Summary: Sortase 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 "Sortase". 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.
Sortase Edit Wikipedia article
Pilus-related Sortase C of Group B Streptococcus. PDB entry 
Sortase refers to a group of prokaryotic enzymes that modify surface proteins by recognizing and cleaving a carboxyl-terminal sorting signal. For most substrates of sortase enzymes, the recognition signal consists of the motif LPXTG (Leu-Pro-any-Thr-Gly), then a highly hydrophobic transmembrane sequence, followed by a cluster of basic residues such as arginine. Cleavage occurs between the Thr and Gly, with transient attachment through the Thr residue to the active site Cys residue, followed by transpeptidation that attaches the protein covalently to cell wall components. Sortases occur in almost all Gram-positive bacteria and the occasional Gram-negative (e.g. Shewanella putrefaciens) or Archaea (e.g. Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported. Although sortase A, the "housekeeping" sortase, typically acts on many protein targets, other forms of sortase recognize variant forms of the cleavage motif, or that catalyze the assembly of pilins into pili.
The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan.
Substrate proteins attached to cell walls by sortases include enzymes, pilins, and adhesion-mediating large surface glycoproteins. These proteins often play important roles in virulence, infection, and colonization by pathogens.
Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope.
Note that exosortase is functionally analogous, but not in any way homologous to sortase.
As an antibiotic target
The sortases are thought to be good targets for new antibiotics as they are important proteins for pathogenic bacteria and some limited commercial interest has been noted by at least one company.
Another sub-family of sortases (C60B in MEROPS) contains bacterial sortase B proteins that are approximately 200 residues long.
Use in structural biology
The transpeptidase activity of sortase is taken advantage of by structural biologists to produce fusion proteins in vitro. The recognition motif (LPXTG) is added to the C-terminus of a protein of interest while an oligo-glycine motif is added to the N-terminus of the second protein to be ligated. Upon addition of sortase to the protein mixture, the two peptides are covalently linked through a native peptide bond. This reaction is employed by NMR spectroscopists to produce NMR invisible solubility tags  and in one example by X-ray crystallographers to promote complex formation.
- Cozzi, R; Malito, E; Nuccitelli, A; d'Onofrio, M; Martinelli, M; Ferlenghi, I; Grandi, G; Telford, J. L.; Maione, D; Rinaudo, C. D. (2011). "Structure analysis and site-directed mutagenesis of defined key residues and motives for pilus-related sortase C1 in group B Streptococcus". The FASEB Journal. 25 (6): 1874–86. doi:10.1096/fj.10-174797. PMID 21357525.
- Schneewind O, Mazmanian SK, Ton-that H (2001). "Sortase-catalysed anchoring of surface proteins to the cell wall of Staphylococcus aureus". Mol. Microbiol. 40 (5): 1049–1057. doi:10.1046/j.1365-2958.2001.02411.x. PMID 11401711.
- Pallen MJ, Henderson IR, Chaudhuri RR (2003). "Genomic analysis of secretion systems". Curr Opin Microbiol. 6 (5): 519–527. doi:10.1016/j.mib.2003.09.005. PMID 14572546.
- Oh S, Budzik J, Schneewind O (September 2008). "Sortases make pili from three ingredients". Proc Natl Acad Sci U S A. 105 (37): 13703–13704. doi:10.1073/pnas.0807334105. PMC . PMID 18784365.
- LeMieux J, Woody S, Camilli A (September 2008). "Roles of the sortases of Streptococcus pneumoniae in assembly of the RlrA pilus". J. Bacteriol. 190 (17): 6002–6013. doi:10.1128/JB.00379-08. PMC . PMID 18606733.
- Kang HJ, Coulibaly F, Proft T, Baker EN (2011). Hofmann A, ed. "Crystal structure of Spy0129, a Streptococcus pyogenes class B sortase involved in pilus assembly". PLoS ONE. 6 (1): e15969. doi:10.1371/journal.pone.0015969. PMC . PMID 21264317.
- Mazmanian SK, Liu G, Ton-That H, Schneewind O (July 1999). "Staphylococcus aureus sortase, an enzyme that anchors surface proteins to the cell wall". Science. 285 (5428): 760–3. doi:10.1126/science.285.5428.760. PMID 10427003.
- Cossart P, Jonquières R (May 2000). "Sortase, a universal target for therapeutic agents against gram-positive bacteria?". Proc. Natl. Acad. Sci. U.S.A. 97 (10): 5013–5. doi:10.1073/pnas.97.10.5013. PMC . PMID 10805759.
- Maresso AW, Schneewind O (March 2008). "Sortase as a target of anti-infective therapy". Pharmacol. Rev. 60 (1): 128–141. doi:10.1124/pr.107.07110. PMID 18321961.
- SIGA Technologies (September 2006). "Schedule 14A". U.S. Securities and Exchange Commission. Retrieved 29 October 2009.
- Pallen MJ, Lam AC, Antonio M, Dunbar K (March 2001). "An embarrassment of sortases - a richness of substrates?". Trends Microbiol. 9 (3): 97–102. doi:10.1016/S0966-842X(01)01956-4. PMID 11239768.
- Kobashigawa Y, Kumeta H, Ogura K, Inagaki F (January 2009). "Attachment of an NMR-invisible solubility enhancememnt tag using a sortase mediated protein ligation method". Journal of Biomolecular NMR. 43 (3): 145–150. doi:10.1007/s10858-008-9296-5. PMID 19140010.
- Wang Y, Pascoe HG, Brautigam CA, He H, Zhang X (October 2013). "Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin". eLIFE. 2: e01279. doi:10.7554/eLife.01279. PMID 24137545.
- doi:10.1096/fj.10-174797. PMID 21357525. ; Cozzi R, Malito E, Nuccitelli A, D'Onofrio M, Martinelli M, Ferlenghi I, Grandi G, Telford JL, Maione D, Rinaudo CD (February 2011). "Structure analysis and site-directed mutagenesis of defined key residues and motives for pilus-related sortase C1 in group B Streptococcus". FASEB J. 25 (6): 1874–1886.
- Kang HJ, Paterson NG, Gaspar AH, Ton-That H, Baker EN (October 2009). "The Corynebacterium diphtheriae shaft pilin SpaA is built of tandem Ig-like modules with stabilizing isopeptide and disulfide bonds". Proceedings of the National Academy of Sciences of the United States of America. 106 (40): 16967–16971. doi:10.1073/pnas.0906826106. PMC . PMID 19805181.
- Kankainen M, Paulin L, Tynkkynen S, et al. (October 2009). "Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein". Proceedings of the National Academy of Sciences of the United States of America. 106 (40): 17193–8. doi:10.1073/pnas.0908876106. PMC . PMID 19805152.
- Neiers F, Madhurantakam C, Fälker S, et al. (October 2009). "Two crystal structures of pneumococcal pilus sortase C provide novel insights into catalysis and substrate specificity". Journal of Molecular Biology. 393 (3): 704–16. doi:10.1016/j.jmb.2009.08.058. PMID 19729023.
- Sillanpää J, Nallapareddy SR, Qin X, et al. (November 2009). "A collagen-binding adhesin, Acb, and ten other putative MSCRAMM and pilus family proteins of Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis Group, biotype I)". Journal of Bacteriology. 191 (21): 6643–53. doi:10.1128/JB.00909-09. PMC . PMID 19717590.
- Kang HJ, Paterson NG, Baker EN (August 2009). "Expression, purification, crystallization and preliminary crystallographic analysis of SpaA, a major pilin from Corynebacterium diphtheriae". Acta Crystallographica F. 65 (Pt 8): 802–804. doi:10.1107/S1744309109027596. PMC . PMID 19652344.
- Guttilla IK, Gaspar AH, Swierczynski A, et al. (September 2009). "Acyl enzyme intermediates in sortase-catalyzed pilus morphogenesis in gram-positive bacteria". Journal of Bacteriology. 191 (18): 5603–12. doi:10.1128/JB.00627-09. PMC . PMID 19592583.
- Suree N, Liew CK, Villareal VA, et al. (September 2009). "The structure of the Staphylococcus aureus sortase-substrate complex reveals how the universally conserved LPXTG sorting signal is recognized". The Journal of Biological Chemistry. 284 (36): 24465–77. doi:10.1074/jbc.M109.022624. PMC . PMID 19592495.
- Kang HJ, Baker EN (July 2009). "Intramolecular isopeptide bonds give thermodynamic and proteolytic stability to the major pilin protein of Streptococcus pyogenes". The Journal of Biological Chemistry. 284 (31): 20729–20737. doi:10.1074/jbc.M109.014514. PMC . PMID 19497855.
- Schlüter S, Franz CM, Gesellchen F, Bertinetti O, Herberg FW, Schmidt FR (August 2009). "The high biofilm-encoding Bee locus: a second pilus gene cluster in Enterococcus faecalis?". Current Microbiology. 59 (2): 206–211. doi:10.1007/s00284-009-9422-y. PMID 19459002.
- Quigley BR, Zähner D, Hatkoff M, Thanassi DG, Scott JR (June 2009). "Linkage of T3 and Cpa pilins in the Streptococcus pyogenes M3 pilus". Molecular Microbiology. 72 (6): 1379–1394. doi:10.1111/j.1365-2958.2009.06727.x. PMID 19432798.
- Solovyova AS, Pointon JA, Race PR, Smith WD, Kehoe MA, Banfield MJ (March 2009). "Solution structure of the major (Spy0128) and minor (Spy0125 and Spy0130) pili subunits from Streptococcus pyogenes". European Biophysics Journal. 39 (3): 469–480. doi:10.1007/s00249-009-0432-2. PMID 19290517.
- Budzik JM, Oh SY, Schneewind O (May 2009). "Sortase D forms the covalent bond that links BcpB to the tip of Bacillus cereus pili". The Journal of Biological Chemistry. 284 (19): 12989–12997. doi:10.1074/jbc.M900927200. PMC . PMID 19269972.
- Kang HJ, Middleditch M, Proft T, Baker EN (February 2009). "Isopeptide bonds in bacterial pili and their characterization by X-ray crystallography and mass spectrometry". Biopolymers. 91 (12): 1126–1134. doi:10.1002/bip.21170. PMID 19226623.
- Manzano C, Contreras-Martel C, El Mortaji L, et al. (December 2008). "Sortase-mediated pilus fiber biogenesis in Streptococcus pneumoniae". Structure. 16 (12): 1838–48. doi:10.1016/j.str.2008.10.007. PMID 19081060.
- Proft T, Baker EN (February 2009). "Pili in Gram-negative and Gram-positive bacteria - structure, assembly and their role in disease". Cellular and Molecular Life Sciences. 66 (4): 613–635. doi:10.1007/s00018-008-8477-4. PMID 18953686.
- Budzik JM, Oh SY, Schneewind O (December 2008). "Cell wall anchor structure of BcpA pili in Bacillus anthracis". The Journal of Biological Chemistry. 283 (52): 36676–36686. doi:10.1074/jbc.M806796200. PMC . PMID 18940793.
- Mandlik A, Das A, Ton-That H (September 2008). "The molecular switch that activates the cell wall anchoring step of pilus assembly in gram-positive bacteria". Proceedings of the National Academy of Sciences of the United States of America. 105 (37): 14147–14152. doi:10.1073/pnas.0806350105. PMC . PMID 18779588.
- Fälker S, Nelson AL, Morfeldt E, et al. (November 2008). "Sortase-mediated assembly and surface topology of adhesive pneumococcal pili". Molecular Microbiology. 70 (3): 595–607. doi:10.1111/j.1365-2958.2008.06396.x. PMC . PMID 18761697.
- Budzik JM, Marraffini LA, Souda P, Whitelegge JP, Faull KF, Schneewind O (July 2008). "Amide bonds assemble pili on the surface of bacilli". Proceedings of the National Academy of Sciences of the United States of America. 105 (29): 10215–10220. doi:10.1073/pnas.0803565105. PMC . PMID 18621716.
- Nobbs AH, Rosini R, Rinaudo CD, Maione D, Grandi G, Telford JL (August 2008). "Sortase A utilizes an ancillary protein anchor for efficient cell wall anchoring of pili in Streptococcus agalactiae". Infection and Immunity. 76 (8): 3550–3560. doi:10.1128/IAI.01613-07. PMC . PMID 18541657.
- Bagnoli F, Moschioni M, Donati C, et al. (August 2008). "A second pilus type in Streptococcus pneumoniae is prevalent in emerging serotypes and mediates adhesion to host cells". Journal of Bacteriology. 190 (15): 5480–92. doi:10.1128/JB.00384-08. PMC . PMID 18515415.
- Zähner D, Scott JR (January 2008). "SipA is required for pilus formation in Streptococcus pyogenes serotype M3". Journal of Bacteriology. 190 (2): 527–535. doi:10.1128/JB.01520-07. PMC . PMID 17993527.
- Swaminathan A, Mandlik A, Swierczynski A, Gaspar A, Das A, Ton-That H (November 2007). "Housekeeping sortase facilitates the cell wall anchoring of pilus polymers in Corynebacterium diphtheriae". Molecular Microbiology. 66 (4): 961–974. doi:10.1111/j.1365-2958.2007.05968.x. PMC . PMID 17919283.
- Budzik JM, Marraffini LA, Schneewind O (October 2007). "Assembly of pili on the surface of Bacillus cereus vegetative cells". Molecular Microbiology. 66 (2): 495–510. doi:10.1111/j.1365-2958.2007.05939.x. PMID 17897374.
- Kemp KD, Singh KV, Nallapareddy SR, Murray BE (November 2007). "Relative contributions of Enterococcus faecalis OG1RF sortase-encoding genes, srtA and bps (srtC), to biofilm formation and a murine model of urinary tract infection". Infection and Immunity. 75 (11): 5399–5404. doi:10.1128/IAI.00663-07. PMC . PMID 17785477.
- Manetti AG, Zingaretti C, Falugi F, et al. (May 2007). "Streptococcus pyogenes pili promote pharyngeal cell adhesion and biofilm formation". Molecular Microbiology. 64 (4): 968–83. doi:10.1111/j.1365-2958.2007.05704.x. PMID 17501921.
- Mandlik A, Swierczynski A, Das A, Ton-That H (April 2007). "Corynebacterium diphtheriae employs specific minor pilins to target human pharyngeal epithelial cells". Molecular Microbiology. 64 (1): 111–124. doi:10.1111/j.1365-2958.2007.05630.x. PMC . PMID 17376076.
- Nallapareddy SR, Singh KV, Sillanpää J, et al. (October 2006). "Endocarditis and biofilm-associated pili of Enterococcus faecalis". The Journal of Clinical Investigation. 116 (10): 2799–807. doi:10.1172/JCI29021. PMC . PMID 17016560.
- Scott JR, Zähner D (October 2006). "Pili with strong attachments: Gram-positive bacteria do it differently". Molecular Microbiology. 62 (2): 320–330. doi:10.1111/j.1365-2958.2006.05279.x. PMID 16978260.
- Swierczynski A, Ton-That H (September 2006). "Type III pilus of corynebacteria: Pilus length is determined by the level of its major pilin subunit". Journal of Bacteriology. 188 (17): 6318–6325. doi:10.1128/JB.00606-06. PMC . PMID 16923899.
- Rosini R, Rinaudo CD, Soriani M, et al. (July 2006). "Identification of novel genomic islands coding for antigenic pilus-like structures in Streptococcus agalactiae". Molecular Microbiology. 61 (1): 126–41. doi:10.1111/j.1365-2958.2006.05225.x. PMID 16824100.
- Dramsi S, Caliot E, Bonne I, et al. (June 2006). "Assembly and role of pili in group B streptococci". Molecular Microbiology. 60 (6): 1401–13. doi:10.1111/j.1365-2958.2006.05190.x. PMID 16796677.
- Gaspar AH, Ton-That H (February 2006). "Assembly of distinct pilus structures on the surface of Corynebacterium diphtheriae". Journal of Bacteriology. 188 (4): 1526–1533. doi:10.1128/JB.188.4.1526-1533.2006. PMC . PMID 16452436.
- Ton-That H, Marraffini LA, Schneewind O (November 2004). "Protein sorting to the cell wall envelope of Gram-positive bacteria". Biochimica et Biophysica Acta. 1694 (1–3): 269–278. doi:10.1016/j.bbamcr.2004.04.014. PMID 15546671.
- Ton-That H, Marraffini LA, Schneewind O (July 2004). "Sortases and pilin elements involved in pilus assembly of Corynebacterium diphtheriae". Molecular Microbiology. 53 (1): 251–261. doi:10.1111/j.1365-2958.2004.04117.x. PMID 15225319.
- Ton-That H, Schneewind O (May 2004). "Assembly of pili in Gram-positive bacteria". Trends in Microbiology. 12 (5): 228–234. doi:10.1016/j.tim.2004.03.004. PMID 15120142.
- Ton-That H, Schneewind O (November 2003). "Assembly of pili on the surface of Corynebacterium diphtheriae". Molecular Microbiology. 50 (4): 1429–1438. doi:10.1046/j.1365-2958.2003.03782.x. PMID 14622427.
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.
Sortase family Provide feedback
The founder member of this family is S.aureus sortase, a transpeptidase that attaches surface proteins by the threonine of an LPXTG motif to the cell wall .
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005754
This family includes Staphylococcus aureus sortase, a transpeptidase that attaches surface proteins by the Thr of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known [PUBMED:10427003].Sortase refers to a group of prokaryotic enzymes which catalyze the assembly of pilins into pili, and the anchoring of pili to the cell wall [PUBMED:2544515]. They act as both proteases and transpeptidases [PUBMED:2519520]. Sortase, a transpeptidase present in almost all Gram-positive bacteria, anchors a range of important surface proteins to the cell wall [PUBMED:11401711, PUBMED:14572546]. The sortases are thought to be good targets for new antibiotics as they are important proteins for pathogenic bacteria [PUBMED:18321961].
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 (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.
|Seed source:||TIGRFAMs (release 2.0);|
|Author:||TIGRFAMs, Finn RD|
|Number in seed:||86|
|Number in full:||3330|
|Average length of the domain:||138.00 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||51.50 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|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 Sortase domain has been found. There are 99 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...