Summary: Caspase domain
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Caspase Edit Wikipedia article
Structure of interleukin-1 beta-converting enzyme.
Caspases (cysteine-aspartic proteases, cysteine aspartases or cysteine-dependent aspartate-directed proteases) are a family of protease enzymes playing essential roles in programmed cell death (including apoptosis, pyroptosis and necroptosis) and inflammation. They are named Caspases due to their specific cysteine protease activity - a cysteine in its active site nucleophilically attacks and cleaves a target protein only at the C-terminal of an aspartic acid amino acid. As of 2009, there are 12 confirmed Caspases in humans and mice, carrying out a variety of cellular functions.
The role of these enzymes in programmed cell death was first identified in 1993, with their functions in apoptosis well characterised. This is a form of programmed cell death, occurring widely during development, and throughout life to maintain cell homeostasis. Activation of Caspases ensure that the cellular components are degraded in a controlled manner, carrying out cell death with minimal effect to surrounding tissues.
Caspases have other identified roles in programmed cell death such as Pyroptosis and Necroptosis. These forms of cell death are important for protecting an organism from stress signals and pathogenic attack. Caspases also have a role in inflammation, whereby it directly processes pro-inflammatory cytokines such as pro-IL1β. These are signalling molecules that allow recruitment of immune cells to an infected cell or tissue. There are other identified roles of caspases such as cell proliferation, tumour suppression, cell differentiation, neural development and axon guidance and ageing
Caspase deficiency has been identified as a cause of tumour development. Tumour growth can occur by a combination of factors, including a mutation in a cell cycle gene which removes the restrains of cell growth, combined with mutations in apoptopic proteins such as Caspases that would respond by inducing cell death in abnormal growing cells. On the contrary, over activation of some caspases such as caspase-3 can lead to excessive programmed cell death. This is seen in several neurodegenerative diseases where neural cells are lost, such as Alzheimers disease. Caspases involved with processing inflammatory signals are also implicated in disease. Insufficient activation of these caspases can increase the organisms susceptibility to infection as an appropriate immune response may not be activated. The integral role caspases play in cell death and disease has led to research for using caspases as a drug target. For example, inflammatory caspase-1 has been implicated in causing autoimmune diseases; drugs blocking the activation of Caspase-1 have been used to improve the health of patients. Additionally, scientists have used caspases as cancer therapy to kill unwanted cells in tumours.
Functional classification of caspases
Most caspases play a role in programmed cell death. These are summarised in the table below. The enzymes are sub classified into three types: Intiator, Executioner and Inflammatory.
|Programmed Cell Death||Type of Caspase||Enzyme||Organism|
|Apoptosis||Initiator||Caspase 2||human and mouse|
|Caspase 8||human and mouse|
|Caspase 9||human and mouse|
|Caspase 10||human and mouse|
|Executioner||Caspase 3||human and mouse|
|Caspase 6||human and mouse|
|Caspase 7||human and mouse|
|Pyroptosis||Inflammatory||Caspase 1||human and mouse|
|Other roles||Other||Caspase 14||human and mouse|
Note that in addition to apoptosis, Caspase-8 is also required for the inhibition of another form of programmed cell death called Necroptosis. Caspase-14 plays a role in epithelial cell keratinocyte differentiation and can form an epidermal barrier that protects against dehydration and UVB radiation.
Activation of caspases
Caspases are synthesised as inactive zymogens (pro-caspases) that are only activated following an appropriate stimulus. This post-translational level of control allows rapid and tight regulation of the enzyme.
Activation involves dimerization and often oligomerisation of pro-caspases, followed by cleavage into a small subunit and large subunit. The large and small subunit associate with each other to form an active heterodimer caspase. The active enzyme often exists as a heterotetramer in the biological environment, where a pro-caspase dimer is cleaved together to form a heterotetramer.
Dimerisation is facilitated by a particular domain called the pro-domain. This domain is larger in Initiator and Inflammatory Caspases, consisting of Caspase Recruitment Domains (CARD) and Death Effector Domains (DED), used to mediate protein-protein interactions between caspases. Adaptor proteins are used by some caspases, to assist this interaction.
Multiprotein complexes often form during pro-caspase activation. Some activating multiprotein complexes includes:
- Apoptosome and Death Induced Signalling Complex (DISC) during apoptosis
- Inflammasome during pyroptosis
Once appropriately dimerised, the Caspases cleaves at inter domain linker regions, forming a large and small subunit. This cleavage allows the active-site loops to take up a conformation favourable for enzymatic activity.
Cleavage of Initiator and Executioner caspases occur by different methods outlined in the table below.
- Initiator caspases auto-proteolytically cleave whereas Executioner caspases are cleaved by intitiator caspases. This hierarchy allows an amplifying chain reaction or cascade for degrading cellular components, during controlled cell death.
Some roles of caspases
Apoptosis is a form of programmed cell death where the cell undergoes morphological changes, to minimize its effect on surrounding cells to avoid inducing an immune response. The cell shrinks and condenses - the cytoskeleton will collapse, the nucleur envelope disassembles and the DNA fragments up. This results in the cell forming self-enclosed bodies called 'blebs', to avoid release of cellular components into the extracellular medium. Additionally, the cell membrane phospholipid content is altered, which makes the dying cell more susceptible to phagocytic attack and removal.
Apoptopic caspases are subcategorised as:
- Initiator Caspases (Caspase 2, Caspase 8, Caspase-9, Caspase 10)
- Executioner Caspases (Caspase 3, Caspase 6 and Caspase 7)
Once initiator caspases are activated, they produce a chain reaction, activating several other executioner caspases. Executioner caspases degrade over 600 cellular components in order to induce the morphological changes for apoptosis.
Examples of caspase cascade during apoptosis:
- Intrinsic apoptopic pathway: During times of cellular stress, mitochondrial cytochrome c is released into the cytosol. This molecule binds an adaptor protein (APAF-1), which recruits initiator Caspase-9 (via CARD-CARD interactions). This leads to the formation of a Caspase activating multiprotein complex called the Apoptosome. Once activated, initiator caspases such as Caspase 9 will cleave and activate other executioner caspases. This leads to degradation of cellular components for apoptosis.
- Extrinsic apoptopic pathway: The caspase cascade is also activated by extracellular ligands, via cell surface Death Receptors. This is done by the formation of a multiprotein Death Inducing Signalling Complex (DISC) that recruits and activates a pro-caspase. For example, the Fas Ligand binds the FasR receptor at the receptor's extracellular surface; this activates the death domains at the cytoplasmic tail of the receptor. The adaptor protein FADD will recruit (by a Death domain-Death domain interaction). The other end of the adaptor contains a DED domain for pro-caspase recruitment. This FasR, FADD and pro-Caspase 8 form the Death Inducing Signalling Complex (DISC) where Caspase-8 is activated. This could lead to either downstream activation of the intrinsic pathway by inducing mitochondrial stress, or direct activation of Executioner Caspases (Caspase 3, Caspase 6 and Caspase 7) to degrade cellular components as shown in the adjacent diagram.
Pyroptosis is a form of programmed cell death that inherently induces an immune response. It is morphologically distinct from other types of cell death – cells swell up, rupture and release pro-inflammatory cellular contents. This is done in response to a range of stimuli including microbial infections as well as heart attacks (myocardial infarctions). Caspase-1, Caspase-4 and Caspase-5 in humans whereas Caspase-1 and Caspase-11 in mice play important roles in inducing cell death by Pyroptosis. This could lead to limiting the life and proliferation time of intracellular and extracellular pathogens.
Pyroptosis by caspase-1
Caspase-1 activation is mediated by a repertoire of proteins, allowing detection of a range of pathogenic ligands. Some mediators of Caspase-1activation are: NOD-like Leucine Rich Repeats (NLRs), AIM2-Like Receptors (ALRs), Pyrin and IFI16.
These proteins allow caspase-1 activation by forming a multiprotein activating complex called Inflammasomes. For example, a NOD Like Leucine Rich Repeat NLRP3 will sense an efflux of potassium ions from the cell. This cellular ion imbalance leads to oligomerisation of NLRP3 molecules to form a multiprotein complex called the NLRP3 Inflammasome. The pro-caspase-1 is brought into close proximity with other pro-caspase molecule in order to dimerise and undergo auto-proteolytic cleavage.
Some pathogenic signals that lead to Pyroptosis by Caspase-1 are listed below:
- DNA in the host cytosol binds to AIM2-Like Receptors inducing Pyroptosis
- Type III secretion system apparatus from bacteria bind NOD Like Leucine Rich Repeats receptors called NAIP’s (1 in humans and 4 in mice)
Pyroptosis by Caspase -4 and Caspase-5 in humans and Caspase-11 in mice
These caspases have the ability to induce direct pyroptosis when LPS molecules (found in the cell wall of gram negative bacteria) are found in the cytoplasm of the host cell. For example, Caspase 4 acts as a receptor and is proteolytically activated, without the need of an inflammasome complex or Caspase-1 activation.
A crucial downstream substrate for pyroptopic caspases is Gasdermin D (GSDMD)
Role in inflammation
Inflammation is a protective attempt by an organism to restore a homeostatic state, following disruption from harmful stimulus, such as tissue damage or bacterial infection.
Caspase-1, Caspase-4, Caspase-5 and Caspase-11 are considered 'Inflammatory Caspases'.
- Caspase-1 is key in activating pro-inflammatory cytokines; these act as signals to immune cells and make the environment favourable for immune cell recruitment to the site of damage. Caspase-1 therefore plays has a fundamental role in the innate immune system. The enzyme is responsible for processing cytokines such as pro-ILβ and pro-IL18, as well as secreting them.
- Caspase-4 and -5 in humans, and Caspase-11 in mice have a unique role as a receptor, whereby it binds to LPS, a molecule abundant in gram negative bacteria. This can lead to the processing and secretion of IL-1β and IL-18 cytokines by activating Caspase-1; this downstream effect is the same as described above. It also leads to the secretion of another inflammatory cytokine that is not processed. This is called pro-IL1α. There is also evidence of an inflammatory caspase, caspase-11 aiding cytokine secretion; this is done by inactivating a membrane channel that blocks IL-1β secretion
- Caspases can also induce an inflammatory response on a transcriptional level. There is evidence where it promotes transcription of nuclear factor-κB (NF-κB), a transcription factor that assists in transcribing inflammatory cytokines such as IFNs, TNF, IL-6 and IL-8. For example, Caspase-1 activates Caspase-7, which in turn cleaves the poly (ADP) ribose – this activates transcription of NF-κB controlled genes.
Discovery of caspases
H. Robert Horvitz initially established the importance of caspases in apoptosis and found that the ced-3 gene is required for the cell death that took place during the development of the nematode C. elegans. Horvitz and his colleague Junying Yuan found in 1993 that the protein encoded by the ced-3 gene is cysteine protease with similar properties to the mammalian interleukin-1-beta converting enzyme (ICE) (now known as caspase 1). At the time, ICE was the only known caspase. Other mammalian caspases were subsequently identified, in addition to caspases in organisms such as fruit fly Drosophila melanogaster.
Researchers decided upon the nomenclature of the caspase in 1996. In many instances, a particular caspase had been identified simultaneously by more than one laboratory, who would each give the protein a different name. For example, caspase 3 was variously known as CPP32, apopain and Yama. Caspases, therefore, were numbered in the order in which they were identified. ICE was, therefore, renamed as caspase 1. ICE was the first mammalian caspase to be characterised because of its similarity to the nematode death gene ced-3, but it appears that the principal role of this enzyme is to mediate inflammation rather than cell death.
- The Proteolysis Map
- Programmed cell death
- Wilson KP, Black JA, Thomson JA; et al. (July 1994). "Structure and mechanism of interleukin-1 beta converting enzyme". Nature 370 (6487): 270–5. doi:10.1038/370270a0. PMID 8035875.
- Rathore, S.; Datta, G.; Kaur, I.; Malhotra, P.; Mohmmed, A. (2015-07-02). "Disruption of cellular homeostasis induces organelle stress and triggers apoptosis like cell-death pathways in malaria parasite". Cell Death & Disease 6 (7): e1803. doi:10.1038/cddis.2015.142. PMC 4650714. PMID 26136076.
- Shalini, S.; Dorstyn, L.; Dawar, S.; Kumar, S. (2015-04-01). "Old, new and emerging functions of caspases". Cell Death & Differentiation 22 (4): 526–539. doi:10.1038/cdd.2014.216. ISSN 1350-9047. PMC 4356345. PMID 25526085.
- Goodsell, David S. (2000-10-01). "The Molecular Perspective: Caspases". The Oncologist 5 (5): 435–436. doi:10.1634/theoncologist.5-5-435. ISSN 1083-7159. PMID 11040280.
- McIlwain, David R.; Berger, Thorsten; Mak, Tak W. (2013-04-01). "Caspase Functions in Cell Death and Disease". Cold Spring Harbor Perspectives in Biology 5 (4): a008656. doi:10.1101/cshperspect.a008656. ISSN 1943-0264. PMC 3683896. PMID 23545416.
- Galluzzi, Lorenzo; López-Soto, Alejandro; Kumar, Sharad; Kroemer, Guido (2016-02-16). "Caspases Connect Cell-Death Signaling to Organismal Homeostasis". Immunity 44 (2): 221–231. doi:10.1016/j.immuni.2016.01.020. ISSN 1074-7613. PMID 26885855.
- Denecker, Geertrui; Ovaere, Petra; Vandenabeele, Peter; Declercq, Wim (2008-02-11). "Caspase-14 reveals its secrets". The Journal of Cell Biology 180 (3): 451–458. doi:10.1083/jcb.200709098. ISSN 0021-9525. PMC 2234247. PMID 18250198.
- Shi, Yigong (2004-06-25). "Caspase Activation". Cell 117 (7): 855–858. doi:10.1016/j.cell.2004.06.007. ISSN 0092-8674. PMID 15210107.
- Riedl, Stefan J.; Shi, Yigong. "Molecular mechanisms of caspase regulation during apoptosis". Nature Reviews Molecular Cell Biology 5 (11): 897–907. doi:10.1038/nrm1496.
- Lavrik, I.; Krueger, A.; Schmitz, I.; Baumann, S.; Weyd, H.; Krammer, P. H.; Kirchhoff, S. (2003-01-01). "The active caspase-8 heterotetramer is formed at the CD95 DISC". Cell Death & Differentiation 10 (1): 144–145. doi:10.1038/sj.cdd.4401156. ISSN 1350-9047.
- Elmore, Susan (2007-06-01). "Apoptosis: A Review of Programmed Cell Death". Toxicologic Pathology 35 (4): 495–516. doi:10.1080/01926230701320337. ISSN 0192-6233. PMC 2117903. PMID 17562483.
- Sollberger, Gabriel; Strittmatter, Gerhard E.; Garstkiewicz, Martha; Sand, Jennifer; Beer, Hans-Dietmar (2014-02-01). "Caspase-1: The inflammasome and beyond". Innate Immunity 20 (2): 115–125. doi:10.1177/1753425913484374. ISSN 1753-4259. PMID 23676582.
- Creagh, Emma M. (December 2014). "Caspase crosstalk: integration of apoptotic and innate immune signalling pathways". Trends in Immunology 35 (12): 631–640. doi:10.1016/j.it.2014.10.004. PMID 25457353.
- Bergsbaken, Tessa; Fink, Susan L.; Cookson, Brad T. "Pyroptosis: host cell death and inflammation". Nature Reviews Microbiology 7 (2): 99–109. doi:10.1038/nrmicro2070. PMC 2910423. PMID 19148178.
- Eldridge, Matthew JG; Shenoy, Avinash R. "Antimicrobial inflammasomes: unified signalling against diverse bacterial pathogens". Current Opinion in Microbiology 23: 32–41. doi:10.1016/j.mib.2014.10.008.
- He, Wan-ting; Wan, Haoqiang; Hu, Lichen; Chen, Pengda; Wang, Xin; Huang, Zhe; Yang, Zhang-Hua; Zhong, Chuan-Qi; Han, Jiahuai (2015-12-01). "Gasdermin D is an executor of pyroptosis and required for interleukin-1β secretion". Cell Research 25 (12): 1285–1298. doi:10.1038/cr.2015.139. ISSN 1001-0602. PMC 4670995. PMID 26611636.
- Yuan, J; et al. (1993). "The C. elegans cell death gene ced-3 encodes a protein similar to mammalian interleukin-1 beta-converting enzyme". Cell 75 (4): 641–652. doi:10.1016/0092-8674(93)90485-9. PMID 8242740.
- Alnemri ES, Emad S; et al. (1996). "Human ICE/CED-3 Protease Nomenclature". Cell 87 (2): 171. doi:10.1016/S0092-8674(00)81334-3. PMID 8861900. Retrieved 6 March 2011.
- Eukaryotic Linear Motif resource motif class CLV_C14_Caspase3-7
- Apoptosis Video Demonstrates a model of a caspase cascade as it occurs in vivo.
- The Mechanisms of Apoptosis Kimball's Biology Pages. Simple explanation of the mechanisms of apoptosis triggered by internal signals (bcl-2), along the caspase-9, caspase-3 and caspase-7 pathway; and by external signals (FAS and TNF), along the caspase 8 pathway. Accessed 25 March 2007.
- Apoptosis & Caspase 7, PMAP-animation
- Caspases at the US National Library of Medicine Medical Subject Headings (MeSH)
- Tumors Beware (from Beaker Blog)
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.
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No Pfam abstract.
Wilson KP, Black JA, Thomson JA, Kim EE, Griffith JP, Navia MA, Murcko MA, Chambers SP, Aldape RA, Raybuck SA, et al , Nature 1994;370:270-275.: Structure and mechanism of interleukin-1 beta converting enzyme. PUBMED:8035875 EPMC:8035875
Internal database links
|SCOOP:||Peptidase_C13 CHAT Raptor_N|
|Similarity to PfamA using HHSearch:||Peptidase_C13|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR011600
This domain can be found in caspases (MEROPS family C12A) and metacaspases (MEROPS family C14B). Metacaspases adopt a caspase fold, with active site loops arranged similarly as other caspases [PUBMED:22761449].
Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases [PUBMED:11517925]. They are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Caspases are mainly involved in mediating cell death (apoptosis) [PUBMED:10578171, PUBMED:10872455, PUBMED:15077141]. They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (EC), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation [PUBMED:15066636].
Metacaspases are arginine/lysine-specific, in contrast to caspases, which are aspartate-specific. They are found only in plants [PUBMED:17998208, PUBMED:23522353], fungi [PUBMED:18355456] and lower eukaryotes, including the protozoa [PUBMED:23506317]. While plant metacaspases have been shown to be involved in cell death pathways, in other organisms they have evolved alternative functions [PUBMED:21949125].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||cysteine-type endopeptidase activity (GO:0004197)|
|Biological process||proteolysis (GO:0006508)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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The members of this clan are all endopeptidase that have the catalytic dyad histidine followed by cysteine. The catalytic histidine is preceded by a block of hydrophobic residues and a glycine, where as the cysteine is preceded by a block of hydrophobic residues and a glutamine and an alanine. The members with a know structure adopt an alpha/beta fold .
The clan contains the following 8 members:CHAT Peptidase_C11 Peptidase_C13 Peptidase_C14 Peptidase_C25 Peptidase_C50 Peptidase_C80 Raptor_N
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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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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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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.
|Seed source:||Bateman A & Pfam-B_2524 (Release 8.0)|
|Number in seed:||115|
|Number in full:||3842|
|Average length of the domain:||237.50 aa|
|Average identity of full alignment:||16 %|
|Average coverage of the sequence by the domain:||49.18 %|
|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:||19|
|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_C14 domain has been found. There are 565 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...