Summary: Sortase family

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Sortase Edit Wikipedia article

Sortase family

Sortase "RCSB Protein Data Bank - Structure Summary for 3O0P - Pilus-related Sortase C of Group B Streptococcus". http://www.rcsb.org/pdb/explore/explore.do?structureId=3O0P.

Identifiers

Symbol

Sortase

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

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, then 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 the cell wall. 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.^[1]^[2] Although sortase A, the "housekeeping" sortase, typically acts on many targets per genome, other forms of sortase occur that recognize variant forms of the cleavage motif, or that catalyze the assembly of pilins into pili. ^[3] ^[4] ^[5]

[edit] Reaction

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.^[6]^[7]

[edit] Biological role

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.

[edit] As an antibiotic target

The sortases are thought to be good targets for new antibiotics^[8] as they are important proteins for pathogenic bacteria and some limited commercial interest has been noted by at least one company.^[9]

[edit] Structure

This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of several subfamilies of sortases.

Another sub-family of sortases (C60B in MEROPS) contains bacterial sortase B proteins that are approximately 200 residues long.^[10]

[edit] References

^ 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, and 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 2544515. PMID 18784365. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2544515/.
^ 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 2519520. PMID 18606733. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2519520/.
^ Kang HJ, Coulibaly F, Proft T, Baker EN (2011). Hofmann, Andreas. 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 3019223. PMID 21264317. //www.ncbi.nlm.nih.gov/pmc/articles/PMC3019223/.
^ 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 33977. PMID 10805759. //www.ncbi.nlm.nih.gov/pmc/articles/PMC33977/.
^ 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. http://www.sec.gov/Archives/edgar/data/1010086/000095013606007825/file1.htm. 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.

[edit] Further reading

PDB 3O0P; 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. doi:10.1096/fj.10-174797. PMID 21357525.
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 2761350. PMID 19805181. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2761350/.
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 2746127. PMID 19805152. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2746127/.
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 2795296. PMID 19717590. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2795296/.
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 2720338. PMID 19652344. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2720338/.
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 2737948. PMID 19592583. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2737948/.
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 2782039. PMID 19592495. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2782039/.
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 2742838. PMID 19497855. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2742838/.
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 2676031. PMID 19269972. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2676031/.
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 2605976. PMID 18940793. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2605976/.
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 2734112. PMID 18779588. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2734112/.
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 2680257. PMID 18761697. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2680257/.
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 2481347. PMID 18621716. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2481347/.
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 2493207. PMID 18541657. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2493207/.
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 2493256. PMID 18515415. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2493256/.
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 2223711. PMID 17993527. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2223711/.
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 2841690. PMID 17919283. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2841690/.
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 2168291. PMID 17785477. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2168291/.
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 2844904. PMID 17376076. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2844904/.
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 1578622. PMID 17016560. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1578622/.
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 1595371. PMID 16923899. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1595371/.
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 1367254. PMID 16452436. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1367254/.
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 article incorporates text from the public domain Pfam and InterPro IPR005754

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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 [1].

Literature references

Mazmanian SK, Liu G, Ton-That H, Schneewind O; , Science 1999;285:760-763.: Staphylococcus aureus sortase, an enzyme that anchors surface proteins to the cell wall. PUBMED:10427003 EPMC:10427003
Pallen MJ, Lam AC, Antonio M, Dunbar K; , Trends Microbiol 2001;9:97-102.: An embarrassment of sortases - a richness of substrates? PUBMED:11239768 EPMC:11239768

External database links

MEROPS:	C60
PANDIT:	PF04203
Pseudofam:	PF04203
SCOP:	1ija
SYSTERS:	Sortase

This tab holds annotation information from the InterPro database.

InterPro entry IPR005754

In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:

Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases.

In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.

Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad [PUBMED:11517925].

This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. 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 [PUBMED:10427003]. Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported [PUBMED:11401711, PUBMED:14572546].

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.

Domain organisation

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Alignments

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...

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We make a range of alignments for each Pfam-A family:

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RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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meta: alignment generated by searching the metagenomics sequence database using the family HMM

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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.

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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.

	Seed (138)	Full (4873)	Representative proteomes				NCBI (3560)	Meta (293)
	Seed (138)	Full (4873)	RP15 (283)	RP35 (543)	RP55 (695)	RP75 (783)	NCBI (3560)	Meta (293)
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¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (138)	Full (4873)	Representative proteomes				NCBI (3560)	Meta (293)
	Seed (138)	Full (4873)	RP15 (283)	RP35 (543)	RP55 (695)	RP75 (783)	NCBI (3560)	Meta (293)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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.

	Seed (138)	Full (4873)	Representative proteomes				NCBI (3560)	Meta (293)
	Seed (138)	Full (4873)	RP15 (283)	RP35 (543)	RP55 (695)	RP75 (783)	NCBI (3560)	Meta (293)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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 logo

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...

Trees

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.

Curation

Seed source:

TIGRFAMs (release 2.0);

Previous IDs:

none

Type:

Family

Author:

TIGRFAMs, Finn RD

Number in seed:

138

Number in full:

4873

Average length of the domain:

135.30 aa

Average identity of full alignment:

24 %

Average coverage of the sequence by the domain:

51.42 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	21.3	21.3
Trusted cut-off	21.3	21.3
Noise cut-off	21.1	21.2

Model length:

128

Family (HMM) version:

8

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. 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:

superkingdom
kingdom
phylum
class
order
family
genus
species

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".

Sub-species

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.

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Species trees

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.

Interactive tree

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

Loading...

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.

Interactions

There is 1 interaction for this family. More...

Sortase

Structures

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 74 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...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Sortase (PF04203)

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Summary: Sortase family

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Editing Wikipedia articles

Before you edit for the first time

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Sortase Edit Wikipedia article

Contents

[edit] Reaction

[edit] Biological role

[edit] As an antibiotic target

[edit] Structure

[edit] References

[edit] Further reading

Sortase family Provide feedback

Literature references

External database links

InterPro entry IPR005754

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures