Summary: LAGLIDADG endonuclease
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This is the Wikipedia entry entitled "Homing endonuclease". More...
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LAGLIDADG endonuclease Provide feedback
No Pfam abstract.
Literature references
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Heath PJ, Stephens KM, Monnat RJ Jr, Stoddard BL; , Nat Struct Biol 1997;4:468-476.: The structure of I-Crel, a group I intron-encoded homing endonuclease. PUBMED:9187655 EPMC:9187655
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Belfort M, Roberts RJ; , Nucleic Acids Res 1997;25:3379-3388.: Homing endonucleases: keeping the house in order. PUBMED:9254693 EPMC:9254693
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Dalgaard JZ, Klar AJ, Moser MJ, Holley WR, Chatterjee A, Mian IS; , Nucleic Acids Res 1997;25:4626-4638.: Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. PUBMED:9358175 EPMC:9358175
Internal database links
SCOOP: | LAGLIDADG_3 |
Similarity to PfamA using HHSearch: | LAGLIDADG_3 |
External database links
SCOP: | 1af5 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR004860
Homing endonucleases (HEnases) form a large and highly diverse class of proteins encoded by introns and inteins that confer mobility to their host genetic elements. LAGLIDADG HEnases are structured into two tandemly repeated homing endonuclease-like domains [ PUBMED:17603302 , PUBMED:8918801 ]. This entry represents the homing endonuclease LAGLIDADG domain [ PUBMED:9358175 ].
Gene Ontology
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) |
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 Homing_endonuc (CL0324), which has the following description:
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_NAlignments
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.
Seed (41) |
Full (825) |
Representative proteomes | UniProt (8805) |
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RP15 (283) |
RP35 (471) |
RP55 (644) |
RP75 (828) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (41) |
Full (825) |
Representative proteomes | UniProt (8805) |
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RP15 (283) |
RP35 (471) |
RP55 (644) |
RP75 (828) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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: | Sarah Teichmann |
Previous IDs: | Intron_maturase; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 41 |
Number in full: | 825 |
Average length of the domain: | 92.9 aa |
Average identity of full alignment: | 20 % |
Average coverage of the sequence by the domain: | 47.78 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 102 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 LAGLIDADG_1 domain has been found. There are 202 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.