kidney). All four isozymes are anchored to the outer surface of the plasma membrane by a covalently attached glycosylphosphatidylinositol (GPI) anchor [PUBMED:17520090]. Human alkaline phosphatases have four metal binding sites: two for zinc, one for magnesium, and one for calcium ion. Placental alkaline phosphatase (ALPP or PLAP) is highly polymorphic, with at least three common alleles [PUBMED:11124260]. Its activity is down-regulated by a number of effectors such as l-phenylalanine, 5'-AMP, and by p-nitrophenyl-phosphonate (PNPPate) [PUBMED:15946677]. The placental-like isozyme (ALPPL or PLAP-like) is elevated in germ cell tumours. The intestinal isozyme (ALPI or IAP) has the ability to detoxify lipopolysaccharide and prevent bacterial invasion across the gut mucosal barrier [PUBMED:18292227]. The tissue-nonspecific isozyme (ALPL) is, and may play a role in skeletal mineralisation. Defects in ALPL are a cause of hypophosphatasia, including infantile-type (OMIM:241500), childhood-type (OMIM:241510) and adult-type (OMIM:146300). Hhypophosphatasia is an inherited metabolic bone disease characterised by defective skeletal mineralisation [PUBMED:17719863].
This entry also contains the related enzyme streptomycin-6-phosphate phosphatase (EC) (encoded by strK) from Streptomyces species. This enzyme is involved in the synthesis of the antibiotic streptomycin, specifically cleaving both streptomycin-6-phosphate and, more slowly, streptomycin-3-phosphate [PUBMED:1654502].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||phosphatase activity (GO:0016791)|
|Biological process||metabolic process (GO:0008152)|
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The members of this clan all share a common structure of their catalytic domains, which contain conserved metal binding residues .
The clan contains the following 10 members:Alk_phosphatase DUF1501 DUF229 DUF4976 Metalloenzyme PglZ Phosphodiest Phosphoesterase Sulfatase Sulfatase_C
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|Number in seed:||10|
|Number in full:||1733|
|Average length of the domain:||368.80 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||78.22 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
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This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Alk_phosphatase domain has been found. There are 216 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...