Summary: Calpain family cysteine protease
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Calpain Edit Wikipedia article
Crystal structure of the peptidase core of Calpain II.
|PDB structures||RCSB PDB PDBe PDBsum|
|PDB structures||RCSB PDB PDBe PDBsum|
A calpain (//; EC 18.104.22.168, EC 22.214.171.124) is a protein belonging to the family of calcium-dependent, non-lysosomal cysteine proteases (proteolytic enzymes) expressed ubiquitously in mammals and many other organisms. Calpains constitute the C2 family of protease clan CA in the MEROPS database. The calpain proteolytic system includes the calpain proteases, the small regulatory subunit CAPNS1, also known as CAPN4, and the endogenous calpain-specific inhibitor, calpastatin.
The history of calpain originates in 1964, when calcium-dependent proteolytic activities caused by a â€œcalcium-activated neutral proteaseâ€ (CANP) were detected in brain, lens of the eye and other tissues. In the late 1960s the enzymes were isolated and characterised independently in both rat brain and skeletal muscle. These activities were caused by an intracellular cysteine protease not associated with the lysosome and having an optimum activity at neutral pH, which clearly distinguished it from the cathepsin family of proteases. The calcium-dependent activity, intracellular localization, along with the limited, specific proteolysis on its substrates, highlighted calpainâ€™s role as a regulatory, rather than a digestive protease. When the sequence of this enzyme became known, it was given the name â€œcalpainâ€, to recognize it as a hybrid of two well-known proteins at the time, the calcium-regulated signalling protein, calmodulin, and the cysteine protease of papaya, papain. Shortly thereafter, the activity was found to be attributable to two main isoforms, dubbed Î¼("mu")-calpain and m-calpain (a.k.a. calpain I and II), that differed primarily in their calcium requirements in vitro. Their names reflect the fact that they are activated by micro- and nearly millimolar concentrations of Ca2+ within the cell, respectively.
To date, these two isoforms remain the best characterised members of the calpain family. Structurally, these two heterodimeric isoforms share an identical small (28k) subunit (CAPNS1 (formerly CAPN4)), but have distinct large (80k) subunits, known as calpain 1 and calpain 2 (each encoded by the CAPN1 and CAPN2 genes, respectively).
No specific amino acid sequence is uniquely recognized by calpains. Amongst protein substrates, tertiary structure elements rather than primary amino acid sequences are likely responsible for directing cleavage to a specific substrate. Amongst peptide and small-molecule substrates, the most consistently reported specificity is for small, hydrophobic amino acids (e.g. leucine, valine and isoleucine) at the P2 position, and large hydrophobic amino acids (e.g. phenylalanine and tyrosine) at the P1 position. Arguably, the best currently available fluorogenic calpain substrate is (EDANS)-Glu-Pro-Leu-Phe=Ala-Glu-Arg-Lys-(DABCYL), with cleavage occurring at the Phe=Ala bond.
The Human Genome Project has revealed that there are more than a dozen other calpain isoforms, some with multiple splice variants. As the first calpain whose three-dimensional structure was determined, m-calpain is the type-protease for the C2 (calpain) family in the MEROPS database.
|Gene||Protein||Aliases||Tissue expression||Disease linkage|
|CAPN1||Calpain 1||Calpain-1 large subunit, Calpain mu-type||Central Nervous System|
|CAPN2||Calpain 2||Calpain-2 large subunit||Central Nervous System|
|CAPN3||Calpain 3||skeletal muscle retina and lens specific||Limb Girdle muscular dystrophy 2A|
|CAPN5||Calpain 5||ubiquitous (high in colon, small intestine and testis)||might be linked to necrosis,
as it is an ortholog of the C. elegans necrosis gene tra-3
|CAPN6||Calpain 6||CAPNX, Calpamodulin|
|CAPN8||Calpain 8||exclusive to stomach mucosa and the GI track||might be linked to colon polyp formation|
|CAPN9||Calpain 9||exclusive to stomach mucosa and the GI track||might be linked to colon polyp formation|
|CAPN10||Calpain 10||susceptibility gene for type II diabetes|
|CAPN12||Calpain 12||ubiquitous but high in hair follicle|
|CAPN13||Calpain 13||testis and lung|
|CAPN17||Calpain 17||Fish and amphibian-only|
|SOLH||Calpain 15||Sol H (homolog of the drosophila gene sol)|
|CAPNS1||Calpain small subunit 1||Calpain 4|
|CAPNS2||Calpain small subunit 2|
Although the physiological role of calpains is still poorly understood, they have been shown to be active participants in processes such as cell mobility and cell cycle progression, as well as cell-type specific functions such as long-term potentiation in neurons and cell fusion in myoblasts. Under these physiological conditions, a transient and localized influx of calcium into the cell activates a small local population of calpains (for example, those close to Ca2+ channels), which then advance the signal transduction pathway by catalyzing the controlled proteolysis of its target proteins. Other reported roles of calpains are in cell function, helping to regulate clotting and the diameter of blood vessels, and playing a role in memory. Calpains have been implicated in apoptotic cell death, and appear to be an essential component of necrosis.
Enhanced calpain activity, regulated by CAPNS1, significantly contributes to platelet reactivity and thrombosis under hypoxic conditions.
In the brain, while Î¼-calpain is mainly located in the cell body and dendrites of neurons and to a lesser extent in axons and glial cells, m-calpain is found in glia and a small amount in axons. Calpain is also involved in skeletal muscle protein breakdown due to exercise and altered nutritional states.
The structural and functional diversity of calpains in the cell is reflected in their involvement in the pathogenesis of a wide range of disorders. At least two well known genetic disorders and one form of cancer have been linked to tissue-specific calpains. When defective, the mammalian calpain 3 (also known as p94) is the gene product responsible for limb-girdle muscular dystrophy type 2A, calpain 10 has been identified as a susceptibility gene for type II diabetes mellitus, and calpain 9 has been identified as a tumour suppressor for gastric cancer. Moreover, the hyperactivation of calpains is implicated in a number of pathologies associated with altered calcium homeostasis such as Alzheimer's disease, and cataract formation, as well as secondary degeneration resulting from acute cellular stress following myocardial ischemia, cerebral (neuronal) ischemia, traumatic brain injury and spinal cord injury. Excessive amounts of calpain can be activated due to Ca2+ influx after cerebrovascular accident (during the ischemic cascade) or some types of traumatic brain injury such as diffuse axonal injury. Increase in concentration of calcium in the cell results in calpain activation, which leads to unregulated proteolysis of both target and non-target proteins and consequent irreversible tissue damage. Excessively active calpain breaks down molecules in the cytoskeleton such as spectrin, microtubule subunits, microtubule-associated proteins, and neurofilaments. It may also damage ion channels, other enzymes, cell adhesion molecules, and cell surface receptors. This can lead to degradation of the cytoskeleton and plasma membrane. Calpain may also break down sodium channels that have been damaged due to axonal stretch injury, leading to an influx of sodium into the cell. This, in turn, leads to the neuron's depolarization and the influx of more Ca2+. A significant consequence of calpain activation is the development of cardiac contractile dysfunction that follows ischemic insult to the heart. Upon reperfusion of the ischemic myocardium, there is development of calcium overload or excess in the heart cell (cardiomyocytes). This increase in calcium leads to activation of calpain.
The exogenous regulation of calpain activity is therefore of interest for the development of therapeutics in a wide array of pathological states. As a few of the many examples supporting the therapeutic potential of calpain inhibition in ischemia, calpain inhibitor AK275 protected against focal ischemic brain damage in rats when administered after ischemia, and MDL28170 significantly reduced the size of damaged infarct tissue in a rat focal ischemia model. There are also known calpain inhibitors with neuroprotective effects: PD150606, SJA6017, ABT-705253, and SNJ-1945.
Calpain may be released in the brain for up to a month after a head injury, and may be responsible for a shrinkage of the brain sometimes found after such injuries. However, calpain may also be involved in a "resculpting" process that helps repair damage after injury.
- Ohno S, Emori Y, Imajoh S, Kawasaki H, Kisaragi M, Suzuki K (1984). "Evolutionary origin of a calcium-dependent protease by fusion of genes for a thiol protease and a calcium-binding protein?". Nature 312 (5994): 566â€“70. doi:10.1038/312566a0. PMID 6095110.
- Glass JD, Culver DG, Levey AI, Nash NR (April 2002). "Very early activation of m-calpain in peripheral nerve during Wallerian degeneration". J. Neurol. Sci. 196 (1-2): 9â€“20. doi:10.1016/S0022-510X(02)00013-8. PMID 11959150.
- Cuerrier D, Moldoveanu T, Davies PL (December 2005). "Determination of peptide substrate specificity for mu-calpain by a peptide library-based approach: the importance of primed side interactions". J. Biol. Chem. 280 (49): 40632â€“41. doi:10.1074/jbc.M506870200. PMID 16216885.
- Thompson V (2002-02-12). "Calpain Nomenclature". College of Agriculture and Life Sciences at the University of Arizona. Retrieved 2010-08-06.
- Huang Y, Wang KK (August 2001). "The calpain family and human disease". Trends Mol Med 7 (8): 355â€“62. doi:10.1016/S1471-4914(01)02049-4. PMID 11516996.
- Suzuki K, Hata S, Kawabata Y, Sorimachi H (February 2004). "Structure, activation, and biology of calpain". Diabetes. 53. Suppl 1: S12â€“8. PMID 14749260.
- Blood. 2014 Feb 20;123(8):1250-60. doi: 10.1182/blood-2013-05-501924. Altered expression of platelet proteins and calpain activity mediate hypoxia-induced prothrombotic phenotype.PMID: 24297866
- Lenzlinger PM, Saatman KE, Raghupathi R, Mcintosh TK (2000). "Chapter 1: Overview of basic mechanisms underlying neuropathological consequences of head trauma". In Newcomb JK, Miller LS, Hayes RL. Head trauma: basic, preclinical, and clinical directions. New York: Wiley-Liss. ISBN 0-471-36015-5.
- Belcastro AN, Albisser TA, Littlejohn B (October 1996). "Role of calcium-activated neutral protease (calpain) with diet and exercise". Can J Appl Physiol 21 (5): 328â€“46. doi:10.1139/h96-029. PMID 8905185.
- Richard I, Broux O, Allamand V et al. (April 1995). "Mutations in the proteolytic enzyme calpain 3 cause limb-girdle muscular dystrophy type 2A". Cell 81 (1): 27â€“40. doi:10.1016/0092-8674(95)90368-2. PMID 7720071.
- Ono Y, Shimada H, Sorimachi H et al. (July 1998). "Functional defects of a muscle-specific calpain, p94, caused by mutations associated with limb-girdle muscular dystrophy type 2A". J. Biol. Chem. 273 (27): 17073â€“8. doi:10.1074/jbc.273.27.17073. PMID 9642272.
- Yamashima T (2013). "Reconsider Alzheimer's disease by the 'calpain-cathepsin hypothesis'--a perspective review". PROGRESS IN NEUROLOGY 105: 1â€“23. doi:10.1016/j.pneurobio.2013.02.004. PMID 23499711.
- Liu J, Liu MC, Wang KK (April 2008). "Calpain in the CNS: from synaptic function to neurotoxicity". Sci Signal. 1 (14): re 1. doi:10.1126/stke.114re1. PMID 18398107.
- Castillo MR, Babson JR (October 1998). "Ca2+-dependent mechanisms of cell injury in cultured cortical neurons". Neuroscience 86 (4): 1133â€“44. doi:10.1016/S0306-4522(98)00070-0. PMID 9697120.
- Iwata A, Stys PK, Wolf JA et al. (May 2004). "Traumatic axonal injury induces proteolytic cleavage of the voltage-gated sodium channels modulated by tetrodotoxin and protease inhibitors". J. Neurosci. 24 (19): 4605â€“13. doi:10.1523/JNEUROSCI.0515-03.2004. PMID 15140932.
- Wang KK, Larner SF, Robinson G, Hayes RL (December 2006). "Neuroprotection targets after traumatic brain injury". Curr. Opin. Neurol. 19 (6): 514â€“9. doi:10.1097/WCO.0b013e3280102b10. PMID 17102687.
- Wang KK, Nath R, Posner A, Raser KJ, Buroker-Kilgore M, Hajimohammadreza I, Probert A W, Marcoux FW, Ye Q, Takano E, Hatanaka M, Maki M, Caner H, Collins JL, Fergus A, Lee KS, Lunney EA, Hays SJ, Yuen P (June 1996). "An alpha-mercaptoacrylic acid derivative is a selective nonpeptide cell-permeable calpain inhibitor and is neuroprotective". Proc. Natl. Acad. Sci. U.S.A. 93 (13): 6687â€“92. doi:10.1073/pnas.93.13.6687. PMC 39087. PMID 8692879.
- Kupina NC, Nath R, Bernath EE, Inoue J, Mitsuyoshi A, Yuen PW, Wang KK, Hall ED (November 2001). "The novel calpain inhibitor SJA6017 improves functional outcome after delayed administration in a mouse model of diffuse brain injury". J. Neurotrauma 18 (11): 1229â€“40. doi:10.1089/089771501317095269. PMID 11721741.
- Lubisch W, Beckenbach E, Bopp S, Hofmann HP, Kartal A, KÃ¤stel C, Lindner T, Metz-Garrecht M, Reeb J, Regner F, Vierling M, MÃ¶ller A (June 2003). "Benzoylalanine-derived ketoamides carrying vinylbenzyl amino residues: discovery of potent water-soluble calpain inhibitors with oral bioavailability". J. Med. Chem. 46 (12): 2404â€“12. doi:10.1021/jm0210717. PMID 12773044.
- Nimmrich V, Reymann KG, Strassburger M, SchÃ¶der UH, Gross G, Hahn A, Schoemaker H, Wicke K, MÃ¶ller A (April 2010). "Inhibition of calpain prevents NMDA-induced cell death and beta-amyloid-induced synaptic dysfunction in hippocampal slice cultures". Br. J. Pharmacol. 159 (7): 1523â€“31. doi:10.1111/j.1476-5381.2010.00652.x. PMC 2850408. PMID 20233208.
- Koumura A, Nonaka Y, Hyakkoku K, Oka T, Shimazawa M, Hozumi I, Inuzuka T, Hara H (November 2008). "A novel calpain inhibitor, ((1S)-1((((1S)-1-benzyl-3-cyclopropylamino-2,3-di-oxopropyl)amino)carbonyl)-3-methylbutyl) carbamic acid 5-methoxy-3-oxapentyl ester, protects neuronal cells from cerebral ischemia-induced damage in mice". Neuroscience 157 (2): 309â€“18. doi:10.1016/j.neuroscience.2008.09.007. PMID 18835333.
- White V (1999-10-21). "â€“ â€˜Biochemical Stormâ€™ Following Brain Trauma An Important Factor In Treatment, University of Florida Researcher Finds". University of Florida News. Retrieved 2010-08-07.
- Liu J, Liu MC, Wang KK (2008). "Calpain in the CNS: from synaptic function to neurotoxicity". Sci Signal 1 (14): re1. doi:10.1126/stke.114re1. PMID 18398107.
- Suzuki K, Hata S, Kawabata Y, Sorimachi H (February 2004). "Structure, activation, and biology of calpain". Diabetes. 53. Suppl 1: S12â€“8. PMID 14749260.
- Yuen P-W, Wang KW (1999). Calpains : Pharmacology and Toxicology of a Cellular Protease. Boca Raton: CRC Press. ISBN 1-56032-713-8.
- Calpain at the US National Library of Medicine Medical Subject Headings (MeSH)
- CaMPDB, Calpain for Modulatory Proteolysis Database
- The Calpain Family of Proteases. (2001). University of Arizona.
- Calpain Info with links in the Cell Migration Gateway
- Alzheimers and calpain protease, PMAP The Proteolysis Map-animation.
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.
Calpain family cysteine protease Provide feedback
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This tab holds annotation information from the InterPro database.
InterPro entry IPR001300
This group of cysteine peptidases belong to the MEROPS peptidase family C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium [PUBMED:2539381]. The protein is a complex of 2 polypeptide chains (light and heavy), with three known forms in mammals [PUBMED:7845226, PUBMED:2555341]: a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only [PUBMED:2555341].
All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [PUBMED:7845226, PUBMED:2539381]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit:
- A 19-amino acid NH2-terminal sequence;
- Active site domain IIa;
- Active site domain IIb.
Domain 2 shows low levels of sequence similarity to papain; although the catalytic His has not been located by biochemical means, it is likely that calpain and papain are related [PUBMED:7845226].
- Domain III;
- An 18-amino acid extended sequence linking domain III to domain IV;
- Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity [PUBMED:7845226]. />]. Ca2+-binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad [PUBMED:11914728].
Calpain-like mRNAs have been identified in other organisms including bacteria, but the molecules encoded by these mRNAs have not been isolated, so little is known about their properties. How calpain activity is regulated in these organisms cells is still unclear In metazoans, the activity of calpain is controlled by a single proteinase inhibitor, calpastatin (INTERPRO). The calpastatin gene can produce eight or more calpastatin polypeptides ranging from 17 to 85 kDa by use of different promoters and alternative splicing events. The physiological significance of these different calpastatins is unclear, although all bind to three different places on the calpain molecule; binding to at least two of the sites is Ca2+ dependent. The calpains ostensibly participate in a variety of cellular processes including remodelling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis. Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma [PUBMED:12843408].
Calpains are a family of cytosolic cysteine proteinases (see PROSITEDOC). Members of the calpain family are believed to function in various biological processes, including integrin-mediated cell migration, cytoskeletal remodeling, cell differentiation and apoptosis [PUBMED:11854009, PUBMED:11950589].
The calpain family includes numerous members from C. elegans to mammals and with homologues in yeast and bacteria. The best characterised members are the m- and mu-calpains, both proteins are heterodimer composed of a large catalytic subunit and a small regulatory subunit. The large subunit comprises four domains (dI-dIV) while the small subunit has two domains (dV-dVI). Domain dI is a short region cleaved by autolysis, dII is the catalytic core, dIII is a C2-like domain, dIV consists of five calcium binding EF-hand motifs [PUBMED:11950589].
The crystal structure of calpain has been solved [PUBMED:10601010, PUBMED:11893336]. The catalytic region consists of two distinct structural domains (dIIa and dIIb). dIIa contains a central helix flanked on three faces by a cluster of alpha-helices and is entirely unrelated to the corresponding domain in the typical thiol proteinases. The fold of dIIb is similar to the corresponding domain in other cysteine proteinases and contains two three-stranded anti-parallel beta-sheets. The catalytic triad residues (C,H,N) are located in dIIa and dIIb. The activation of the domain is dependent on the binding of two calcium atoms in two non EF-hand calcium binding sites located in the catalytic core, one close to the Cys active site in dIIa and one at the end of dIIb. Calcium-binding induced conformational changes in the catalytic domain which align the active site [PUBMED:11893336][PUBMED:11914728].
The profile covers the whole catalytic domain.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||intracellular (GO:0005622)|
|Molecular function||calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|
|Biological process||proteolysis (GO:0006508)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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This clan includes peptidases with the papain-like fold.
The clan contains the following 60 members:Acetyltransf_2 Amidase_5 Amidase_6 BtrH_N CHAP DUF1175 DUF1287 DUF1460 DUF2272 DUF3335 DUF553 EDR1 Guanylate_cyc_2 LRAT NLPC_P60 OTU Peptidase_C1 Peptidase_C10 Peptidase_C101 Peptidase_C12 Peptidase_C16 Peptidase_C1_2 Peptidase_C2 Peptidase_C21 Peptidase_C23 Peptidase_C27 Peptidase_C28 Peptidase_C31 Peptidase_C32 Peptidase_C33 Peptidase_C34 Peptidase_C36 Peptidase_C39 Peptidase_C39_2 Peptidase_C42 Peptidase_C47 Peptidase_C48 Peptidase_C5 Peptidase_C54 Peptidase_C58 Peptidase_C6 Peptidase_C65 Peptidase_C7 Peptidase_C70 Peptidase_C71 Peptidase_C78 Peptidase_C8 Peptidase_C9 Peptidase_C92 Peptidase_C93 Peptidase_C97 Peptidase_C98 Phytochelatin Rad4 Transglut_core Transglut_core2 Transglut_core3 UCH UCH_1 Viral_protease
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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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.
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MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
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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:||194|
|Number in full:||4049|
|Average length of the domain:||261.50 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||34.02 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- 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 4 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 Peptidase_C2 domain has been found. There are 27 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...