Summary: Galactoside-binding lectin
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Galectin Edit Wikipedia article
Galectins are a class of proteins that bind specifically to Î²-galactoside sugars, such as N-acetyllactosamine (GalÎ²1-3GlcNAc or GalÎ²1-4GlcNAc), which can be bound to proteins by either N-linked or O-linked glycosylation. They are also termed S-type lectins due to their dependency on disulphide bonds for stability and carbohydrate binding. There have been 15 galectins discovered in mammals, encoded by the LGALS genes, which are numbered in a consecutive manner. Only galectin-1, -2, -3, -4, -7, -8, -9, -10 and -12 have been identified in humans. Galectin-5 and -6 are found in rodents, whereas galectin-11, -14 and -15 are uniquely found in sheep and goats. Members of the galectin family have also been discovered in other mammals, birds, amphibians, fish, nematodes, sponges, and some fungi. Unlike the majority of lectins they are not membrane bound, but soluble proteins with both intra- and extracellular functions. They have distinct but overlapping distributions but found primarily in the cytosol, nucleus, extracellular matrix or in circulation. Although many galectins must be secreted, they do not have a typical signal peptide required for classical secretion. The mechanism and reason for this non-classical secretion pathway is unknown.
- 1 Structure
- 2 Function
- 3 Galectins and disease
- 4 Table of Human Galectins
- 5 References
- 6 External links
There are three different forms of galectin structure: dimeric, tandem or chimera. Dimeric galectins, also called prototypical galectins, are homodimers, consisting of two identical galectin subunits that have associated with one another. The galectins that fall under this category are galectin-1, -2, -5, -7, -10, -11, -14 and -15. Tandem galectins contain at least two distinct carbohydrate recognition domains (CRD) within one polypeptide, thus are considered intrinsically divalent. The CRDs are linked with a small peptide domain. Tandem galectins include galectin-4, -6, -8, -9 and -12. The final galectin is galectin-3 which is the only galectin found in the chimera category in vertebrates. Galectin-3 has one CRD and a long non-lectin domain. Galectin-3 can exist in monomeric form or can associate via the non-lectin domain into multivalent complexes up to a pentameric form. This allows galectin-3 to bridge effectively between different ligands and form adhesive networks. The formation of multimers is concentration dependent. When Galectin-3 is at a low concentration it is monomeric and likely to inhibit adhesion. It binds to adhesion proteins such as integrins and blocks further binding to other cells or the extracellular matrix. When concentrations of galectin-3 are high it forms large complexes that assist in adhesion by bridging between cells or cells and the extracellular matrix. Many isoforms of galectins have been found due to different splicing variants. For example, Galectin-8 has seven different mRNAs encoding for both tandem and dimeric forms. The type of galectin-8 that is expressed is dependent on the tissue. Galectin-9 has three different isoforms which differ in the length of the linker region.
The galectin carbohydrate recognition domain (CRD) is constructed from beta-sheet of about 135 amino acids. The two sheets are slightly bent with 6 strands forming the concave side and 5 strands forming the convex side. The concave side forms a groove in which the carbohydrate ligand can bind, and which is long enough to hold about a linear tetrasaccharide.
Galectins essentially bind to glycans featuring galactose and its derivatives. However, physiologically, they are likely to require lactose or N-aceyllactosamine for significantly strong binding. Generally, the longer the sugar the stronger the interactions. For example, galectin-9 binds to polylactosamine chains with stronger affinity than to an N-acetyllactosamine monomer. This is because more Van der Waals interactions can occur between sugar and binding pocket. Carbohydrate binding is calcium independent, unlike C-type lectins. The strength of ligand binding is determined by a number of factors: The multivalency of both of ligand and the galectin, the length of the carbohydrate and the mode of presentation of ligand to carbohydrate recognition domain. Different galectins have distinct binding specificities for binding oligosaccharides depending on the tissue in which they are expressed and the function that they possess. However, in each case, galactose is essential for binding. Crystallisation experiments of galectins in complex with N-acetyllactosamine show that binding arises due to hydrogen bonding interactions from the carbon-4 and carbon-6 hydroxyl groups of galactose and carbon-3 of N-acetylglucosamine (GlcNAc) to the side chains of amino acids in the protein. They cannot bind to other sugars such as mannose because this sugar will not fit inside the carbohydrate recognition domain without steric hindrance. Due to the nature of the binding pocket, galectins can bind terminal sugars or internal sugars within a glycan. This allows bridging between two ligands on the same cell or between two ligands on different cells.
Galectins are a large family with relatively broad specificity. Thus, they have a broad variety of functions including mediation of cellâ€“cell interactions, cellâ€“matrix adhesion and transmembrane signalling. Their expression and secretion is well regulated, suggesting they may be expressed at different times during development. There are no serious defects when individual galectin genes are deleted in knock-out mouse models. This is because there is substantial overlap for the essential functions. The list of functions for galectins is extensive and it is unlikely they have all been discovered. A handful of the main functions are described below.
Galectins are distinct in that they can regulate cell death both intracellularly and extracellularly. Extracellularly, they cross link glycans on the outside of cells and transduce signals across the membrane to directly cause cell death or activate downstream signaling that triggers apoptosis. Intracellularly, they can directly regulate proteins that control cell fate. Many galectins have roles in apoptosis:
- One essential way galectins regulate apoptosis is to control positive and negative selection of T cells in the thymus. This process prevents the circulation of T cells that are self-reactive and recognise self antigen. Both galectin-1 and galectin-9 are secreted by epithelial cells in the thymus and mediate T cell apoptosis. T cell death is also necessary to kill activated and infected T cells after an immune response. This is also mediated by galectin-1 and galectin-9. Galectin-1 binds many proteins on the T cell surface, but specifically CD7, CD43 and CD45 are involved in apoptosis.
- Galectin-7 is expressed under the p53 promoter and may have a key role in regulating apoptosis of keratinocytes after DNA damage, such as that caused by UV radiation.
- Galectin-12 expression induces apoptosis of adipocytes.
- Galectin-3 has been shown to be the only galectin with anti-apoptotic activity, proven by knock-out in mice increasing rates of apoptosis. Intracellularly, galectin-3 can associate with Bcl-2 proteins, an antiapoptotic family of proteins, and thus may enhance Bcl-2 binding to the target cell. On the other hand, galectin-3 can also be pro-apoptotic and mediate T cell and neutrophil death.
Suppression of T-cell receptor activation
Galectin-3 has an essential role in negatively regulating T cell receptor (TCR) activation. Crosslinking of T cell receptors and other glycoproteins by galectin-3 on the membrane of T cells prevents clustering of TCRs and ultimately suppresses activation. This prevents auto-activation. Experiments in transgenic mice with deficient N-acetylglucosamine transferase V (GnTV) have increased susceptibility to autoimmune diseases. GnTV is the enzyme required to synthesise polylactosamine chains, which are the ligand for galectin-3 on T cell receptors. This knock-out means galectin-3 cannot prevent auto-activation of TCR so T cells are hypersensitive. Also within the immune system, galectins have been proven to act as chemoattractants to immune cells and activate secretion of inflammatory cytokines.
Galectins can both promote and inhibit integrin-mediated adhesion. To enhance integrin-mediated adhesion, they cross link between two glycans on different cells. This brings the cells closer together so integrin binding occurs. They can also hinder adhesion by binding to two glycans on the same cell, which blocks the integrin binding site. Galectin-8 is specific for the glycans bound to integrin and has a direct role in adhesion as well as activating integrin-specific signaling cascades.
Nuclear pre-mRNA splicing
Galectin-1 and galectin-3 have been found, surprisingly, to associate with nuclear ribonucleoprotein complexes including the spliceosome. Studies revealed that galectin-1 and -3 are required splicing factors, since removal of the galectins by affinity chromatography with lactose resulted in loss of splicing activity. It appears that the splicing capability of galectins is independent of their sugar-binding specificities. Site-directed mutagenesis studies to the carbohydrate recognition domain removes glycan binding but does not prevent association with the spliceosome.
Cytoplasmic galectin-8 and galectin-9 have been shown to control mTOR (mTORC1) and PRKAA (AMPK) in response to lysosomal membrane damage. Lysosomal perforation and other endomembrane damage can be inflicted by various agents such as some chemicals yielding osmotically active products, crystalline silica, possibly amyloid aggregates and cytoplasmic organic or inorganic crystals, as well as intracellular microbial pathogens such as Mycobacterium tuberculosis; such injury can be modeled using membrane-permeant dipeptide precursors that polymerize in lysosomes,. Under resting, homeostatic conditions galectin-8 interacts with mTOR, which it=n its active state resides on the cytosolic (cytofacial) side of lysosomal membranes. However, under lysosome damaging conditions leading to exposure of the exofacially, i.e., lumenaly, oriented glycans (glycoporteins and glycolipids), galectin-8 recognizes the cytofacial glycans exposed due to membrane damage and releases mTOR. Galectin-8 instead now binds to the mTOR-regulatory complex located on the lysosomal membrane including SLC38A9, LAMTOR1, and RRAGA/RRAGB (RagA/B). This complex loses affinity for mTOR causing mTOR's inactivation and translocation from the lysosome to the cytosol. The damage-responsive complex containing galectin-8, SLC38A9, LAMTOR1, and RRAGA/RRAGB is known as GALTOR. Galectin-3 and galectin-8 also interact with autophagy receptor-regulator TRIM16 that assembles autophagy initiation machinery on damaged lysosomes, whereas galectin-8 also interacts with the autophagy receptor NDP52 recognizing Salmonella-damaged vacuole.
The functional roles of galectins in cellular response to membrane damage are expanding, e.g. Galectin-3 recruits ESCRTs to damaged lysosomes so that lysosomes can be repaired. This occurs before autophagy is induced to repair endosomes and lysosomes lest they are removed by autophagy.
Galectins and disease
Galectins are abundant, distributed widely around the body and have some distinct functions. It is because of these that they are often implicated in a wide range of diseases such as cancer, HIV, autoimmune disease, chronic inflammation, graft vs host disease (GVHD) and allergic reactions. The most studied and characterised mechanisms are for cancer and HIV, which are described below.
The best understood galectin in terms of cancer is galectin-3. Evidence suggests that galectin-3 plays a considerable part in processes linked to tumorigenesis, including transformation to a malignant form, metastasis and increased invasive properties of tumour cells. There is some significant evidence that galectin-3 is involved in cancer since it interacts with oncogenes such as Ras and activates downstream signalling that promotes proliferation. It can also regulate some of the proteins of the cell cycle, such as cyclin E and c-myc, which may give it additional tumorigenic properties. The concentration of galectin-3 is elevated in the circulation of patients with some types of cancer including breast cancer. It has also been identified bound to glycans on the surface of breast cancer cells. In cancer patients whose cancer has metastasised, galectin-3 is higher still, suggesting that this galectin has a crucial role in metastasis. Galectin-3 also binds to MUC-1, a very large transmembrane mucin, which on cancer cells changes expression from long core 2 type O-glycosylation to shorter core 1 type O-glycosylation. Core 2 glycans terminate in galactose or sialic acid, whereas core 1 is branched and has potential for large carbohydrate extensions. High levels of MUC-1 are associated with poor prognosis and increased potential of metastasis. This cancer-associated MUC-1 is a natural ligand for galectin-3. In normal cells, MUC-1 has distinct polarisation and acts as a protective barrier around the cell, reducing cell-cell interactions. In breast cancer cells, it is hypothesised that galectin-3 has high affinity for cancer-associated MUC-1, causing depolarisation and breaking the cell's protective shield. This exposes small adhesion molecules on the surface of the cell, which interact with adhesion proteins on endothelial cell walls, such as E-selectin, promoting intravastion into the blood stream. Experiments shows that overexpression of MUC-1 alone is not enough to increase metastatic potential, and in fact it inhibits tumour cell entry into the blood stream. It requires the presence of upregulated galectin-3 in addition to MUC-1 to increase invasive and metastatic properties of the cancer. This is supported by other studies showing that inhibition of galectin-3 in human breast cancer cells lose their malignancy in vitro. This may provide a clue towards developing therapeutics for cancer, such as galectin-3 inhibitors.
Galectin-8, which increases integrin-mediated adhesion, has been shown to be downregulated in some cancers. This benefits the cancer since integrin interactions with the extracellular matrix prevent metastasis. Lung cancer studies, however, have demonstrated increased adhesion to galectin-8 with increased metastatic potential, which may be mediated by elevated surface expression and activation of integrin Î±3Î²1.
Intracellular Pathogen Invasion
Galectin-8 has been shown to play a specific role in assessing endosomal integrity. After pathogens, such as bacteria or viruses, are engulfed by cells, they typically try to exit the endosome to gain access to nutrients in the cytosol. Galectin-8 specifically binds to glycosylation found within the endosome, and recruits adapter molecule CALCOCO2 which activates antibacterial autophagy. Galectin-3, galectin 8 and galectin-9 have been shown to play additional roles in autophagy both through control of mTOR (galectin-8) and AMPK (galectin-9), and as a factor (galectin-3) in the assembly of the ULK1-Beclin 1-ATG16L1 initiator complex on TRIM16 during endomembrane damage.
Galectin-1 has been shown to enhance HIV infection due to its galactose binding specificity. HIV preferentially infects CD4+ T cells and other cells of the immune system, immobilising the adaptive immune system. HIV is a virus that infects CD4+ cells via binding of its viral envelope glycoprotein complex, which consists of gp120 and gp41. The gp120 glycoprotein contains two types of N-glycan, high mannose oligomers and N-acetyllactosamine chains on a trimannose core. The high mannose oligomers are pathogen-associated molecular pattern (PAMPs) and are recognised by the C-type lectin DC-SIGN found on dendritic cells. The N-acetyllactosamine chains are ligands for galectin-1. Galectin-1 is expressed in the thymus. In particular it is secreted in abundance by Th1 cells. In its normal function, galectin-1 binds to glycans on the CD4 co-receptor of T cells to prevent auto reactivity. When HIV is present, the galectin bridges between the CD4 co-receptor and gp120 ligands, thus facilitating HIV infection of the T cell. Galectin-1 is not essential for HIV infection but assists it by accelerating the binding kinetics between gp120 and CD4. Knowledge of the mechanism between galectin and HIV may provide important therapeutic opportunities. A galectin-1 inhibitor can be used in conjunction with antiretroviral drugs to decrease the infectivity of the HIV and increase the efficacy of the drug. Galectin-3 binds TRIM5Î±, a cytosolic restriction factor against HIV acting during HIV capsid uncoating, although the precise role of this association remains to be determined. Several galectins bind other TRIMs  some of which are known to contribute to antiviral restriction.
T. cruzi infection of cardiac cells reduced by galectinâ€“1.
Table of Human Galectins
|Human galectin||Location||Function||Implication in disease|
|Galectin-1||Secreted by immune cells such as by T helper cells in the thymus or by stromal cells surrounding B cells 
Also found in abundance in muscle, neurons and kidney
|Negatively regulate B cell receptor activation
Activate apoptosis in T cells
Suppression of Th1 and Th17 immune responses
Contributes to nuclear splicing of pre-mRNA
|Can enhance HIV infection
Found upregulated in tumour cells
|Galectin-2||Gastrointestinal tract ||Binds selectively to Î²-galactosides of T cells to induce apoptosis||None found|
|Galectin-3||Wide distribution||Can be pro- or anti-apoptotic (cell dependent)
Contributes to nuclear splicing of pre-mRNA
Crosslinking and adhesive properties
In the cytoplasm, helps form the ULK1-Beclin-1-ATG16L1-TRIM16 complex following endomembrane damage
|Upregulation occurs in some cancers, including breast cancer, gives increased metastatic potential|
|Galectin-4||Intestine and stomach||Binds with high affinity to lipid rafts suggesting a role in protein delivery to cells||Inflammatory bowel disease (IBD)|
|Galectin-7||Stratified squamous epithelium||Differentiation of keratinocytes
May have a role in apoptosis and cellular repair mediated by p53
|Implications in cancer|
|Galectin-8||Wide distribution||Binds to integrins of the extracellular matrix. In the cytoplasm, alternatively binds to mTOR or forms the GALTOR complex with SLC38A9, LAMTOR1, and RagA/B||Downregulation in some cancers
Implicated in tuberculosis defense
|Functions as a urate transporter in the kidney 
Enhances maturation of dendritic cells to secrete inflammatory cytokines. In the cytoplasm, associates upon lysosomal damage with AMPK and activates it
|Galectin-10||Expressed in eosinophils and basophils||Essential role in immune system by suppression of T cell proliferation||Found in Charcot Leyden crystals in asthma|
|Galectin-12||Adipose tissue||Stimulates apoptosis of adipocytes
Involved in adipocyte differentiation
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- Galectin: Definition and History by Jun Hirabayashi
- Handbook of Animal Lectins by David Kilpatrick
- Galectin at the US National Library of Medicine Medical Subject Headings (MeSH)
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.
Galactoside-binding lectin Provide feedback
This family contains galactoside binding lectins. The family also includes enzymes such as human eosinophil lysophospholipase (Q05315 EC:126.96.36.199).
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001079
Galectins (also known as galaptins or S-lectin) are a family of proteins defined by having at least one characteristic carbohydrate recognition domain (CRD) with an affinity for beta-galactosides and sharing certain sequence elements. Members of the galectins family are found in mammals, birds, amphibians, fish, nematodes, sponges, and some fungi. Galectins are known to carry out intra- and extracellular functions through glycoconjugate-mediated recogntion. From the cytosol they may be secreted by non-classical pathways, but they may also be targeted to the nucleus or specific sub-cytosolic sites. Within the same peptide chain some galectins have a CRD with only a few additional amino acids, whereas others have two CRDs joined by a link peptide, and one (galectin-3) has one CRD joined to a different type of domain [PUBMED:16051274, PUBMED:14758066].
The galectin carbohydrate recognition domain (CRD) is a beta-sandwich of about 135 amino acid. The two sheets are slightly bent with 6 strands forming the concave side and 5 strands forming the convex side. The concave side forms a groove in which carbohydrate is bound, and which is long enough to hold about a linear tetrasaccharide [PUBMED:8262940, PUBMED:8747464].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||carbohydrate binding (GO:0030246)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This superfamily includes a diverse range of carbohydrate binding domains and glycosyl hydrolase enzymes that share a common structure.
The clan contains the following 49 members:Alginate_lyase2 ArabFuran-catal Arabino_trans_N Bac_rhamnosid Bact_lectin Calreticulin Cleaved_Adhesin DUF1080 DUF1349 DUF1583 DUF1961 DUF2401 DUF3472 DUF4975 Exotox-A_bind Gal-bind_lectin GalBD_like GH131_N GH43_C2 Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_32C Glyco_hydro_7 HA1 Laminin_G_1 Laminin_G_2 Laminin_G_3 Lectin_leg-like Lectin_legB MAM Methyltransf_FA Neuralized Pentaxin Peptidase_A4 Polysacc_lyase PRY Reoviridae_Vp9 Sial-lect-inser Sialidase SKN1 Spike_NTD SPRY TgMIC1 Toxin_R_bind_N TSP_C VP4_haemagglut XET_C YrpD
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 , Griffiths-Jones SR|
|Number in seed:||53|
|Number in full:||5599|
|Average length of the domain:||135.70 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||49.84 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||22|
|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 Gal-bind_lectin domain has been found. There are 535 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.
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