Summary: Phosphoenolpyruvate carboxylase
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "Phosphoenolpyruvate carboxylase". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at firstname.lastname@example.org and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Phosphoenolpyruvate carboxylase Edit Wikipedia article
the Phosphoenolpyruvate (PEP) carboxylase single subunit structure (generated by PyMOL)]
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
|SCOPe||1fiy / SUPFAM|
Phosphoenolpyruvate carboxylase (also known as PEP carboxylase, PEPCase, or PEPC; EC 188.8.131.52, PDB ID: 3ZGE) is an enzyme in the family of carboxy-lyases found in plants and some bacteria that catalyzes the addition of bicarbonate (HCO3âˆ’) to phosphoenolpyruvate (PEP) to form the four-carbon compound oxaloacetate and inorganic phosphate:
- PEP + HCO3âˆ’ â†’ oxaloacetate + Pi
This reaction is used for carbon fixation in CAM (crassulacean acid metabolism) and C4 organisms, as well as to regulate flux through the citric acid cycle (also known as Krebs or TCA cycle) in bacteria and plants. The enzyme structure and its two step catalytic, irreversible mechanism have been well studied. PEP carboxylase is highly regulated, both by phosphorylation and allostery.
The PEP carboxylase enzyme is present in plants and some types of bacteria, but not in fungi or animals (including humans). The genes vary between organisms, but are strictly conserved around the active and allosteric sites discussed in the mechanism and regulation sections. Tertiary structure of the enzyme is also conserved.
The crystal structure of PEP carboxylase in multiple organisms, including Zea mays (maize), and Escherichia coli has been determined. The overall enzyme exists as a dimer-of-dimers: two identical subunits closely interact to form a dimer through salt bridges between arginine (R438 - exact positions may vary depending on the origin of the gene) and glutamic acid (E433) residues. This dimer assembles (more loosely) with another of its kind to form the four subunit complex. The monomer subunits are mainly composed of alpha helices (65%), and have a mass of 106kDa each. The sequence length is about 966 amino acids.
The enzyme active site is not completely characterized. It includes a conserved aspartic acid (D564) and a glutamic acid (E566) residue that non-covalently bind a divalent metal cofactor ion through the carboxylic acid functional groups. This metal ion can be magnesium, manganese or cobalt depending on the organism, and its role is to coordinate the phosphoenolpyruvate molecule as well as the reaction intermediates. A histidine (H138) residue at the active site is believed to facilitate proton transfer during the catalytic mechanism.
The mechanism of PEP carboxylase has been well studied. The enzymatic mechanism of forming oxaloacetate is very exothermic and thereby irreversible; the biological Gibbs free energy change (â–³GÂ°â€™) is -30kJmolâˆ’1. The substrates and cofactor bind in the following order: metal cofactor (either Co2+, Mg2+, or Mn2+), PEP, bicarbonate (HCO3âˆ’). The mechanism proceeds in two major steps, as described below and shown in figure 2:
- The bicarbonate acts as a nucleophile to attack the phosphate group in PEP. This results in the splitting of PEP into a carboxyphosphate and the (very reactive) enolate form of pyruvate.
- Proton transfer takes place at the carboxyphosphate. This is most likely modulated by a histidine (H138) residue that first deprotonates the carboxy side, and then, as an acid, protonates the phosphate part. The carboxyphosphate then exothermically decomposes into carbon dioxide and inorganic phosphate, at this point making this an irreversible reaction. Finally, after the decomposition, the carbon dioxide is attacked by the enolate to form oxaloacetate.
The metal cofactor is necessary to coordinate the enolate and carbon dioxide intermediates; the CO2 molecule is only lost 3% of the time. The active site is hydrophobic to exclude water, since the carboxyphosphate intermediate is susceptible to hydrolysis.
The primary mechanism of carbon dioxide assimilation in plants is through the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (also known as RuBisCO), that adds CO2 to ribulose-1,5-bisphosphate (a 5 carbon sugar), to form two molecules of 3-phosphoglycerate (2x3 carbon sugars). However, at higher temperatures and lower CO2 concentrations, RuBisCO adds oxygen instead of carbon dioxide, to form the unusable product glycolate in a process called photorespiration. To prevent this wasteful process, plants increase the local CO2 concentration in a process called the C4 cycle. PEP carboxylase plays the key role of binding CO2 in the form of bicarbonate with PEP to create oxaloacetate in the mesophyll tissue. This is then converted back to pyruvate (through a malate intermediate), to release the CO2 in the deeper layer of bundle sheath cells for carbon fixation by RuBisCO and the Calvin cycle. Pyruvate is converted back to PEP in the mesophyll cells, and the cycle begins again, thus actively pumping CO2.
The second important and very similar biological significance of PEP carboxylase is in the CAM cycle. This cycle is common in organisms living in arid habitats. Plants cannot afford to open stomata during the day to take in CO2, as they would lose too much water by transpiration. Instead, stomata open at night, when water evaporation is minimal, and take in CO2 by fixing with PEP to form oxaloacetate though PEP carboxylase. Oxaloacetate is converted to malate by malate dehydrogenase, and stored for use during the day when the light dependent reaction generates energy (mainly in the form of ATP) and reducing equivalents such as NADPH to run the Calvin cycle.
Third, PEP carboxylase is significant in non-photosynthetic metabolic pathways. Figure 3 shows this metabolic flow (and its regulation). Similar to pyruvate carboxylase, PEP carboxylase replenishes oxaloacetate in the citric acid cycle. At the end of glycolysis, PEP is converted to pyruvate, which is converted to acetyl-coenzyme-A (acetyl-CoA), which enters the citric acid cycle by reacting with oxaloacetate to form citrate. To increase flux through the cycle, some of the PEP is converted to oxaloacetate by PEP carboxylase. Since the citric acid cycle intermediates provide a hub for metabolism, increasing flux is important for the biosynthesis of many molecules, such as for example amino acids.
Phosphorylation by phosphoenolpyruvate carboxylase kinase turns the enzyme on, whereas phosphoenolpyruvate carboxylase phosphatase turns it back off. Both kinase and phosphate are regulated by transcription. It is further believed that malate acts as a feedback inhibitor of kinase expression levels, and as an activator for phosphatase expression (transcription). Since oxaloacetate is converted to malate in CAM and C4 organisms, high concentrations of malate activate phosphatase expression - the phosphatase subsequently de-phosphorylates and thus de-actives PEP carboxylase, leading to no further accumulation of oxaloacetate and thus no further conversion of oxaloacetate to malate. Hence malate production is down-regulated.
The main allosteric inhibitors of PEP carboxylase are the carboxylic acids malate (weak) and aspartate (strong). Since malate is formed in the next step of the CAM and C4 cycles after PEP carboxylase catalyses the condensation of CO2 and PEP to oxaloacetate, this works as a feedback inhibition pathway. Oxaloacetate and aspartate are easily inter-convertible through a transaminase mechanism; thus high concentrations of aspartate are also a pathway of feedback inhibition of PEP carboxylase.
The main allosteric activators of PEP carboxylase are acetyl-CoA and fructose-1,6-bisphosphate (F-1,6-BP). Both molecules are indicators of increased glycolysis levels, and thus positive feed-forward effectors of PEP carboxylase. They signal the need to produce oxaloacetate to allow more flux through the citric acid cycle. Additionally, increased glycolysis means a higher supply of PEP is available, and thus more storage capacity for binding CO2 in transport to the Calvin cycle. It is also noteworthy that the negative effectors aspartate competes with the positive effector acetyl-CoA, suggesting that they share an allosteric binding site.
The magnitudes of the allosteric effects of these different molecules on PEP carboxylase activity depend on individual organisms.
- Kai Y, Matsumura H, Izui K (June 2003). "Phosphoenolpyruvate carboxylase: three-dimensional structure and molecular mechanisms". Archives of Biochemistry and Biophysics. 414 (2): 170â€“9. doi:10.1016/S0003-9861(03)00170-X. PMID 12781768.
- Chollet R, Vidal J, O'Leary MH (June 1996). "Phosphoenolpyruvate Carboxylase: A Ubiquitous, Highly Regulated Enzyme in Plants". Annual Review of Plant Physiology and Plant Molecular Biology. 47 (1): 273â€“298. doi:10.1146/annurev.arplant.47.1.273. PMID 15012290.
- Paulus JK, Schlieper D, Groth G (2013). "Greater efficiency of photosynthetic carbon fixation due to single amino-acid substitution". Nature Communications. 4 (2): 1518. doi:10.1038/ncomms2504. PMC 3586729. PMID 23443546.
- Kai Y, Matsumura H, Inoue T, Terada K, Nagara Y, Yoshinaga T, Kihara A, Tsumura K, Izui K (February 1999). "Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition". Proceedings of the National Academy of Sciences of the United States of America. 96 (3): 823â€“8. doi:10.1073/pnas.96.3.823. PMC 15309. PMID 9927652.
- Gonzalez DH, Iglesias AA, Andreo CS (February 1986). "Active-site-directed inhibition of phosphoenolpyruvate carboxylase from maize leaves by bromopyruvate". Archives of Biochemistry and Biophysics. 245 (1): 179â€“86. doi:10.1016/0003-9861(86)90203-1. PMID 3947097.
- "Greater efficiency of photosynthetic carbon fixation due to single amino-acid substitution". Nature Communications. 4: 1518. doi:10.1038/ncomms2504. PMC 3586729. PMID 23443546. ; Paulus JK, Schlieper D, Groth G (19 April 2018).
- Fujita N, Izui K, Nishino T, Katsuki H (April 1984). "Reaction mechanism of phosphoenolpyruvate carboxylase. Bicarbonate-dependent dephosphorylation of phosphoenol-alpha-ketobutyrate". Biochemistry. 23 (8): 1774â€“9. doi:10.1021/bi00303a029. PMID 6326809.
- Leegood RC (May 2007). "A welcome diversion from photorespiration". Nature Biotechnology. 25 (5): 539â€“40. doi:10.1038/nbt0507-539. PMID 17483837.
- Hatch MD (2002). "C(4) photosynthesis: discovery and resolution". Photosynthesis Research. 73 (1â€“3): 251â€“6. doi:10.1023/A:1020471718805. PMID 16245128.
- Keeley JE, Rundel PW (2003). "Evolution of CAM and C4Carbonâ€Concentrating Mechanisms". International Journal of Plant Sciences. 164 (S3): S55â€“S77. doi:10.1086/374192.
- Cousins AB, Baroli I, Badger MR, Ivakov A, Lea PJ, Leegood RC, von Caemmerer S (November 2007). "The role of phosphoenolpyruvate carboxylase during C4 photosynthetic isotope exchange and stomatal conductance". Plant Physiology. 145 (3): 1006â€“17. doi:10.1104/pp.107.103390. PMC 2048775. PMID 17827274.
- Nimmo HG (February 2000). "The regulation of phosphoenolpyruvate carboxylase in CAM plants". Trends in Plant Science. 5 (2): 75â€“80. doi:10.1016/S1360-1385(99)01543-5. PMID 10664617.
- Morikawa M, Izui K, Taguchi M, Katsuki H (February 1980). "Regulation of Escherichia coli phosphoenolpyruvate carboxylase by multiple effectors in vivo. Estimation of the activities in the cells grown on various compounds". Journal of Biochemistry. 87 (2): 441â€“9. doi:10.1093/oxfordjournals.jbchem.a132764. PMID 6987214.
- Smith TE (April 1970). "Escherichia coli phosphoenolpyruvate carboxylase: competitive regulation by acetyl-coenzyme A and aspartate". Archives of Biochemistry and Biophysics. 137 (2): 512â€“22. doi:10.1016/0003-9861(70)90469-8. PMID 4909168.
- Coombs J, Maw SL, Baldry CW (December 1974). "Metabolic regulation in C4 photosynthesis: PEP-carboxylase and energy charge". Planta. 117 (4): 279â€“92. doi:10.1007/BF00388023. PMID 24458459.
- Schuller KA, Plaxton WC, Turpin DH (August 1990). "Regulation of Phosphoenolpyruvate Carboxylase from the Green Alga Selenastrum minutum: Properties Associated with Replenishment of Tricarboxylic Acid Cycle Intermediates during Ammonium Assimilation". Plant Physiology. 93 (4): 1303â€“11. doi:10.1104/pp.93.4.1303. PMC 1062672. PMID 16667617.
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.
Phosphoenolpyruvate carboxylase Provide feedback
No Pfam abstract.
Internal database links
|Similarity to PfamA using HHSearch:||PEPcase_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR021135
Phosphoenolpyruvate carboxylase (PEPCase), an enzyme found in all multicellular plants, catalyses the formation of oxaloacetate from phosphoenolpyruvate (PEP) and a hydrocarbonate ion [PUBMED:1450389]. This reaction is harnessed by C4 plants to capture and concentrate carbon dioxide into the photosynthetic bundle sheath cells. It also plays a key role in the nitrogen fixation pathway in legume root nodules: here it functions in concert with glutamine, glutamate and asparagine synthetases and aspartate amido transferase, to synthesise aspartate and asparagine, the major nitrogen transport compounds in various amine-transporting plant species [PUBMED:1421147].
PEPCase also plays an antipleurotic role in bacteria and plant cells, supplying oxaloacetate to the TCA cycle, which requires continuous input of C4 molecules in order to replenish the intermediates removed for amino acid biosynthesis [PUBMED:2779518]. The C terminus of the enzyme contains the active site that includes a conserved lysine residue, involved in substrate binding, and other conserved residues important for the catalytic mechanism [PUBMED:1508152].
Based on sequence similarity, PEPCase enzymes can be grouped into two distinct families, one found primarily in bacteria and plants, and another found primarily in archaea.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||phosphoenolpyruvate carboxylase activity (GO:0008964)|
|Biological process||tricarboxylic acid cycle (GO:0006099)|
|carbon fixation (GO:0015977)|
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
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
This superfamily consists of a number of TIM barrel domains found in enzymes such as pyruvate kinase, malate synthase and citrate lyase.
The clan contains the following 11 members:C-C_Bond_Lyase HpcH_HpaI ICL Malate_synthase Pantoate_transf PEP-utilizers_C PEP_hydrolase PEP_mutase PEPcase PEPcase_2 PK
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Author:||Finn RD , Coggill P|
|Number in seed:||49|
|Number in full:||5799|
|Average length of the domain:||587.70 aa|
|Average identity of full alignment:||30 %|
|Average coverage of the sequence by the domain:||82.22 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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 PEPcase domain has been found. There are 21 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 sequence.
Loading structure mapping...