Summary: Phosphoglycerate kinase
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 "Phosphoglycerate kinase". 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 email@example.com 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.
Phosphoglycerate kinase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
Structure of yeast phosphoglycerate kinase.
Phosphoglycerate kinase (EC 18.104.22.168) (PGK) is an enzyme that catalyzes the reversible transfer of a phosphate group from 1,3-bisphosphoglycerate (1,3-BPG) to ADP producing 3-phosphoglycerate (3-PG) and ATP. Like all kinases it is a transferase. PGK is a major enzyme used in glycolysis, in the first ATP-generating step of the glycolytic pathway. In gluconeogenesis, the reaction catalyzed by PGK proceeds in the opposite direction, generating ADP and 1,3-BPG.
In humans, two isozymes of PGK have been so far identified, PGK1 and PGK2. The isozymes have 87-88% identical amino acid sequence identity and though they are structurally and functionally similar, they have different localizations: PGK2, encoded by an autosomal gene, is unique to meiotic and postmeiotic spermatogenic cells, while PGK1, encoded on the X-chromosome, is ubiquitously expressed in all cells.
PGK is present in all living organisms as one of the two ATP-generating enzymes in glycolysis. In the gluconeogenic pathway, PGK catalyzes the reverse reaction. Under biochemical standard conditions, the glycolytic direction is favored.
PGK has been reported to exhibit thiol reductase activity on plasmin, leading to angiostatin formation, which inhibits angiogenesis and tumor growth. The enzyme was also shown to participate in DNA replication and repair in mammal cell nuclei.
The human isozyme PGK2, which is only expressed during spermatogenesis, was shown to be essential for sperm function in mice.
Interactive pathway map
Click on genes, proteins and metabolites below to link to respective articles. [Â§ 1]
- The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534".
PGK is found in all living organisms and its sequence has been highly conserved throughout evolution. The enzyme exists as a 415-residue monomer containing two nearly equal-sized domains that correspond to the N- and C-termini of the protein. 3-phosphoglycerate (3-PG) binds to the N-terminal, while the nucleotide substrates, MgATP or MgADP, bind to the C-terminal domain of the enzyme. This extended two-domain structure is associated with large-scale 'hinge-bending' conformational changes, similar to those found in hexokinase. The two domains of the protein are separated by a cleft and linked by two alpha-helices. At the core of each domain is a 6-stranded parallel beta-sheet surrounded by alpha helices. The two lobes are capable of folding independently, consistent with the presence of intermediates on the folding pathway with a single domain folded. Though the binding of either substrate triggers a conformational change, only through the binding of both substrates does domain closure occur, leading to the transfer of the phosphate group.
The enzyme has a tendency to exist in the open conformation with short periods of closure and catalysis, which allow for rapid diffusion of substrate and products through the binding sites; the open conformation of PGK is more conformationally stable due to the exposure of a hydrophobic region of the protein upon domain closure.
Role of magnesium
Magnesium ions are normally complexed to the phosphate groups the nucleotide substrates of PGK. It is known that in the absence of magnesium, no enzyme activity occurs. The bivalent metal assists the enzyme ligands in shielding the bound phosphate group's negative charges, allowing the nucleophilic attack to occur; this charge-stabilization is a typical characteristic of phosphotransfer reaction. It is theorized that the ion may also encourage domain closure when PGK has bound both substrates.
Without either substrate bound, PGK exists in an "open" conformation[disambiguation needed]. After both the triose and nucleotide substrates are bound to the N- and C-terminal domains, respectively, an extensive hinge-bending motion occurs, bringing the domains and their bound substrates into close proximity and leading to a "closed" conformation. Then, in the case of the forward glycolytic reaction, the beta-phosphate of ADP initiates a nucleophilic attack on the 1-phosphate of 1,3-BPG in an SN2 substitution reaction. The Lys219 on the enzyme guides the phosphate group to the substrate.
PGK proceeds through a charge-stabilized transition state that is favored over the arrangement of the bound substrate in the closed enzyme because in the transition state, all three phosphate oxygens are stabilized by ligands, as opposed to only two stabilized oxygens in the initial bound state.
In the glycolytic pathyway, 1,3-BPG is the phosphate donor and has a high phosphoryl-transfer potential. The PGK-catalyzed transfer of the phosphate group from 1,3-BPG to ADP to yield ATP can power the carbon-oxidation reaction of the previous glycolytic step (converting glyceraldehyde 3-phosphate to 3-phosphoglycerate).
The enzyme is activated by low concentrations of various multivalent anions, such as pyrophosphate, sulfate, phosphate, and citrate. High concentrations of MgATP and 3-PG activates PGK, while Mg2+ at high concentrations non-competitively inhibits the enzyme.
Macromolecular crowding has been shown to increase PGK activity in both computer simluations and in vitro environments simulating a cell interior; as a result of crowding, the enzyme becomes more enyzmatically active and more compact.
Phosphoglycerate kinase (PGK) deficiency is an X-linked recessive trait associated with hemolytic anemia, mental disorders and myopathy in humans. Since the trait is X-linked, it is usually fully expressed in males, who have one X chromosome; affected females are typically asymptomatic. The condition results from mutations in Pgk1, the gene encoding PGK1, and twenty mutations have been identified. On a molecular level, the mutation in Pgk1 impairs the thermal stability and inhibits the catalytic activity of the enzyme. PGK is the only enzyme in the immediate glycolytic pathway encoded by an X-linked gene. In the case of hemolytic anemia, PGK deficiency occurs in the erythrocytes. Currently, no definitive treatment exists for PGK deficiency.
PGK1 overexpression has been associated with gastric cancer and has been found to increase the invasiveness of gastric cancer cells in vitro. The enzyme is secreted by tumor cells and participates in the angiogenic process, leading to the release of angiostatin and the inhibition of tumor blood vessel growth.
- Watson HC, Walker NP, Shaw PJ et al. (1982). "Sequence and structure of yeast phosphoglycerate kinase". EMBO J. 1 (12): 1635â€“40. PMC 553262. PMID 6765200.
- Chiarelli LR, Morera SM, Bianchi P, Fermo E, Zanella A, Galizzi A, Valentini G (2012). "Molecular insights on pathogenic effects of mutations causing phosphoglycerate kinase deficiency". PLoS ONE 7 (2): e32065. doi:10.1371/journal.pone.0032065. PMC 3279470. PMID 22348148.
- Hogg, Philip J.; Lay, Angelina J.; Jiang, Xing-Mai; Kisker, Oliver; Flynn, Evelyn; Underwood, Anne; Condron, Rosemary (14 December 2000). Nature 408 (6814): 869â€“873. doi:10.1038/35048596. Missing or empty
- Danshina, Polina; GB Geyer; Q Dai; EH Goulding; WD Willis et al. (1 January 2010). "Phosphoglycerate Kinase 2 (PGK2) Is Essential for Sperm Function and Male Fertility in Mice". Biology of Reproduction 82 (1): 136â€“145. doi:10.1095/biolreprod.109.079699.
- Dhar, A.; Samiotakis, A.; Ebbinghaus, S.; Nienhaus, L.; Homouz, D.; Gruebele, M.; Cheung, M. S. (4 October 2010). "Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding". Proceedings of the National Academy of Sciences 107 (41): 17586â€“17591. doi:10.1073/pnas.1006760107.
- Kumar S, Ma B, Tsai CJ, Wolfson H, Nussinov R (1999). "Folding funnels and conformational transitions via hinge-bending motions". Cell Biochem. Biophys. 31 (2): 141â€“64. doi:10.1007/BF02738169. PMID 10593256.
- Yon JM, Desmadril M, Betton JM, Minard P, Ballery N, Missiakas D, Gaillard-Miran S, Perahia D, Mouawad L (1990). "Flexibility and folding of phosphoglycerate kinase". Biochimie 72 (6-7): 417â€“29. doi:10.1016/0300-9084(90)90066-p. PMID 2124145.
- Zerrad L, Merli A, SchrÃ¶der GF, Varga A, GrÃ¡czer Ã‰, Pernot P, Round A, Vas M, Bowler MW (April 2011). "A spring-loaded release mechanism regulates domain movement and catalysis in phosphoglycerate kinase". J. Biol. Chem. 286 (16): 14040â€“8. doi:10.1074/jbc.M110.206813. PMC 3077604. PMID 21349853.
- Varga, Andrea; Palmai, Zoltan; Gugolya, ZoltÃ¡n; GrÃ¡czer, Ã‰va; Vonderviszt, Ferenc; ZÃ¡vodszky, PÃ©ter; Balog, Erika; Vas, MÃ¡ria (21 December 2012). "Importance of Aspartate Residues in Balancing the Flexibility and Fine-Tuning the Catalysis of Human 3-Phosphoglycerate Kinase". Biochemistry 51 (51): 10197â€“10207. doi:10.1021/bi301194t.
- Cliff, MJ; Bowler MW; Varga A; Marston JP et al. (12 May 2010). "Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis". J Am Chem Soc 132 (18): 6507â€“6516. doi:10.1021/ja100974t. PMID 20397725. Retrieved 6 March 2013.
- Banks, R. D.; Blake, C. C. F.; Evans, P. R.; Haser, R.; Rice, D. W.; Hardy, G. W.; Merrett, M.; Phillips, A. W. (28 June 1979). "Sequence, structure and activity of phosphoglycerate kinase: a possible hinge-bending enzyme". Nature 279 (5716): 773â€“777. doi:10.1038/279773a0.
- "Phosphoglycerate kinase". Mechanism, Annotation and Classification In Enzymes (MACiE). Retrieved 4 March 2013.
- Bernstein, Bradley E; Wim G; Hol J (17 March 1998). "Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism". Biochemistry 37 (13): 4429â€“4436. doi:10.1021/bi9724117.
- Larsson-RaÅºnikiewicz M (January 1967). "Kinetic studies on the reaction catalyzed by phosphoglycerate kinase. II. The kinetic relationships between 3-phosphoglycerate, MgATP2-and activating metal ion". Biochim. Biophys. Acta 132 (1): 33â€“40. doi:10.1016/0005-2744(67)90189-1. PMID 6030358.
- Varga, A; Chaloin K; Sagi G; Sendula R et al. (20 April 2011). "Nucleotide promiscuity of 3-phosphoglycerate kinase is in focus: implications for the design of better anti-HIV analogues". Mol Biosyst 7 (6): 1863â€“73. doi:10.1039/c1mb05051f. PMID 21505655.
- Larsson-RaÅºnikiewicz, MÃ¤rtha; Wiksell, Eva (1 March 1978). "Inhibition of phosphoglycerate kinase by salicylates". Biochimica et Biophysica Acta (BBA) - Enzymology 523 (1): 94â€“100. doi:10.1016/0005-2744(78)90012-8.
- Yoshida A, Tani K (1983). "Phosphoglycerate kinase abnormalities: functional, structural and genomic aspects". Biomed. Biochim. Acta 42 (11-12): S263â€“7. PMID 6689547.
- Beutler E (January 2007). "PGK deficiency". Br. J. Haematol. 136 (1): 3â€“11. doi:10.1111/j.1365-2141.2006.06351.x. PMID 17222195.
- Rhodes, Melissa; Ashford, Linda; Manes, Becky; Calder, Cassie; Domm, Jennifer; Frangoul, Haydar (1 February 2011). "Bone marrow transplantation in phosphoglycerate kinase (PGK) deficiency". British Journal of Haematology 152 (4): 500â€“502. doi:10.1111/j.1365-2141.2010.08474.x.
- Zieker, Derek; KÃ¶nigsrainer, Ingmar; Tritschler, Isabel; LÃ¶ffler, Markus; Beckert, Stefan; Traub, Frank; Nieselt, Kay; BÃ¼hler, Sarah; Weller, Michael; Gaedcke, Jochen; Taichman, Russell S.; Northoff, Hinnak; BrÃ¼cher BL; KÃ¶nigsrainer, Alfred (1 January 2010). "Phosphoglycerate kinase 1 a promoting enzyme for peritoneal dissemination in gastric cancer". International Journal of Cancer: NAâ€“NA. doi:10.1002/ijc.24835.
- Gallois-Mantbrun, Sarah; Faraj A; Seclaman E; Sommadossi JP et al. (1 November 2004). "Broad specificity of human phosphoglycerate kinase for antiviral nucleoside analogs". Biochemical Pharmacology 68 (9): 1749â€“1756. doi:10.1016/j.bcp.2004.06.012. PMID 15450940.
- -858783685 at GPnotebook
- Phosphoglycerate kinase at the US National Library of Medicine Medical Subject Headings (MeSH)
- Illustration at arizona.edu
|Glycolysis Metabolic Pathway|
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.
Phosphoglycerate kinase Provide feedback
No Pfam abstract.
Internal database links
|SCOOP:||DUF1082 Phage-Gp8 DUF3172|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001576
Phosphoglycerate kinase (EC) (PGK) is an enzyme that catalyses the formation of ATP to ADP and vice versa. In the second step of the second phase in glycolysis, 1,3-diphosphoglycerate is converted to 3-phosphoglycerate, forming one molecule of ATP. If the reverse were to occur, one molecule of ADP would be formed. This reaction is essential in most cells for the generation of ATP in aerobes, for fermentation in anaerobes and for carbon fixation in plants.
PGK is found in all living organisms and its sequence has been highly conserved throughout evolution. The enzyme exists as a monomer containing two nearly equal-sized domains that correspond to the N- and C-termini of the protein (the last 15 C-terminal residues loop back into the N-terminal domain). 3-phosphoglycerate (3-PG) binds to the N-terminal, while the nucleotide substrates, MgATP or MgADP, bind to the C-terminal domain of the enzyme. This extended two-domain structure is associated with large-scale 'hinge-bending' conformational changes, similar to those found in hexokinase [PUBMED:10593256]. At the core of each domain is a 6-stranded parallel beta-sheet surrounded by alpha helices. Domain 1 has a parallel beta-sheet of six strands with an order of 342156, while domain 2 has a parallel beta-sheet of six strands with an order of 321456. Analysis of the reversible unfolding of yeast phosphoglycerate kinase leads to the conclusion that the two lobes are capable of folding independently, consistent with the presence of intermediates on the folding pathway with a single domain folded [PUBMED:2124145].
Phosphoglycerate kinase (PGK) deficiency is associated with haemolytic anaemia and mental disorders in man [PUBMED:6689547].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||phosphoglycerate kinase activity (GO:0004618)|
|Biological process||glycolytic process (GO:0006096)|
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...
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...
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 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.
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
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.
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...
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.
|Number in seed:||949|
|Number in full:||21331|
|Average length of the domain:||368.00 aa|
|Average identity of full alignment:||50 %|
|Average coverage of the sequence by the domain:||94.48 %|
|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:||15|
|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 PGK domain has been found. There are 66 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...