Summary: Phosphatidylinositol 3- and 4-kinase
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Phosphoinositide 3-kinase Edit Wikipedia article
PIK-93 inhibitor (yellow) bound to the PI3 Kinase 110 gamma subunit .
|PDB structures||RCSB PDB PDBe PDBsum|
Phosphatidylinositol-4,5-bisphosphate 3-kinase (also called phosphatidylinositide 3-kinases, phosphatidylinositol-3-kinases, PI 3-kinases, PI(3)Ks, PI-3Ks or by the HUGO official stem symbol for the gene family, PI3K(s)) are a family of enzymes involved in cellular functions such as cell growth, proliferation, differentiation, motility, survival and intracellular trafficking, which in turn are involved in cancer.
PI3Ks are a family of related intracellular signal transducer enzymes capable of phosphorylating the 3 position hydroxyl group of the inositol ring of phosphatidylinositol (PtdIns). The pathway, with oncogene PIK3CA and tumor suppressor PTEN, is implicated in insensitivity of cancer tumors to insulin and IGF1, and in calorie restriction.
- 1 Discovery
- 2 Classes
- 3 Human genes
- 4 Mechanism
- 5 Function
- 6 PI 3-kinases as protein kinases
- 7 Inhibition
- 8 See also
- 9 References
- 10 Further reading
- 11 External links
The discovery of PI 3-kinases by Lewis Cantley and colleagues began with their identification of a previously unknown phosphoinositide kinase associated with the polyoma middle T protein. They observed unique substrate specificity and chromatographic properties of the products of the lipid kinase, leading to the discovery that this phosphoinositide kinase had the unprecedented ability to phosphorylate phosphoinositides on the 3' position of the inositol ring. Subsequently, Cantley and colleagues demonstrated that in vivo the enzyme prefers PtdIns(4,5)P2 as a substrate, producing the novel phosphoinositide PtdIns(3,4,5)P3.
The phosphoinositol-3-kinase family is divided into four different classes: Class I, Class II, Class III, and Class IV. The classifications are based on primary structure, regulation, and in vitro lipid substrate specificity.
Class I PI3Ks are responsible for the production of phosphatidylinositol 3-phosphate (PI(3)P), phosphatidylinositol (3,4)-bisphosphate (PI(3,4)P2), and phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P3). The PI3K is activated by G protein-coupled receptors and tyrosine kinase receptors.
Class I PI3K are heterodimeric molecules composed of a regulatory and a catalytic subunit; they are further divided between IA and IB subsets on sequence similarity. Class IA PI3K is composed of a heterodimer between a p110 catalytic subunit and a p85 regulatory subunit. There are five variants of the p85 regulatory subunit, designated p85α, p55α, p50α, p85β, and p55γ. There are also three variants of the p110 catalytic subunit designated p110α, β, or δ catalytic subunit. The first three regulatory subunits are all splice variants of the same gene (Pik3r1), the other two being expressed by other genes (Pik3r2 and Pik3r3, p85β, and p55γ, respectively). The most highly expressed regulatory subunit is p85α; all three catalytic subunits are expressed by separate genes (Pik3ca, Pik3cb, and Pik3cd for p110α, p110β, and p110δ, respectively). The first two p110 isoforms (α and β) are expressed in all cells, but p110δ is expressed primarily in leukocytes, and it has been suggested that it evolved in parallel with the adaptive immune system. The regulatory p101 and catalytic p110γ subunits comprise the class IB PI3Ks and are encoded by a single gene each.
The p85 subunits contain SH2 and SH3 domains (Online 'Mendelian Inheritance in Man' (OMIM) 171833). The SH2 domains bind preferentially to phosphorylated tyrosine residues in the amino acid sequence context Y-X-X-M.
Classes II and III
Class II and III PI3K are differentiated from the Class I by their structure and function. The distinct feature of Class II PI3Ks is the C-terminal C2 domain. This domain lacks critical Asp residues to coordinate binding of Ca2+, which suggests class II PI3Ks bind lipids in a Ca2+-independent manner.
Class II comprises three catalytic isoforms (C2α, C2β, and C2γ), but, unlike Classes I and III, no regulatory proteins. Class II catalyse the production of PI(3)P from PI and PI(3,4)P2 from PIP; however, little is known about their role in immune cells. C2α and C2β are expressed through the body, but expression of C2γ is limited to hepatocytes.
Class III produces only PI(3)P from PI  but are more similar to Class I in structure, as they exist as heterodimers of a catalytic (Vps34) and a regulatory (Vps15/p150) subunits. Class III seems to be primarily involved in the trafficking of proteins and vesicles. There is, however, evidence to show that they are able to contribute to the effectiveness of several process important to immune cells, not least phagocytosis.
A group of more distantly related enzymes are sometimes referred to as class IV PI 3-kinases. It is composed of ataxia telangiectasia mutated (ATM), ataxia telangiectasia and Rad3 related (ATR), DNA-dependent protein kinase (DNA-PK) and mammalian target of rapamycin (mTOR). They are protein serine/threonine kinases.
|class 1 catalytic||PIK3CA||PI3K, catalytic, alpha polypeptide||p110-α||126.96.36.199|
|PIK3CB||PI3K, catalytic, beta polypeptide||p110-β|
|PIK3CG||PI3K, catalytic, gamma polypeptide||p110-γ|
|PIK3CD||PI3K, catalytic, delta polypeptide||p110-δ|
|class 1 regulatory||PIK3R1||PI3K, regulatory subunit 1 (alpha)||p85-α||N/A|
|PIK3R2||PI3K, regulatory subunit 2 (beta)||p85-β|
|PIK3R3||PI3K, regulatory subunit 3 (gamma)||p55-γ|
|PIK3R4||PI3K, regulatory subunit 4||p150|
|PIK3R5||PI3K, regulatory subunit 5||p101|
|PIK3R6||PI3K, regulatory subunit 6||p87|
|class 2||PIK3C2A||PI3K, class 2, alpha polypeptide||PI3K-C2α||188.8.131.52|
|PIK3C2B||PI3K, class 2, beta polypeptide||PI3K-C2β|
|PIK3C2G||PI3K, class 2, gamma polypeptide||PI3K-C2γ|
|class 3||PIK3C3||PI3K, class 3||Vps34||184.108.40.206|
The various 3-phosphorylated phosphoinositides that are produced by PI 3-kinases (PtdIns3P, PtdIns(3,4)P2, PtdIns(3,5)P2, and PtdIns(3,4,5)P3) function in a mechanism by which an assorted group of signalling proteins, containing PX domain, pleckstrin homology domains (PH domains), FYVE domains and other phosphoinositide-binding domains, are recruited to various cellular membranes.
PI 3-kinases have been linked to an extraordinarily diverse group of cellular functions, including cell growth, proliferation, differentiation, motility, survival and intracellular trafficking. Many of these functions relate to the ability of class I PI 3-kinases to activate protein kinase B (PKB, aka Akt) as in the PI3K/AKT/mTOR pathway. The p110δ and p110γ isoforms regulate different aspects of immune responses. PI 3-kinases are also a key component of the insulin signaling pathway. Hence there is great interest in the role of PI 3-kinase signaling in diabetes mellitus.
The pleckstrin homology domain of AKT binds directly to PtdIns(3,4,5)P3 and PtdIns(3,4)P2, which are produced by activated PI 3-kinase. Since PtdIns(3,4,5)P3 and PtdIns(3,4)P2 are restricted to the plasma membrane, these results in translocation of AKT to the plasma membrane. Likewise, the phosphoinositide-dependent kinase-1 (PDK1 or, rarely referred to as PDPK1) also contains a pleckstrin homology domain that binds directly to PtdIns(3,4,5)P3 and PtdIns(3,4)P2, causing it to also translocate to the plasma membrane upon activation of PI 3-kinase. The interaction of activated PDK1 and AKT allows AKT to become phosphorylated by PDK1 on threonine 308, leading to partial activation of AKT. Full activation of AKT occurs upon phosphorylation of serine 473 by the TORC2 complex of the mTOR protein kinase.
The "PI3-k/AKT" signaling pathway has been shown to be required for an extremely diverse array of cellular activities - most notably cellular proliferation and survival. The phosphatidylinositol 3-kinase/protein kinase B pathway is stimulated in protection of astrocytes from ceramide-induced apoptosis.
Many other proteins have been identified that are regulated by PtdIns(3,4,5)P3, including Bruton's tyrosine kinase (BTK), General Receptor for Phosphoinositides-1 (GRP1), and the O-linked N-acetylglucosamine (O-GlcNAc) transferase.
The class IA PI 3-kinase p110α is mutated in many cancers. Many of these mutations cause the kinase to be more active. It is the single most mutated kinase in glioblastoma, the most malignant primary brain tumor. The PtdIns(3,4,5)P3 phosphatase PTEN that antagonises PI 3-kinase signaling is absent from many tumours. In addition, the epidermal growth factor receptor EGFR that functions upstream of PI 3-kinase is mutationally activated or overexpressed in cancer. Hence, PI 3-kinase activity contributes significantly to cellular transformation and the development of cancer.
Learning and memory
PI3K has also been implicated in long-term potentiation (LTP). Whether it is required for the expression or the induction of LTP is still debated. In mouse hippocampal CA1 neurons, PI3K is complexed with AMPA receptors and compartmentalized at the postsynaptic density of glutamatergic synapses. PI3K is phosphorylated upon NMDA receptor-dependent CaMKII activity, and it then facilitates the insertion of AMPA-R GluR1 subunits into the plasma membrane. This suggests that PI3K is required for the expression of LTP. Furthermore, PI3K inhibitors abolished the expression of LTP in rat hippocampal CA1, but do not affect its induction. Notably, the dependence of late-phase LTP expression on PI3K seems to decrease over time.
However, another study found that PI3K inhibitors suppressed the induction, but not the expression, of LTP in mouse hippocampal CA1. The PI3K pathway also recruits many other proteins downstream, including mTOR, GSK3β, and PSD-95. The PI3K-mTOR pathway leads to the phosphorylation of p70S6K, a kinase that facilitates translational activity, further suggesting that PI3K is required for the protein-synthesis phase of LTP induction instead.
PI3Ks interact with the insulin receptor substrate (IRS) to regulate glucose uptake through a series of phosphorylation events.
PI 3-kinases as protein kinases
Many of the PI 3-kinases appear to have a serine/threonine kinase activity in vitro; however, it is unclear whether this has any role in vivo.
PI 3-kinases inhibitors as therapeutics
As wortmannin and LY294002 are broad inhibitors against PI 3-kinases and a number of unrelated proteins at higher concentrations they are too toxic to be used as therapeutics. A number of pharmaceutical companies have recently been working on PI 3-kinase isoform specific inhibitors including the class I PI 3-kinase, p110δ isoform specific inhibitors, IC486068 and IC87114, ICOS Corporation.. GDC-0941 is a highly selective inhibitor of p110α with little activity against mTOR.
- "A pharmacological map of the PI3-K family defines a role for p110alpha in insulin signaling". Cell 125 (4): 733–47. doi:10.1016/j.cell.2006.03.035. PMC 2946820. PMID 16647110.; Knight ZA, Gonzalez B, Feldman ME, Zunder ER, Goldenberg DD, Williams O, Loewith R, Stokoe D, Balla A, Toth B, Balla T, Weiss WA, Williams RL, Shokat KM (May 2006).
- Giese N (2009-03-11). "Cell pathway on overdrive prevents cancer response to dietary restriction". PhysOrg.com. Retrieved 2009-04-22.
- Kalaany NY, Sabatini DM (Apr 2009). "Tumours with PI3K activation are resistant to dietary restriction". Nature 458 (7239): 725–31. doi:10.1038/nature07782. PMC 2692085. PMID 19279572.
- Whitman M, Kaplan DR, Schaffhausen B, Cantley L, Roberts TM (1985). "Association of phosphatidylinositol kinase activity with polyoma middle-T competent for transformation". Nature 315 (6016): 239–42. doi:10.1038/315239a0. PMID 2987699.
- Whitman M, Downes CP, Keeler M, Keller T, Cantley L (Apr 1988). "Type I phosphatidylinositol kinase makes a novel inositol phospholipid, phosphatidylinositol-3-phosphate". Nature 332 (6165): 644–6. doi:10.1038/332644a0. PMID 2833705.
- Auger KR, Serunian LA, Soltoff SP, Libby P, Cantley LC (Apr 1989). "PDGF-dependent tyrosine phosphorylation stimulates production of novel polyphosphoinositides in intact cells". Cell 57 (1): 167–75. doi:10.1016/0092-8674(89)90182-7. PMID 2467744.
- Leevers SJ, Vanhaesebroeck B, Waterfield MD (Apr 1999). "Signalling through phosphoinositide 3-kinases: the lipids take centre stage". Current Opinion in Cell Biology 11 (2): 219–25. doi:10.1016/S0955-0674(99)80029-5. PMID 10209156.
- Okkenhaug K (January 2013). "Signaling by the phosphoinositide 3-kinase family in immune cells". Annual Review of Immunology 31 (2): 675–704. doi:10.1146/annurev-immunol-032712-095946. PMID 23330955.
- Carpenter CL, Duckworth BC, Auger KR, Cohen B, Schaffhausen BS, Cantley LC (Nov 1990). "Purification and characterization of phosphoinositide 3-kinase from rat liver". The Journal of Biological Chemistry 265 (32): 19704–11. PMID 2174051.
- Songyang Z, Shoelson SE, Chaudhuri M, Gish G, Pawson T, Haser WG, King F, Roberts T, Ratnofsky S, Lechleider RJ (Mar 1993). "SH2 domains recognize specific phosphopeptide sequences". Cell 72 (5): 767–78. doi:10.1016/0092-8674(93)90404-E. PMID 7680959.
- Yoakim M, Hou W, Songyang Z, Liu Y, Cantley L, Schaffhausen B (Sep 1994). "Genetic analysis of a phosphatidylinositol 3-kinase SH2 domain reveals determinants of specificity". Molecular and Cellular Biology 14 (9): 5929–38. doi:10.1128/MCB.14.9.5929. PMC 359119. PMID 8065326.
- Franke TF, Kaplan DR, Cantley LC, Toker A (Jan 1997). "Direct regulation of the Akt proto-oncogene product by phosphatidylinositol-3,4-bisphosphate". Science 275 (5300): 665–8. doi:10.1126/science.275.5300.665. PMID 9005852.
- Gómez Del Pulgar T, De Ceballos ML, Guzmán M, Velasco G (Sep 2002). "Cannabinoids protect astrocytes from ceramide-induced apoptosis through the phosphatidylinositol 3-kinase/protein kinase B pathway". The Journal of Biological Chemistry 277 (39): 36527–33. doi:10.1074/jbc.M205797200. PMID 12133838.
- Bleeker FE, Lamba S, Zanon C, Molenaar RJ, Hulsebos TJ, Troost D, van Tilborg AA, Vandertop WP, Leenstra S, van Noorden CJ, Bardelli A (26 September 2014). "Mutational profiling of kinases in glioblastoma". BMC Cancer 14: 718. doi:10.1186/1471-2407-14-718. PMID 25256166.
- Bleeker FE, Molenaar RJ, Leenstra S (May 2012). "Recent advances in the molecular understanding of glioblastoma". Journal of Neuro-Oncology 108 (1): 11–27. doi:10.1007/s11060-011-0793-0. PMC 3337398. PMID 22270850.
- Man HY, Wang Q, Lu WY, Ju W, Ahmadian G, Liu L, D'Souza S, Wong TP, Taghibiglou C, Lu J, Becker LE, Pei L, Liu F, Wymann MP, MacDonald JF, Wang YT (May 2003). "Activation of PI3-kinase is required for AMPA receptor insertion during LTP of mEPSCs in cultured hippocampal neurons". Neuron 38 (4): 611–24. doi:10.1016/S0896-6273(03)00228-9. PMID 12765612.
- Joyal JL, Burks DJ, Pons S, Matter WF, Vlahos CJ, White MF, Sacks DB (Nov 1997). "Calmodulin activates phosphatidylinositol 3-kinase". The Journal of Biological Chemistry 272 (45): 28183–6. doi:10.1074/jbc.272.45.28183. PMID 9353264.
- Sanna PP, Cammalleri M, Berton F, Simpson C, Lutjens R, Bloom FE, Francesconi W (May 2002). "Phosphatidylinositol 3-kinase is required for the expression but not for the induction or the maintenance of long-term potentiation in the hippocampal CA1 region". The Journal of Neuroscience 22 (9): 3359–65. PMID 11978812.
- Karpova A, Sanna PP, Behnisch T (Feb 2006). "Involvement of multiple phosphatidylinositol 3-kinase-dependent pathways in the persistence of late-phase long term potentiation expression". Neuroscience 137 (3): 833–41. doi:10.1016/j.neuroscience.2005.10.012. PMID 16326012.
- Opazo P, Watabe AM, Grant SG, O'Dell TJ (May 2003). "Phosphatidylinositol 3-kinase regulates the induction of long-term potentiation through extracellular signal-related kinase-independent mechanisms". The Journal of Neuroscience 23 (9): 3679–88. PMID 12736339.
- Yang PC, Yang CH, Huang CC, Hsu KS (Feb 2008). "Phosphatidylinositol 3-kinase activation is required for stress protocol-induced modification of hippocampal synaptic plasticity". The Journal of Biological Chemistry 283 (5): 2631–43. doi:10.1074/jbc.M706954200. PMID 18057005.
- Peineau S, Taghibiglou C, Bradley C, Wong TP, Liu L, Lu J, Lo E, Wu D, Saule E, Bouschet T, Matthews P, Isaac JT, Bortolotto ZA, Wang YT, Collingridge GL (Mar 2007). "LTP inhibits LTD in the hippocampus via regulation of GSK3beta". Neuron 53 (5): 703–17. doi:10.1016/j.neuron.2007.01.029. PMID 17329210.
- Toker A, Cantley LC (Jun 1997). "Signalling through the lipid products of phosphoinositide-3-OH kinase". Nature 387 (6634): 673–6. doi:10.1038/42648. PMID 9192891.
- Cammalleri M, Lütjens R, Berton F, King AR, Simpson C, Francesconi W, Sanna PP (Nov 2003). "Time-restricted role for dendritic activation of the mTOR-p70S6K pathway in the induction of late-phase long-term potentiation in the CA1". Proceedings of the National Academy of Sciences of the United States of America 100 (24): 14368–73. doi:10.1073/pnas.2336098100. PMC 283598. PMID 14623952.
- Vanhaesebroeck B, Leevers SJ, Ahmadi K, Timms J, Katso R, Driscoll PC, Woscholski R, Parker PJ, Waterfield MD (2001). "Synthesis and function of 3-phosphorylated inositol lipids". Annual Review of Biochemistry 70: 535–602. doi:10.1146/annurev.biochem.70.1.535. PMID 11395417. 
- Schild C, Wirth M, Reichert M, Schmid RM, Saur D, Schneider G (Dec 2009). "PI3K signaling maintains c-myc expression to regulate transcription of E2F1 in pancreatic cancer cells". Molecular Carcinogenesis 48 (12): 1149–58. doi:10.1002/mc.20569. PMID 19603422.
- Williams R, Berndt A, Miller S, Hon WC, Zhang X (Aug 2009). "Form and flexibility in phosphoinositide 3-kinases". Biochemical Society Transactions 37 (Pt 4): 615–26. doi:10.1042/BST0370615. PMID 19614567.
- Quaresma AJ, Sievert R, Nickerson JA (Apr 2013). "Regulation of mRNA export by the PI3 kinase/AKT signal transduction pathway". Molecular Biology of the Cell 24 (8): 1208–21. doi:10.1091/mbc.E12-06-0450. PMC 3623641. PMID 23427269.
- Eukaryotic Linear Motif resource motif class MOD_PIKK_1
- Proteopedia Phosphoinositide_3-Kinases to explore the structure in interactive 3D
- PI-3 Kinase at the US National Library of Medicine Medical Subject Headings (MeSH)
- PI3K/Akt Signaling Pathway
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000403
Phosphatidylinositol 3-kinase (PI3-kinase) (EC) [PUBMED:1322797] is an enzyme that phosphorylates phosphoinositides on the 3-hydroxyl group of the inositol ring. The three products of PI3-kinase - PI-3-P, PI-3,4-P(2) and PI-3,4,5-P(3) function as secondary messengers in cell signalling. Phosphatidylinositol 4-kinase (PI4-kinase) (EC) [PUBMED:8194527] is an enzyme that acts on phosphatidylinositol (PI) in the first committed step in the production of the secondary messenger inositol-1'4'5'-trisphosphate. This domain is also present in a wide range of protein kinases, involved in diverse cellular functions, such as control of cell growth, regulation of cell cycle progression, a DNA damage checkpoint, recombination, and maintenance of telomere length. Despite significant homology to lipid kinases, no lipid kinase activity has been demonstrated for any of the PIK-related kinases [PUBMED:12456783].
The PI3- and PI4-kinases share a well conserved domain at their C-terminal section; this domain seems to be distantly related to the catalytic domain of protein kinases [PUBMED:8387896, PUBMED:12151228]. The catalytic domain of PI3K has the typical bilobal structure that is seen in other ATP-dependent kinases, with a small N-terminal lobe and a large C-terminal lobe. The core of this domain is the most conserved region of the PI3Ks. The ATP cofactor binds in the crevice formed by the N-and C-terminal lobes, a loop between two strands provides a hydrophobic pocket for binding of the adenine moiety, and a lysine residue interacts with the alpha-phosphate. In contrast to protein kinases, the PI3K loop which interacts with the phosphates of the ATP and is known as the glycine-rich or P-loop, contains no glycine residues. Instead, contact with the ATP -phosphate is maintained through the side chain of a conserved serine residue.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||phosphotransferase activity, alcohol group as acceptor (GO:0016773)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This superfamily includes the Serine/Threonine- and Tyrosine- protein kinases as well as related kinases that act on non-protein substrates.
The clan contains the following 23 members:ABC1 Act-Frag_cataly Alpha_kinase APH APH_6_hur Choline_kinase DUF1679 DUF2252 EcKinase Fructosamin_kin Kdo Kinase-like KIND PI3_PI4_kinase PIP49_C Pkinase Pkinase_Tyr Pox_ser-thr_kin RIO1 Seadorna_VP7 UL97 WaaY YrbL-PhoP_reg
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Prosite & Pfam-B_6771 (Rlease 7.6)|
|Author:||Sonnhammer ELL, Finn RD|
|Number in seed:||41|
|Number in full:||5590|
|Average length of the domain:||208.70 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||13.98 %|
|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:||24|
|Download:||download the raw HMM for this family|
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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 are 12 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PI3_PI4_kinase domain has been found. There are 207 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...