Summary: Yersinia pseudo-tuberculosis mitogen
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 "Yersinia pseudotuberculosis". 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.
Yersinia pseudotuberculosis Edit Wikipedia article
Smith & Thal 1965
Yersinia pseudotuberculosis is a Gram-negative bacterium that causes Far East scarlet-like fever in humans, who occasionally get infected zoonotically, most often through the food-borne route. Animals are also infected by Y. pseudotuberculosis. The bacterium is urease positive.
Yersinia scanned with electron micrograph
|Classification and external resources|
In humans, symptoms of Far East scarlet-like fever are similar to those of infection with Yersinia enterocolitica (fever and right-sided abdominal pain), except that the diarrheal component is often absent, which sometimes makes the resulting condition difficult to diagnose. Y. pseudotuberculosis infections can mimic appendicitis, especially in children and younger adults, and, in rare cases, the disease may cause skin complaints (erythema nodosum), joint stiffness and pain (reactive arthritis), or spread of bacteria to the blood (bacteremia).
Far East scarlet-like fever usually becomes apparent five to 10 days after exposure and typically lasts one to three weeks without treatment. In complex cases or those involving immunocompromised patients, antibiotics may be necessary for resolution; ampicillin, aminoglycosides, tetracycline, chloramphenicol, or a cephalosporin may all be effective.
The recently described syndrome "Izumi-fever" has been linked to infection with Y. pseudotuberculosis.
The symptoms of fever and abdominal pain mimicking appendicitis (actually from mesenteric lymphadenitis)  associated with Y. pseudotuberculosis infection are not typical of the diarrhea and vomiting from classical food poisoning incidents. Although Y. pseudotuberculosis is usually only able to colonize hosts by peripheral routes and cause serious disease in immunocompromised individuals, if this bacterium gains access to the blood stream, it has an LD50 comparable to Y. pestis at only 10 CFU.
Relationship to Y. pestis
To facilitate attachment, invasion, and colonization of its host, this bacterium possesses many virulence factors. Superantigens, bacterial adhesions, and the actions of Yops (which are bacterial proteins once thought to be "Yersinia outer membrane proteins") that are encoded on the "[plasmid] for Yersinia virulence" â€“ commonly known as the pYV â€“ cause host pathogenesis and allow the bacteria to live parasitically.
The 70-kb pYV is critical to Yersinia's pathogenicity, since it contains many genes known to encode virulence factors and its loss gives avirulence of all Yersinia species. A 26-kb "core region" in the pYV contains the ysc genes, which regulate the expression and secretion of Yops. Many Ysc proteins also amalgamate to form a type-III secretory apparatus, which secretes many Yops into the host cell cytoplasm with the assistance of the "translocation apparatus", constructed of YopB and YopD. The core region also includes yopN, yopB, yopD, tyeA, lcrG, and lcrV, which also regulate Yops gene expression and help to translocate secretory Yops to the target cell. For example, YopN and TyeA are positioned as a plug on the apparatus so only their conformational change, induced by their interaction with certain host cell membrane proteins, will cause the unblocking of the secretory pathway. Secretion is regulated in this fashion so that proteins are not expelled into the extracellular matrix and elicit an immune response. Since this pathway gives secretion selectivity, it is a virulence factor.
In contrast to the ysc and yop genes listed above, the Yops that act directly on host cells to cause cytopathologic effects â€“ "effector Yops" â€“ are encoded by pYV genes external to this core region. The sole exception is LcrV, which is also known as the "versatile Yop" for its two roles as an effector Yop and as a regulatory Yop. The combined function of these effector Yops permits the bacteria to resist internalization by immune and intestinal cells and to evade the bactericidal actions of neutrophils and macrophages. Inside the bacterium, these Yops are bound by pYV-encoded Sycs (specific Yop chaperones), which prevent premature interaction with other proteins and guide the Yops to a type-III secretory apparatus. In addition to the Syc-Yop complex, Yops are also tagged for type III secretion either by the first 60nt in their corresponding mRNA transcript or by their corresponding first 20 N-terminal amino acids. LcrV, YopQ, YopE, YopT, YopH, YpkA, YopJ, YopM, and YadA are all secreted by the type-III secretory pathway. LcrV inhibits neutrophil chemotaxis and cytokine production, allowing Y. pseudotuberculosis to form large colonies without inducing systemic failure and, with YopQ, contributes to the translocation process by bringing YopB and YopD to the eukaryotic cell membrane for pore-formation. By causing actin filament depolymerisation, YopE, YopT, and YpkA resist endocytosis by intestinal cells and phagocytosis while giving cytotoxic changes in the host cell. YopT targets Rho GTPase, commonly named "RhoA", and uncouples it from the membrane, leaving it in an inactive RhoA-GDI (guanine nucleotide dissociation inhibitor)-bound state whereas YopE and YpkA convert Rho proteins to their inactive GDP-bound states by expressing GTPase activity. YpkA also catalyses serine autophosporylation, so it may have regulatory functions in Yersinia or undermine host cell immune response signal cascades since YpkA is targeted to the cytoplasmic side of the host cell membrane. YopH acts on host focal adhesion sites by dephosphorylating several phosphotyrosine residues on focal adhesion kinase (FAK) and the focal adhesion proteins paxillin and p130. Since FAK phosphorylation is involved in uptake of yersiniae as well as T cell and B cell responses to antigen-binding, YopH elicits antiphagocytic and other anti-immune effects. YopJ, which shares an operon with YpkA, "...interferes with the mitogen-activated protein (MAP) kinase activities of c-Jun N-terminal kinase (JNK), p38, and extracellular signal-regulated kinase", leading to macrophage apoptosis. In addition, YopJ inhibits TNF-Î± release from many cell types, possibly through an inhibitory action on NF-ÎºB, suppressing inflammation and the immune response. By secretion through a type III pathway and localization in the nucleus by a vesicle-associated, microtubule-dependent method, YopM may alter host cell growth by binding to RSK (ribosomal S6 kinase), which regulates cell cycle regulation genes. Interestingly, YadA has lost its adhesion, opsonisation-resisting, phagocytosis-resisting, and respiratory burst-resisting functions in Y. pseudotuberculosis due to a frameshift mutation by a single base-pair deletion in yadA in comparison to yadA in Y. enterocolitica, yet it still is secreted by type III secretion. The yop genes, yadA, ylpA, and the virC operon are considered the "Yop regulon" since they are coregulated by pYV-encoded VirF. virF is in turn thermoregulated. At 37 degrees Celsius, chromosomally encoded Ymo, which regulates DNA supercoiling around the virF gene, changes conformation, allowing for VirF expression, which then up-regulates the Yop regulon.
Y. pseudotuberculosis adheres strongly to intestinal cells via chromosomally encoded proteins so that Yop secretion may occur, to avoid being removed by peristalsis, and to invade target host cells. A transmembrane protein, Invasin, facilitates these functions by binding to host cell Î±Î²1 integrins. Through this binding, the integrins cluster, thereby activating FAK, and causing a corresponding reorganization of the cytoskeleton. Subsequent internalization of bound bacteria occurs when the actin-depolymerising Yops are not being expressed. The protein encoded on the "attachment invasion locus" named Ail also bestows attachment and invasive abilities upon Yersiniae while interfering with the binding of complement on the bacterial surface. To increase binding specificity, the fibrillar pH6 antigen targets bacteria to target intestinal cells only when thermoinduced.
Certain strains of Yersinia pseudotuberculosis express a superantigenic exotoxin, YPM, or the Y. pseudotuberculosis-derived mitogen, from the chromosomal ypm gene. YPM specifically binds and causes the proliferation of T lymphocytes expressing the VÎ²3, VÎ²7, VÎ²8, VÎ²9, VÎ²13.1, and VÎ²13.2 variable regions  with CD4+ T cell preference, although activation of some CD8+ T cells occurs. This T cell expansion can cause splenomegaly coupled with IL-2 and IL-4 overproduction. Since administering anti-TNF-Î± and anti-IFN-Î³ monoclonal antibodies neutralizes YPM toxicity in vivo, these cytokines are largely responsible for the damage caused indirectly by the exotoxin. Strains that carry the exotoxin gene are rare in Western countries, where the disease, when at all apparent, manifests itself largely with minor symptoms, whereas more than 95% of strains from Far Eastern countries contain ypm and are correlated with Izumi fever and Kawasaki disease. Although the superantigen poses the greatest threat to host health, all virulence factors contribute to Y. pseudotuberculosis viability in vivo and define the bacteriumâ€™s pathogenic characteristics. Y. pseudotuberculosis can live extracellularly due to its formidable mechanisms of phagocytosis and opsonisation resistance through the expression of Yops and the type III pathway; yet, by limited pYV action, it can populate host cells, especially macrophages, intracellularly to further evade immune responses and be disseminated throughout the body.
crystal structure of yersinia pseudotuberculosis-derived mitogen (ypm)
Yersinia pseudotuberculosis-derived mitogens (YpM) are superantigens, which are able to excessively activate T cells by binding to the T cell receptor. Since YpM can activate large numbers of the T cell population, this leads the release of inflammatory cytokines.
Members of this family of Yersinia pseudotuberculosis mitogens adopt a sandwich structure consisting of 9 strands in two beta sheets, in a jelly-roll topology. YpM molecular weight is about 14 kDa. Structurally, it is unlike any other superantigen, but is remarkably similar to the tumour necrosis factor and viral capsid proteins. This suggests a possible evolutionary relationship.
Some highly homologous variants of YPM have been characterized, including YPMa, YPMb, and YPMc.
- Ryan KJ; Ray CG (editors) (2004). Sherris Medical Microbiology (4th ed. ed.). McGraw Hill. ISBN 0-8385-8529-9.
- Jani, Asim (2003). "Pseudotuberculosis (Yersina)". Retrieved 2006-03-04.
- Carnoy, C.; Lemaitre, N.; Simonet, M. (2005). "The superantigenic toxin of Yersinia pseudotuberculosis". In Ladant, Daniel; Alouf, Joseph E.; Popoff, Michel R. The Comprehensive Sourcebook of Bacterial Protein Toxins. Academic Press. pp. 862â€“871. ISBN 978-0-08-045698-0.
- Robins-Browne, R.; Hartland, E. (2003). "Yersinia species". In Miliotis, Marianne D.; Bier, Jeffrey W. International Handbook of Foodborne Pathogens. CRC Press. pp. 323â€“355. ISBN 978-0-203-91206-5.
- Lindler, L. (2004). "Virulence plasmids of Yersinia: characteristics and comparison". In Funnell, B.E.; Phillips, G.J. Plasmid biology. ASM Press. pp. 423â€“437. ISBN 1555812651.
- Brubaker RR (1983). "The Vwa+ virulence factor of yersiniae: the molecular basis of the attendant nutritional requirement for Ca++". Rev. Infect. Dis. 5 (Suppl 4): S748â€“58. PMID 6195719.
- Achtman, M.; Zurth, K.; Morelli, G.; Torrea, G.; Guiyoule, A.; Carniel, E. (23 November 1999). "Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis". Proc. Natl. Acad. Sci. U.S.A. 96 (24): 14043â€“8. doi:10.1073/pnas.96.24.14043. PMC 24187. PMID 10570195.
- Iriarte M, Cornelis GR (1999). "Identification of SycN, YscX, and YscY, three new elements of the Yersinia yop virulon". J. Bacteriol. 181 (2): 675â€“80. PMC 93427. PMID 9882687.
- Cornelis GR, Boland A, Boyd AP, Geuijen C, Iriarte M, Neyt C, Sory MP, Stainier I (1998). "The virulence plasmid of Yersinia, an antihost genome". Microbiol. Mol. Biol. Rev. 62 (4): 1315â€“52. PMC 98948. PMID 9841674.
- Lee VT, Tam C, Schneewind O (2000). "LcrV, a substrate for Yersinia enterocolitica type III secretion, is required for toxin targeting into the cytosol of HeLa cells". J. Biol. Chem. 275 (47): 36869â€“75. doi:10.1074/jbc.M002467200. PMID 10930402.
- Zumbihl R, Aepfelbacher M, Andor A, Jacobi CA, Ruckdeschel K, Rouot B, Heesemann J (1999). "The cytotoxin YopT of Yersinia enterocolitica induces modification and cellular redistribution of the small GTP-binding protein RhoA". J. Biol. Chem. 274 (41): 29289â€“93. doi:10.1074/jbc.274.41.29289. PMID 10506187.
- Persson C, Carballeira N, Wolf-Watz H, FÃ¤llman M (1997). "The PTPase YopH inhibits uptake of Yersinia, tyrosine phosphorylation of p130Cas and FAK, and the associated accumulation of these proteins in peripheral focal adhesions". EMBO J. 16 (9): 2307â€“18. doi:10.1093/emboj/16.9.2307. PMC 1169832. PMID 9171345.
- HÃ¥kansson S, Galyov EE, Rosqvist R, Wolf-Watz H (1996). "The Yersinia YpkA Ser/Thr kinase is translocated and subsequently targeted to the inner surface of the HeLa cell plasma membrane". Mol. Microbiol. 20 (3): 593â€“603. doi:10.1046/j.1365-2958.1996.5251051.x. PMID 8736538.
- Ruckdeschel K, Machold J, Roggenkamp A, Schubert S, Pierre J, Zumbihl R, Liautard JP, Heesemann J, Rouot B (1997). "Yersinia enterocolitica promotes deactivation of macrophage mitogen-activated protein kinases extracellular signal-regulated kinase-1/2, p38, and c-Jun NH2-terminal kinase. Correlation with its inhibitory effect on tumor necrosis factor-alpha production". J. Biol. Chem. 272 (25): 15920â€“7. doi:10.1074/jbc.272.25.15920. PMID 9188492.
- Alrutz MA, Isberg RR (1998). "Involvement of focal adhesion kinase in invasin-mediated uptake". Proc. Natl. Acad. Sci. U.S.A. 95 (23): 13658â€“63. doi:10.1073/pnas.95.23.13658. PMC 24875. PMID 9811856.
- Galyov EE, HÃ¥kansson S, Forsberg A, Wolf-Watz H (1993). "A secreted protein kinase of Yersinia pseudotuberculosis is an indispensable virulence determinant". Nature 361 (6414): 730â€“2. doi:10.1038/361730a0. PMID 8441468.
- Boland A, Cornelis GR (1998). "Role of YopP in suppression of tumor necrosis factor alpha release by macrophages during Yersinia infection". Infect. Immun. 66 (5): 1878â€“84. PMC 108138. PMID 9573064.
- Skurnik M, el Tahir Y, Saarinen M, Jalkanen S, Toivanen P (1994). "YadA mediates specific binding of enteropathogenic Yersinia enterocolitica to human intestinal submucosa". Infect. Immun. 62 (4): 1252â€“61. PMC 186266. PMID 8132332.
- China B, Sory MP, N'Guyen BT, De Bruyere M, Cornelis GR (1993). "Role of the YadA protein in prevention of opsonization of Yersinia enterocolitica by C3b molecules". Infect. Immun. 61 (8): 3129â€“36. PMC 280979. PMID 8335343.
- China B, N'Guyen BT, de Bruyere M, Cornelis GR (1994). "Role of YadA in resistance of Yersinia enterocolitica to phagocytosis by human polymorphonuclear leukocytes". Infect. Immun. 62 (4): 1275â€“81. PMC 186269. PMID 8132334.
- Han YW, Miller VL (1997). "Reevaluation of the virulence phenotype of the inv yadA double mutants of Yersinia pseudotuberculosis". Infect. Immun. 65 (1): 327â€“30. PMC 174597. PMID 8975933.
- Cornelis GR, Sluiters C, Delor I, Geib D, Kaniga K, Lambert de Rouvroit C, Sory MP, Vanooteghem JC, Michiels T (1991). "ymoA, a Yersinia enterocolitica chromosomal gene modulating the expression of virulence functions". Mol. Microbiol. 5 (5): 1023â€“34. PMID 1956283.
- Isberg RR, Van Nhieu GT (1994). "Two mammalian cell internalization strategies used by pathogenic bacteria". Annu. Rev. Genet. 28: 395â€“422. doi:10.1146/annurev.ge.28.120194.002143. PMID 7893133.
- Miller, V. (1992). "Yersinia invasion genes and their products". ASM News 58: 26â€“33.
- Bliska JB, Falkow S (1992). "Bacterial resistance to complement killing mediated by the Ail protein of Yersinia enterocolitica". Proc. Natl. Acad. Sci. U.S.A. 89 (8): 3561â€“5. doi:10.1073/pnas.89.8.3561. PMC 48908. PMID 1565652.
- Lindler LE, Tall BD (1993). "Yersinia pestis pH 6 antigen forms fimbriae and is induced by intracellular association with macrophages". Mol. Microbiol. 8 (2): 311â€“24. doi:10.1111/j.1365-2958.1993.tb01575.x. PMID 8100346.
- Miyoshi-Akiyama T, Fujimaki W, Yan XJ, Yagi J, Imanishi K, Kato H, Tomonari K, Uchiyama T (1997). "Identification of murine T cells reactive with the bacterial superantigen Yersinia pseudotuberculosis-derived mitogen (YPM) and factors involved in YPM-induced toxicity in mice". Microbiol. Immunol. 41 (4): 345â€“52. doi:10.1111/j.1348-0421.1997.tb01211.x. PMID 9159409.
- Uchiyama T, Miyoshi-Akiyama T, Kato H, Fujimaki W, Imanishi K, Yan XJ (1993). "Superantigenic properties of a novel mitogenic substance produced by Yersinia pseudotuberculosis isolated from patients manifesting acute and systemic symptoms". J. Immunol. 151 (8): 4407â€“13. PMID 8409410.
- Carnoy C, Loiez C, Faveeuw C, Grangette C, Desreumaux P, Simonet M (2003). "Impact of the Yersinia pseudotuberculosis-derived mitogen (YPM) on the murine immune system". Adv. Exp. Med. Biol. 529: 133â€“5. doi:10.1007/0-306-48416-1_26. PMID 12756744.
- Yoshino K, Ramamurthy T, Nair GB, Fukushima H, Ohtomo Y, Takeda N, Kaneko S, Takeda T (1995). "Geographical heterogeneity between Far East and Europe in prevalence of ypm gene encoding the novel superantigen among Yersinia pseudotuberculosis strains". J. Clin. Microbiol. 33 (12): 3356â€“8. PMC 228710. PMID 8586739.
- Fukushima H, Matsuda Y, Seki R, Tsubokura M, Takeda N, Shubin FN, Paik IK, Zheng XB (2001). "Geographical heterogeneity between Far Eastern and Western countries in prevalence of the virulence plasmid, the superantigen Yersinia pseudotuberculosis-derived mitogen, and the high-pathogenicity island among Yersinia pseudotuberculosis strains". J. Clin. Microbiol. 39 (10): 3541â€“7. doi:10.1128/JCM.39.10.3541-3547.2001. PMC 88386. PMID 11574570.
- Nikolova S, Najdenski H, Wesselinova D, Vesselinova A, Kazatchca D, Neikov P (1997). "Immunological and electronmicroscopic studies in pigs infected with Yersinia enterocolitica 0:3". Zentralbl. Bakteriol. 286 (4): 503â€“10. doi:10.1016/s0934-8840(97)80053-9. PMID 9440199.
- Smith MG (1992). "Destruction of bacteria on fresh meat by hot water". Epidemiol. Infect. 109 (3): 491â€“6. doi:10.1017/s0950268800050482. PMC 2271933. PMID 1468533.
- Donadini R, Liew CW, Kwan AH, Mackay JP, Fields BA (January 2004). "Crystal and solution structures of a superantigen from Yersinia pseudotuberculosis reveal a jelly-roll fold". Structure 12 (1): 145â€“56. doi:10.1016/j.str.2003.12.002. PMID 14725774.
|Wikispecies has information related to: Yersinia pseudotuberculosis|
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.
Yersinia pseudo-tuberculosis mitogen Provide feedback
Members of this family of Yersinia pseudo-tuberculosis mitogens adopt a sandwich structure consisting of nine strands in two beta sheets, in a jelly-roll topology. As with other super-antigens, they are able to excessively activate T cells by binding to the T cell receptor .
Donadini R, Liew CW, Kwan AH, Mackay JP, Fields BA; , Structure. 2004;12:145-156.: Crystal and solution structures of a superantigen from Yersinia pseudotuberculosis reveal a jelly-roll fold. PUBMED:14725774 EPMC:14725774
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015227
Members of this family of Yersinia pseudotuberculosis mitogens adopt a sandwich structure consisting of nine strands in two beta sheets, in a jelly-roll topology. As with other superantigens, they are able to excessively activate T cells by binding to the T cell receptor [PUBMED:14725774].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Number in seed:||2|
|Number in full:||5|
|Average length of the domain:||116.60 aa|
|Average identity of full alignment:||88 %|
|Average coverage of the sequence by the domain:||77.42 %|
|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:||6|
|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 YpM domain has been found. There are 4 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...