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123  structures 6674  species 0  interactions 24274  sequences 278  architectures

Family: SLT (PF01464)

Summary: Transglycosylase SLT domain

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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.

Transglycosylase SLT domain Provide feedback

This family is distantly related to PF00062. Members are found in phages, type II, type III and type IV secretion systems (reviewed in [4]).

Literature references

  1. Koonin EV, Rudd KE; , Trends Biochem Sci 1994;19:106-107.: A conserved domain in putative bacterial and bacteriophage transglycosylases. PUBMED:8203016 EPMC:8203016

  2. Mushegian AR, Fullner KJ, Koonin EV, Nester EW; , Proc Natl Acad Sci U S A 1996;93:7321-7326.: A family of lysozyme-like virulence factors in bacterial pathogens of plants and animals. PUBMED:8692991 EPMC:8692991

  3. Thunnissen AM, Rozeboom HJ, Kalk KH, Dijkstra BW; , Biochemistry 1995;34:12729-12737.: Structure of the 70-kDa soluble lytic transglycosylase complexed with bulgecin A. Implications for the enzymatic mechanism. PUBMED:7548026 EPMC:7548026

  4. Koraimann G; , Cell Mol Life Sci 2003;60:2371-2388.: Lytic transglycosylases in macromolecular transport systems of Gram-negative bacteria. PUBMED:14625683 EPMC:14625683

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008258

Bacterial lytic transglycosylases degrade murein via cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine, with the concomitant formation of a 1,6-anhydrobond in the muramic acid residue. There are both soluble (Slt enzymes) and membrane-bound (Mlt enzymes) lytic transglycosylases that differ in size, sequence, activity, specificity and location. The multi-domain structure of the 70 Kd soluble lytic transglycosylase Slt70 is known [ PUBMED:10452894 ]. Slt70 has 3 distinct domains, each rich in alpha helices: an N-terminal superhelical U-shaped domain, a superhelical linker domain (L-domain, INTERPRO ), and a C-terminal catalytic domain ( INTERPRO ). Both the U- and L-domain share a similar superhelical structure. These two domains are connected, and together form a closed ring with a large central hole; the catalytic domain is packed on top of, and interacts with, this ring. The catalytic domain has a lysosome-like fold.

This domain is found mainly in proteins from phages and type II, type III and type IV secretion systems [ PUBMED:8203016 , PUBMED:8692991 , PUBMED:14625683 , PUBMED:14625683 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Lysozyme (CL0037), which has the following description:

Barley chitinase, bacterial chitosanase, and lysozymes from phage and animals all hydrolyse related polysaccharides. The proteins little amino-acid similarity, but have a structurally invariant core consisting of two helices and a three-stranded beta-sheet which form the substrate-binding and catalytic cleft [1].

The clan contains the following 21 members:

Destabilase DUF3218 Glucosaminidase Glyco_hydro_108 Glyco_hydro_19 Glyco_hydro_46 Glyco_hydro_80 Lys Lysozyme_like Peptidase_U40 Pesticin Phage_lysozyme Phage_lysozyme2 SLT SLT_2 SLT_3 SLT_4 TraH_2 Transgly Transglycosylas Utp11


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 and the UniProtKB sequence database. More...

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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.

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

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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...


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.

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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 View help on the curation process

Seed source: Prodom_3175 (release 99.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 26
Number in full: 24274
Average length of the domain: 111.90 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 28.05 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -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 21.2 21.2
Model length: 117
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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...

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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 SLT domain has been found. There are 123 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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