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18  structures 41  species 0  interactions 70  sequences 2  architectures

Family: zf-His_Me_endon (PF05551)

Summary: Zinc-binding loop region of homing endonuclease

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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.

Zinc-binding loop region of homing endonuclease Provide feedback

This domain [1] is the short zinc-binding loops region of a number of much longer chain homing endonucleases. Such loops are probably stabilised by the zinc and may be viewed as small but separate domains. The common structural feature of these domains is that at least three zinc ligands lie very close to each other in the sequence and are not incorporated into regular secondary structural elements. The biological roles played by these small zinc-binding domains are presently unknown [2].

Literature references

  1. Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat RJ Jr, Stoddard BL;, Nat Struct Biol. 1999;6:1096-1099.: A novel endonuclease mechanism directly visualized for I-PpoI. PUBMED:10581547 EPMC:10581547

  2. Krishna SS, Majumdar I, Grishin NV; , Nucleic Acids Res. 2003;31:532-550.: Structural classification of zinc fingers: survey and summary. PUBMED:12527760 EPMC:12527760


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008704

This entry consists of several putative homing endonuclease proteins of around 245 residues in length which appear to be found exclusively in some fungi and in Naegleria species. The proteins belong to the His-Me finger endonucleases superfamily. The exact function of these proteins are unknown.

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 His-Me_finger (CL0263), which has the following description:

This superfamily defined originally by SCOP contains a diverse range of endonucleases. Later Grishin identified the MH1 domain as belonging to the superfamily [1].

The clan contains the following 19 members:

AHH Colicin-DNase DUF1524 Endonuclea_NS_2 Endonuclease_1 Endonuclease_7 Endonuclease_NS GH-E HNH HNH_2 HNH_3 HNH_4 HNH_5 ICEA LHH MH1 NinG WHH zf-His_Me_endon

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...

View options

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
(11)
Full
(70)
Representative proteomes NCBI
(82)
Meta
(4)
RP15
(12)
RP35
(17)
RP55
(20)
RP75
(21)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(11)
Full
(70)
Representative proteomes NCBI
(82)
Meta
(4)
RP15
(12)
RP35
(17)
RP55
(20)
RP75
(21)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(11)
Full
(70)
Representative proteomes NCBI
(82)
Meta
(4)
RP15
(12)
RP35
(17)
RP55
(20)
RP75
(21)
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 View help on the curation process

Seed source: Pfam-B_7681 (release 8.0)
Previous IDs: Naegl_SSU_RRNA; DUF1519;
Type: Domain
Author: Moxon SJ, Coggill P
Number in seed: 11
Number in full: 70
Average length of the domain: 122.00 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 40.93 %

HMM information View help on HMM parameters

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 27.0 27.0
Trusted cut-off 27.2 27.2
Noise cut-off 26.8 26.8
Model length: 131
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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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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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 zf-His_Me_endon domain has been found. There are 18 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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