Summary: Lactococcin-like family
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 "Bacteriocin". 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.
Bacteriocin Edit Wikipedia article
Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s). They are phenomenologically analogous to yeast and paramecium killing factors, and are structurally, functionally, and ecologically diverse. Applications of bacteriocins are being tested to assess their application as narrow-spectrum antibiotics.
Bacteriocins were first discovered by A. Gratia in 1925. He was involved in the process of searching for ways to kill bacteria, which also resulted in the development of antibiotics and the discovery of bacteriophage, all within a span of a few years. He called his first discovery a colicine because it killed E. coli.
Classification of bacteriocins
Bacteriocins are categorized in several ways, including producing strain, common resistance mechanisms, and mechanism of killing. There are several large categories of bacteriocin which are only phenomenologically related. These include the bacteriocins from gram-positive bacteria, the colicins, the microcins, and the bacteriocins from Archaea. The bacteriocins from E. coli are called colicins (formerly called 'colicines,' meaning 'coli killers'). They are the longest studied bacteriocins. They are a diverse group of bacteriocins and do not include all the bacteriocins produced by E. coli. For example the bacteriocins produced by Staphylococcus warneri are called as warnerin or warnericin. In fact, one of the oldest known so-called colicins was called colicin V and is now known as microcin V. It is much smaller and produced and secreted in a different manner than the classic colicins.
This naming system is problematic for a number of reasons. First, naming bacteriocins by what they putatively kill would be more accurate if their killing spectrum were contiguous with genus or species designations. The bacteriocins frequently possess spectra that exceed the bounds of their named taxa and almost never kill the majority of the taxa for which they are named. Further, the original naming is generally derived not from the sensitive strain the bacteriocin kills, but instead the organism that produces the bacteriocin. This makes the use of this naming system a problematic basis for theory; thus the alternative classification systems.
Methods of classification
Alternative methods of classification include: method of killing (pore-forming, DNase, nuclease, murein production inhibition, etc.), genetics (large plasmids, small plasmids, chromosomal), molecular weight and chemistry (large protein, polypeptide, with/without sugar moiety, containing atypical amino acids like lanthionine) and method of production (ribosomal, post-ribosomal modifications, non-ribosomal).
One method of classification fits the bacteriocins into Class I, Class IIa/b/c, and Class III. 
Class I bacteriocins
Class II bacteriocins
The class II bacteriocins are small (<10 kDa) heat-stable proteins. This class is subdivided into five subclassses. The class IIa bacteriocins (pediocin-like bacteriocins) are the largest subgroup and contain an N-terminal consensus sequence -Tyr-Gly-Asn-Gly-Val-Xaa-Cys across this group. The C-terminal is responsible for species-specific activity, causing cell-leakage by permeabilizing the target cell wall.
Class IIa bacteriocins have a large potential for use in food preservation as well medical applications, due to their strong antilisterial activity, and broad range of activity. One example of Class IIa bacteriocin is pediocin PA-1.
The class IIb bacteriocins (two-peptide bacteriocins) require two different peptides for activity. One such an example is lactococcin G, which permeabilizes cell membranes for monovalent ions such as Na and K, but not for divalents ones. Almost all of this bacteriocins have a GxxxG motifs. This motif is also found in transmembrane proteins where they are involved in helix-helix interactions. The bacteriocins GxxxG motifs can interact with the motifs in the membranes of the bacterial cells and kill the bacteria by doing so.
Class IIc encompasses cyclic peptides, which possesses the N-terminal and C-terminal regions covalentely linked. Enterocin AS-48 is the prototype of this group.
Class IId cover single-peptide bacteriocins, which are not post-translated modified and do not show the pediocin-like signature. The best example of this group is the highly stable aureocin A53. This bacteriocin is stable under highly acidic environment (HCl 6 N), not affected by proteases and thermoresistant.
The most recently proposed subclass is the Class IIe, which encompasses those bacteriocins composed by three or four non-pediocin like peptides. The best example is aureocin A70, a four-peptides bacteriocin, highly active against L. monocytogenes, with potential biotechnological applications.
Class III bacteriocins
Class III bacteriocins are large, heat-labile (>10 kDa) protein bacteriocins. This class is subdivided in two subclasses: subclass IIIa or bacteriolysins and subclass IIIb. Subclass IIIa comprises those peptides that kill bacterial cells by cell-wall degradation, thus causing cell lysis. The best studied bacteriolysin is lysostaphin, a 27 kDa peptide that hydrolises several Staphylococcus spp. cell walls, principally S. aureus. Subclass IIIb, in contrast, comprises those peptides that do not cause cell lysis, killing the target cells by disrupting the membrane potential, which causes ATP efflux .
Class IV bacteriocins
Class IV bacteriocins are defined as complex bacteriocins containing lipid or carbohydrate moities. Confirmatory experimental data was only recently established with the characterisation of Sublancin and Glycocin F (GccF) by two independent groups.
Bacteriocins are of interest in medicine because they are made by non-pathogenic bacteria that normally colonize the human body. Loss of these harmless bacteria following antibiotic use may allow opportunistic pathogenic bacteria to invade the human body .
Bacteriocins have also been suggested as a cancer treatment. They have shown distinct promise as a diagnostic agent for some cancers, but their status as a form of therapy remains experimental and outside the main thread of cancer research. Partly this is due to questions about their mechanism of action and the presumption that anti-bacterial agents have no obvious connection to killing mammalian tumor cells. Some of these questions have been addressed, at least in part.
Bacteriocins[which?] were tested as AIDS drugs around 1990, but did not progress beyond in-vitro tests on cell lines. Bacteriocins can target individual bacterial species, or provide broad-spectrum killing of many microbes. As with today's antibiotics, bacteria can evolve to resist bacteriocins. However, they can be bioengineered to regain their effectiveness. Further, they could be produced in the body by intentionally introduced beneficial bacteria, as some probiotics do.
There are many ways to demonstrate bacteriocin production, depending on the sensitivity and labor intensiveness desired. To demonstrate their production, technicians stab inoculate multiple strains on separate multiple nutrient agar Petri dishes, incubate at 30 Â°C for 24 h., overlay each plate with one of the strains (in soft agar), incubate again at 30 Â°C for 24 h. After this process, the presence of bacteriocins can be inferred if there are zones of growth inhibition around stabs. This is the simplest and least sensitive way. It will often mistake phage for bacteriocins. Some methods prompt production with UV radiation, Mitomycin C, or heat shock. UV radiation and Mitomycin C are used because the DNA damage they produce stimulates the SOS response. Cross streaking may be substituted for lawns. Similarly, production in broth may be followed by dripping the broth on a nascent bacterial lawn, or even filtering it. Precipitation (ammonium sulfate) and some purification (e.g. column or HPLC) may help exclude lysogenic and lytic phage from the assay.
Bacteriocins by name
- aureocin A53
- aureocin A70
- circularin A
- gassericin A
- lactocin S
- microcin S
- reutericin 6
- thuricin 17
- Cotter, Paul D.; Ross, R. Paul; Hill, Colin (2012). "Bacteriocins â€” a viable alternative to antibiotics?". Nature Reviews Microbiology 11 (2): 95â€“105. doi:10.1038/nrmicro2937. ISSN 1740-1526.
- Gratia A (1925). "Sur un remarquable example d'antagonisme entre deux souches de colibacille". Compt. Rend. Soc. Biol. 93: 1040â€“2.
- Gratia JP (October 2000). "AndrÃ© Gratia: a forerunner in microbial and viral genetics". Genetics 156 (2): 471â€“6. PMC 1461273. PMID 11014798.
- Cascales E, Buchanan SK, DuchÃ© D et al. (March 2007). "Colicin Biology". Microbiol. Mol. Biol. Rev. 71 (1): 158â€“229. doi:10.1128/MMBR.00036-06. PMC 1847374. PMID 17347522.
- Prema P, Bharathy S, Palavesam A, Sivasubramanian M, Immanuel G (2006). "Detection, purification and efficacy of warnerin produced by Staphylococcus warneri". World Journal of Microbiology and Biotechnology 22 (8): 865â€“72. doi:10.1007/s11274-005-9116-y.
- Cotter PD, Hill C, Ross RP (2006). "What's in a name? Class distinction for bacteriocins". Nature Reviews Microbiology 4 (2). doi:10.1038/nrmicro1273-c2. is author reply to comment on article :Cotter PD, Hill C, Ross RP (2005). "Bacteriocins: developing innate immunity for food". Nature Reviews Microbiology 3 (?): 777â€“88. doi:10.1038/nrmicro1273. PMID 16205711.
- HENG, C. K. N., WESCOMBE, P. A., BURTON, J. P., JACK, R. W., & TAGG, J. R. (2007). The diversity of bacteriocins in Gram-positive bacteria. In: Bacteriocins: Ecology and Evolution. 1st ed., Riley, M. A. & Chavan, M. A., Eds. Springer, Hildberg, p. 45-83.
- "Structure-function relationships of th... [Curr Pharm Biotechnol. 2009] - PubMed - NCBI". Ncbi.nlm.nih.gov. 2013-08-12. PMID 19149588. Retrieved 2013-12-21.
- NETZ D. J., POHL , BECK-SICKINGER A. G., SELMER , PIERIK , SAHL H. G. (2002). "Biochemical characterisation and genetic analysis of aureocin A53, a new, atypical bacteriocin from Staphylococcus aureus". J. Mol. Biol 319: 745â€“756. doi:10.1016/s0022-2836(02)00368-6.
- NETZ D. J. A., SAHL , NASCIMENTO , OLIVEIRA , SOARES , BASTOS M. C. F. (2001). "Molecular characterisation of aureocin A70, a multiple-peptide bacteriocin isolated from Staphylococcus aureus". J. Mol. Biol 311: 939â€“949. doi:10.1006/jmbi.2001.4885.
- Bastos M.C.F., Coutinho B.G., Coelho M.L.V. Lysostaphin: A Staphylococcal Bacteriolysin with Potential Clinical Applications. Pharmaceuticals. 2010; 3(4):1139-1161.
- Oman T. J., Boettcher J. M., Wang H., Okalibe X. N., & Van der Donk W. A: Sublancin is not a Lantibiotic but an s-Linked Glycopeptide. Nat Chem Biol. 2011; 7(2):78-80.
- Stepper J., Shastri S., Loo T. S., Preston J. C., Novak P., Man P., Moore C. H., HavlÃÄek V., Patchett M. L., and Norris G. E:Cysteine s-Glycosylation, A New Post-Translational Modification Found In Glycopeptide Bacteriocins. FEBS letters. 2011; 585:645-650.
- de Jong A, van Hijum S A F T, Bijlsma J J E, Kok J, Kuipers O P (2006). "BAGEL: a web-based bacteriocin genome mining tool". Nucleic Acids Research 34 (9): W273â€“W279. doi:10.1093/nar/gkl237. PMID 1538908.
- Hammami R, Zouhir A, Ben Hamida J, Fliss I (2007). "BACTIBASE: a new web-accessible database for bacteriocin characterization". BMC Microbiology 7: 89. doi:10.1186/1471-2180-7-89. PMC 2211298. PMID 17941971.
- Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I (2010). "BACTIBASE second release: a database and tool platform for bacteriocin characterization". BMC Microbiology 10: 22. doi:10.1186/1471-2180-10-22. PMC 2824694. PMID 20105292.
- Farkas-Himsley H, Yu H (1985). "Purified colicin as cytotoxic agent of neoplasia: comparative study with crude colicin". Cytobios 42 (167â€“168): 193â€“207. PMID 3891240.
- Baumal R, Musclow E, Farkas-Himsley H, Marks A (1982). "Variants of an interspecies hybridoma with altered tumorigenicity and protective ability against mouse myeloma tumors". Cancer Res. 42 (5): 1904â€“8. PMID 7066902.
- Saito H, Watanabe T, Osasa S, Tado O (1979). "Susceptibility of normal and tumor cells to mycobacteriocin and mitomycin C". Hiroshima J. Med. Sci. 28 (3): 141â€“6. PMID 521305.
- Cruz-Chamorro L, Puertollano MA, Puertollano E, de Cienfuegos GA, de Pablo MA (2006). "In vitro biological activities of magainin alone or in combination with nisin". Peptides 27 (6): 1201â€“9. doi:10.1016/j.peptides.2005.11.008. PMID 16356589.
- Sand SL, Haug TM, Nissen-Meyer J, Sand O (2007). "The bacterial peptide pheromone plantaricin A permeabilizes cancerous, but not normal, rat pituitary cells and differentiates between the outer and inner membrane leaflet". J. Membr. Biol. 216 (2â€“3): 61â€“71. doi:10.1007/s00232-007-9030-3. PMID 17639368.
- Farkas-Himsley H, Hill R, Rosen B, Arab S, Lingwood CA (1995). "The bacterial colicin active against tumor cells in vitro and in vivo is verotoxin 1". Proceedings of the National Academy of Sciences of the United States of America 92 (15): 6996â€“7000. doi:10.1073/pnas.92.15.6996. PMC 41458. PMID 7624357.
- Musclow CE, Farkas-Himsley H, Weitzman SS, Herridge M (1987). "Acute lymphoblastic leukemia of childhood monitored by bacteriocin and flowcytometry". Eur J Cancer Clin Oncol 23 (4): 411â€“8. doi:10.1016/0277-5379(87)90379-8. PMID 3475205.
- Farkas-Himsley H, Zhang YS, Yuan M, Musclow CE (1992). "Partially purified bacteriocin kills malignant cells by apoptosis: programmed cell death". Cell. Mol. Biol. (Noisy-le-grand) 38 (5â€“6): 643â€“51. PMID 1483114.
- Farkas-Himsley H, Musclow CE (1986). "Bacteriocin receptors on malignant mammalian cells: are they transferrin receptors?". Cell. Mol. Biol. 32 (5): 607â€“17. PMID 3779762.
- Farkas-Himsley H, Freedman J, Read SE, Asad S, Kardish M (1991). "Bacterial proteins cytotoxic to HIV-1-infected cells". AIDS 5 (7): 905â€“7. doi:10.1097/00002030-199107000-00025. PMID 1892605.
Could someone please quote the relevant text
- "What Comes After Antibiotics? 5 Alternatives to Stop Superbugs". Popular Mechanics. Retrieved 2013-12-21.
- Kawai Y, Kemperman R, Kok J, Saito T (2004). "The circular bacteriocins gassericin A and circularin A". Current Protein & Peptide Science 5 (5): 393â€“8. PMID 15544534. Retrieved 2015-01-19.
- Pandey N, Malik RK, Kaushik JK, Singroha G (2013). "Gassericin A: a circular bacteriocin produced by lactic acid bacteria Lactobacillus gasseri". World Journal of Microbiology & Biotechnology 29 (11): 1977â€“87. doi:10.1007/s11274-013-1368-3. PMID 23712477. Retrieved 2015-01-19.
- MÃ¸rtvedt, C. I.; Nissen-Meyer, J.; Sletten, K.; Nes, I. F. (1991). "Purification and amino acid sequence of lactocin S, a bacteriocin produced by Lactobacillus sake L45". Applied and environmental microbiology 57 (6): 1829â€“1834. PMC 183476. PMID 1872611.
- Michel-Briand, Y.; Baysse, C. (2002). "The pyocins of Pseudomonas aeruginosa". Biochimie 84 (5â€“6): 499â€“510. doi:10.1016/s0300-9084(02)01422-0. PMID 12423794.
- Kabuki T, Saito T, Kawai Y, Uemura J, Itoh T (1997). "Production, purification and characterization of reutericin 6, a bacteriocin with lytic activity produced by Lactobacillus reuteri LA6". International Journal of Food Microbiology 34 (2): 145â€“56. doi:10.1016/s0168-1605(96)01180-4. PMID 9039561. Retrieved 2015-01-19.
|Wikimedia Commons has media related to Bacteriocin.|
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.
Lactococcin-like family Provide feedback
Family of bacteriocins from lactic acid bacteria.
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR007464
Bacteriocins are produced by bacteria to inhibit the growth of similar or closely related bacterial strains. The class II bacteriocins are small heat-stable proteins for which disulphide bonds are the only modification to the peptide.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||extracellular region (GO:0005576)|
|Biological process||defense response to bacterium (GO:0042742)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
This is a collection of short bacterial families that carry a distinctive GG-cleavage motif. Conservation C-terminal to the GG-motif is not apparent. However, the families are all interconnected with critical virulence attributes of one kind or another.
The clan contains the following 5 members:Antimicrobial17 Bacteriocin_IIc ComC L_biotic_typeA Lactococcin
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:||3|
|Number in full:||73|
|Average length of the domain:||47.10 aa|
|Average identity of full alignment:||30 %|
|Average coverage of the sequence by the domain:||73.70 %|
|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:||9|
|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.