Summary: Homoserine dehydrogenase
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 "Homoserine dehydrogenase". 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.
Homoserine dehydrogenase Edit Wikipedia article
Homoserine dehydrogenase complex with NAD+ analogue and L-homoserine.
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
- L-homoserine + NAD(P)+ L-aspartate 4-semialdehyde + NAD(P)H + H+
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is L-homoserine:NAD(P)+ oxidoreductase. Other names in common use include HSDH, and HSD.
Homoserine dehydrogenase catalyses the third step in the aspartate pathway; the NAD(P)-dependent reduction of aspartate beta-semialdehyde into homoserine. Homoserine is an intermediate in the biosynthesis of threonine, isoleucine, and methionine.
The enzyme can be found in a monofunctional form, in some bacteria and yeast. Structural analysis of the yeast monofunctional enzyme indicates that the enzyme is a dimer composed of three distinct regions; an N-terminal nucleotide-binding domain, a short central dimerisation region, and a C-terminal catalytic domain. The N-terminal domain forms a modified Rossman fold, while the catalytic domain forms a novel alpha-beta mixed sheet.
The enzyme can also be found in a bifunctional form consisting of an N-terminal aspartokinase domain and a C-terminal homoserine dehydrogenase domain, as found in bacteria such as Escherichia coli and in plants.
The bifunctional aspartokinase-homoserine dehydrogenase (AK-HSD) enzyme has a regulatory domain that consists of two subdomains with a common loop-alpha helix-loop-beta strand loop-beta strand motif. Each subdomain contains an ACT domain that allows for complex regulation of several different protein functions. The AK-HSD gene codes for aspartate kinase, an intermediate domain (coding for the linker region between the two enzymes in the bifunctional form), and finally the coding sequence for homoserine dehydrogenase.
Homoserine dehydrogenase catalyzes the reaction of aspartate-semialdehyde (ASA) to homoserine. The overall reaction reduces the C4 carboxylic acid functional group of ASA to a primary alcohol and oxidizes the C1 aldehyde to a carboxylic acid. Residues Glu 208 and Lys 117 are thought to be involved in the active catalytic site of the enzyme. Asp 214 and Lys 223 have been shown to be important for hydride transfer in the catalyzed reaction.
Once the C4 carboxylic acid is reduced to an aldehyde and the C1 aldehyde is oxidized to a carboxylic acid, experiments suggest that Asp 219, Glu 208 and a water molecule bind ASA in the active site while Lys 223 donates a proton to the aspartate-semialdehyde C4 oxygen. Homoserine dehydrogenase has an NAD(P)H cofactor, which then donates a hydrogen to the same carbon, effectively reducing the aldehyde to an alcohol. (Refer to figures 1 and 2).
However, the precise mechanism of complete homoserine dehydrogenase catalysis remains unknown.
The homoserine dehydrogenase-catalyzed reaction has been postulated to proceed through a bi-bi kinetic mechanism, where the NAD(P)H cofactor binds the enzyme first and is the last to dissociate from the enzyme once the reaction is complete. Additionally, while both NADH and NADPH are adequate cofactors for the reaction, NADH is preferred. The Km of the reaction is four-times smaller with NADH and the Kcat/Km is three-times greater, indicating a more efficient reaction.
Homoserine dehydrogenase also exhibits multi-order kinetics at subsaturating levels of substrate. Additionally, the variable kinetics for homoserine dehydrogenase is an artifact of the faster dissociation of the amino acid substrate from the enzyme complex as compared to cofactor dissociation.
The aspartate metabolic pathway is involved in both storage of asparagine and in synthesis of aspartate-family amino acids. Homoserine dehydrogenase catalyzes an intermediate step in this nitrogen and carbon storage and utilization pathway. (Refer to figure 3).
In photosynthetic organisms, glutamine, glutamate, and aspartate accumulate during the day and are used to synthesize other amino acids. At night, aspartate is converted to asparagine for storage. Additionally, the aspartate kinase-homoserine dehydrogenase gene is primarily expressed in actively growing, young plant tissues, particularly in the apical and lateral meristems.
Mammals lack the enzymes involved in the aspartate metabolic pathway, including homoserine dehydrogenase. As lysine, threonine, methionine, and isoleucine are made in this pathway, they are considered essential amino acids for mammals.
Homoserine dehydrogenase and aspartate kinase are both subject to significant regulation (refer to figure 3). HSD is inhibited by downstream products of the aspartate metabolic pathway, mainly threonine. Threonine acts as a competitive inhibitor for both HSD and aspartate kinase. In AK-HSD expressing organisms, one of the threonine binding sites is found in the linker region between AK and HSD, suggesting potential allosteric inhibition of both enzymes.
However, some threonine-resistant HSD forms exist that require concentrations of threonine much greater than physiologically present for inhibition. These threonine-insensitive forms of HSD are used in genetically engineered plants to increase both threonine and methionine production for higher nutritional value.
Homoserine dehydrogenase is also subject to transcriptional regulation. Its promoter sequence contains a cis-regulatory element TGACTC sequence, which is known to be involved in other amino acid biosynthetic pathways. The Opaque2 regulatory element has also been implicated in homoserine dehydrogenase regulation, but its effects are still not well defined.
In plants, there is also environmental regulation of AK-HSD gene expression. Light exposure has been demonstrated to increase expression of the AK-HSD gene, presumably related to photosynthesis.
In humans, there has been a significant increase in disease from pathogenic fungi, so developing anti-fungal drugs is an important biochemical task. As homoserine dehydrogenase is found mainly in plants, bacteria, and yeast, but not mammals, it is a strong target for antifungal drug development. Recently, 5-hydroxy-4-oxonorvaline (HON) was discovered to target and inhibit HSD activity irreversibly. HON is structurally similar to aspartate semialdehyde, so it is postulated that it serves as a competitive inhibitor for HSD. Likewise, (S) 2-amino-4-oxo-5-hydroxypentanoic acid (RI-331), another amino acid analog, has also been shown to inhibit HSD. Both of these compounds are effective against Cryptococcus neoformans and Cladosporium fulvum, among others.
In addition to amino acid analogs, several phenolic compounds have been shown to inhibit HSD activity. Like HON and RI-331, these molecules are competitive inhibitors that bind to the enzyme active site. Specifically, the phenolic hydroxyl group interacts with the amino acid binding site.
- Thomas D, Barbey R, Surdin-Kerjan Y (June 1993). "Evolutionary relationships between yeast and bacterial homoserine dehydrogenases". FEBS Lett. 323 (3): 289–93. doi:10.1016/0014-5793(93)81359-8. PMID 8500624.
- Cami B, Clepet C, Patte JC (1993). "Evolutionary comparisons of three enzymes of the threonine biosynthetic pathway among several microbial species". Biochimie 75 (6): 487–95. doi:10.1016/0300-9084(93)90115-9. PMID 8395899.
- Ferreira RR, Meinhardt LW, Azevedo RA (2006). "Lysine and threonine biosynthesis in sorghum seeds: characterisation of aspartate kinase and homoserine dehydrogenase isoenzymes". Ann. Appl. Biol. 149 (1): 77–86. doi:10.1111/j.1744-7348.2006.00074.x.
- DeLaBarre B, Thompson PR, Wright GD, Berghuis AM (March 2000). "Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases". Nat. Struct. Biol. 7 (3): 238–44. doi:10.1038/73359. PMID 10700284.
- Paris S, Viemon C, Curien G, Dumas R (February 2003). "Mechanism of Control of Arabidopsis thaliana Aspartate Kinase-Homoserine Dehydrogenase by Threonine". J. Biol. Chem. 278 (7): 5361–5366. doi:10.1074/jbc.M207379200. PMID 12435751.
- Schroeder AC, Zhu C, Yanamadala SR, Cahoon RE, Arkus KAJ, Wachsstock L, Bleeke J, Krishnan HB, Jez JM (January 2010). "Threonine-insensitive Homoserine Dehydrogenase from Soybean: Genomic Organization, Kinetic Mechanism, and in vivo Activity". J. Biol. Chem. 285 (2): 827–834. doi:10.1074/jbc.M109.068882. PMID 19897476.
- Ghislain M, Frankard V, Vandenbossche, Matthews BF, Jacobs M (March 1994). "Molecular analysis of the aspartate kinase-homoserine dehydrogenase gene from Arabidopsis thaliana". Plant Mol. Biol. 24 (6): 835–851. doi:10.1007/bf00014439. PMID 8204822.
- Wedler FC, Ley BW, Shames SL, Rembish SJ, Kushmaul DL (March 1992). "Preferred order random kinetic mechanism for homoserine dehydrogenase of Escherichia coli (Thr-sensitive) aspartokinase/homoserine dehydrogenase-I: Equilibrium Isotope Exchange Kinetics". Biochim. Biophys. Acta. 1119 (3): 247–249. doi:10.1016/0167-4838(92)90209-v. PMID 1547269.
- Jacques SL, Nieman C, Bareicha D, Broadhead G, Kinach R, Honek JF, Wright GD (January 2001). "Characterization of yeast homoserine dehydrogenase, an antifungal target: the invariant histidine 309 is important for enzyme integrity". BBA – Protein Struct. M. 1544 (1-2): 28–41. doi:10.1016/S0167-4838(00)00203-X. PMID 11341914.
- Wedler FC and Ley BW (March 1993). "Kinetic and Regulatory Mechanisms for Escherichia coli Homoserine Dehydrogenase-I: Equilibrium Isotope Exchange Kinetics". J. Biol. Chem. 268 (1): 4880–4888. PMID 8444866.
- Azevedo RA (2002). "Analysis of the aspartic acid metabolic pathway using mutant genes". Amino Acids 22 (3): 217–230. PMID 12083066.
- Zhu-Shimoni JX and Galili G (March 1998). "Expression of an Arabidopsis Aspartate Kinase/Homoserine Dehydrogenase Gene Is Metabolically Regulated by Photosynthesis-Related Signals but Not by Nitrogenous Compounds". Plant Physiol. 116 (3): 1023–1028. doi:10.1104/pp.116.3.1023. PMC 35071. PMID 9501134.
- Zhu-Shimoni JX, Lev-Yadun S, Matthews B, Calili C (March 1997). "Expression of an Aspartate Kinase Homoserine Dehydrogenase Gene IS Subject to Specific Spatial and Temporal Regulation in Vegetative Tissues, Flowers, and Developing Seeds". Plant Physiol. 113 (3): 695–706. doi:10.1104/pp.113.3.695. PMID 12223636.
- Park SD, Lee JY, Sim SY, Kim Y, Lee HS (July 2007). "Characteristics of methionine production by an engineered Corynebacterium glutamicum strain". Metab. Eng. 9 (4): 327–336. doi:10.1016/j.ymben.2007.05.001. PMID 17604670.
- Bareich DC, Nazi I, Wright GD (October 2003). "Simultaneous In Vitro Assay of the First Four Enzymes in the Fungal Aspartate Pathway Identifies a New Class of Aspartate Kinase Inhibitor". Chem. Biol. 10 (10): 967–973. doi:10.1016/j.chembiol.2003.09.016. PMID 14583263.
- Yamaki H, Yamaguchi M, Tsuruo T, Yamaguchi H (May 1992). "Mechanism of action of an antifungal antibiotich, RI-331, (S) 2-amino-4-oxo-5-hydroxypentanoic acid; kinetics of inactivation of homoserine dehydrogenase from Saccharomyces cerevisiae". J. Antibiot. (Tokyo) 25 (5): 750–755. PMID 1352515.
- Jacques SL, Mirza IA, Ejim L, Koteva K, Hughes DW, Green K, Kinach R, Honek JF, Lai HK, Berghuis AM, Wright GD (October 2003). "Enzyme-Assisted Suicide: Molecular Basis for the Antifungal Activity of 5-Hydroxy-4-Oxonorvaline by Potent Inhibition of Homoserine Dehydrogenase". Chem. Biol. 10 (10): 989–995. doi:10.1016/j.chembiol.2003.09.015. PMID 14583265.
- Ejim L, Mirza IA, Capone C, Nazi I, Jenkins S, Chee GL, Berghui AM, Wright GD (July 2004). "New phenolic inhibitors of yeast homoserine dehydrogenase". Bioorg. Med. Chem. 12 (14): 3825–3830. doi:10.1016/j.bmc.2004.05.009. PMID 15210149.
- Black S, Wright NG (1955). "Homoserine dehydrogenase". J. Biol. Chem. 213 (1): 51–60. PMID 14353905.
- Starnes WL, Munk P, Maul SB, Cunningham GN, Cox DJ, Shive W (1972). "Threonine-sensitive aspartokinase-homoserine dehydrogenase complex, amino acid composition, molecular weight, and subunit composition of the complex". Biochemistry 11 (5): 677–87. doi:10.1021/bi00755a003. PMID 4551091.
- Veron M, Falcoz-Kelly F, Cohen GN (1972). "The threonine-sensitive homoserine dehydrogenase and aspartokinase activities of Escherichia coli K12. The two catalytic activities are carried by two independent regions of the polypeptide chain". Eur. J. Biochem. 28 (4): 520–7. doi:10.1111/j.1432-1033.1972.tb01939.x. PMID 4562990.
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.
Homoserine dehydrogenase Provide feedback
No Pfam abstract.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001342
Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see [PUBMED:11352712].
Homoserine dehydrogenase (EC) catalyses the third step in the aspartate pathway; theNAD(P)-dependent reduction of aspartate beta-semialdehyde into homoserine [PUBMED:8500624, PUBMED:8395899]. Homoserine is an intermediate in the biosynthesis of threonine, isoleucine, and methionine. The enzyme can be found in a monofunctional form, in some bacteria and yeast, or a bifunctional form consisting of an N-terminal aspartokinase domain and a C-terminal homoserine dehydrogenase domain, as found in bacteria such as Escherichia coli and in plants. Structural analysis of the yeast monofunctional enzyme (SWISSPROT) indicates that the enzyme is a dimer composed of three distinct regions; an N-terminal nucleotide-binding domain, a short central dimerisation region, and a C-terminal catalytic domain [PUBMED:10700284]. The N-terminal domain forms a modified Rossman fold, while the catalytic domain forms a novel alpha-beta mixed sheet.
This entry represents the catalytic domain of homoserine dehydrogenase.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||cellular amino acid metabolic process (GO:0006520)|
|oxidation-reduction process (GO:0055114)|
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.
|Seed source:||Pfam-B_459 (release 2.1)|
|Author:||Bateman A, Griffiths-Jones SR|
|Number in seed:||147|
|Number in full:||5558|
|Average length of the domain:||185.10 aa|
|Average identity of full alignment:||37 %|
|Average coverage of the sequence by the domain:||33.91 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|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 are 2 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 Homoserine_dh domain has been found. There are 19 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...