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0  structures 543  species 0  interactions 574  sequences 8  architectures

Family: LYRM2-like (PF20263)

Summary: LYR motif-containing protein 2-like

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LYR motif-containing protein 2-like Provide feedback

This entry represents LYR motif-containing proteins, including LYR motif-containing protein 2 from animals, whose function is not clear, and Cup1 (caffeine unstable phenotype 1, previously known as uncharacterised protein C17G9.13c) from S. pombe [1]. Cup1 has been characterised; it is a mitochondrial protein whose silencing by heterochromatin island formation results in caffeine resistance. LYR-motif containing proteins are basic polypeptides carrying a conserved tripeptide L-Y-R (leucine/tyrosine/arginine) sequence close to the N-terminus in addition to some basic arginine/lysine residues and a highly-conserved phenylalanine downstream of the LYR motif [2].

Literature references

  1. Torres-Garcia S, Yaseen I, Shukla M, Audergon PNCB, White SA, Pidoux AL, Allshire RC;, Nature. 2020;585:453-458.: Epigenetic gene silencing by heterochromatin primes fungal resistance. PUBMED:32908306 EPMC:32908306

  2. Angerer H;, Biology (Basel). 2015;4:133-150.: Eukaryotic LYR Proteins Interact with Mitochondrial Protein Complexes. PUBMED:25686363 EPMC:25686363

Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 LYR-like (CL0491), which has the following description:

This is a superfamily of sequences with the characteristic LYR, or similar, motif. In some yeasts this family plays a role in Fe-S cluster biogenesis in mitochondria.

The clan contains the following 5 members:

Complex1_LYR Complex1_LYR_1 Complex1_LYR_2 LYRM2-like UQCC2_CBP6


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.

Representative proteomes UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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Representative proteomes UniProt

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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.

Representative proteomes UniProt
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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...


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

This family is new in this Pfam release.

Seed source: Wood V
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Chuguransky S
Number in seed: 15
Number in full: 574
Average length of the domain: 87.4 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 23.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 26.8 26.8
Noise cut-off 26.7 26.7
Model length: 86
Family (HMM) version: 1
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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The tree shows the occurrence of this domain across different species. More...


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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.

Protein Predicted structure External Information
A0A0D2HFA7 View 3D Structure Click here
A0A175WF71 View 3D Structure Click here
A0A1C1CCA7 View 3D Structure Click here
C0NDI0 View 3D Structure Click here
C1GNE0 View 3D Structure Click here
Q9UUD9 View 3D Structure Click here