Summary: LAGLIDADG-like domain
LAGLIDADG-like domain Provide feedback
This domain is part of the LAGLIDADG superfamily .
Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibes A, Serrano L, Grizot S, Duchateau P, Paques F, Blanco FJ, Montoya G;, Proc Natl Acad Sci U S A. 2008;105:16888-16893.: Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. PUBMED:18974222 EPMC:18974222
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR027434
Homing endonucleases are rare-cutting enzymes encoded by inteins and introns. They are found inserted within host genes in eukaryotes, bacteria, archaebacteria and viruses [PUBMED:10754232]. By making a site-specific double-strand break in the intronless or inteinless alleles, these nucleases create recombinogenic ends which engage in a gene conversion process that duplicates the intron or intein [PUBMED:9254693, PUBMED:10487208]. There are four families of homing endonucleases classified by the conserved sequence motifs LAGLIDADG, GIY-YIG, H-N-H and His-Cys box [PUBMED:9254693]. Endonucleases of the DOD family contain one or two copies of the 10-residue sequence known as a dodecapeptide or LAGLIDADG motif. LAGLIDADG endonucleases are either monomers, such as I-SceI, that are composed of two pseudosymmetric subdomains, or homodimers, such as I-CreI. In both cases, the LAGLIDADG endonuclease folds into a beta-saddle architecture, a common motif for nucleic acid binding proteins [PUBMED:18424798].
This entry represents the homing endonuclease domain.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||endonuclease activity (GO:0004519)|
- 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
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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This superfamily includes a variety of LAGLIDADG-like homing endonuclease like families.
The clan contains the following 7 members:Endonuc_subdom Hom_end LAGLIDADG_1 LAGLIDADG_2 LAGLIDADG_3 LAGLIDADG_WhiA WhiA_N
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:
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- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Number in seed:||115|
|Number in full:||4735|
|Average length of the domain:||84.80 aa|
|Average identity of full alignment:||41 %|
|Average coverage of the sequence by the domain:||10.57 %|
|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:||2|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There are 5 interactions 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 LAGLIDADG_3 domain has been found. There are 67 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.
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