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2  structures 1209  species 0  interactions 5243  sequences 50  architectures

Family: LOR (PF04525)

Summary: LURP-one-related

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

LURP-one-related Provide feedback

The structure of this family has been solved. It comprises a 12-stranded beta barrel with a central C-terminal alpha helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein [1]. In plants it plays a role in defense against pathogens [2].

Literature references

  1. Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Soding J;, Bioinformatics. 2009;25:159-162.: Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. PUBMED:19010806 EPMC:19010806

  2. Knoth C, Eulgem T;, Plant J. 2008;55:53-64.: The oomycete response gene LURP1 is required for defense against Hyaloperonospora parasitica in Arabidopsis thaliana. PUBMED:18346188 EPMC:18346188


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007612

The structure of protein LURP-one-related 15 (At5g01750) has been solved. It comprises a 12-stranded beta barrel with a central C-terminal alpha helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein [ PUBMED:19010806 ]. In plants LURP1 plays a role in defense against pathogens [ PUBMED:18346188 ].

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 Tubby_C (CL0395), which has the following description:

This superfamily contains the scramblase protein family, the Tub family and the DUF567, a family of plant and bacterial proteins of hitherto unknown function. All members are membrane-tethered transcription factors.

The clan contains the following 4 members:

DUF3527 LOR Scramblase Tub

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(15)
Full
(5243)
Representative proteomes UniProt
(9908)
RP15
(624)
RP35
(2479)
RP55
(4493)
RP75
(6313)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(15)
Full
(5243)
Representative proteomes UniProt
(9908)
RP15
(624)
RP35
(2479)
RP55
(4493)
RP75
(6313)
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
(15)
Full
(5243)
Representative proteomes UniProt
(9908)
RP15
(624)
RP35
(2479)
RP55
(4493)
RP75
(6313)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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_4998 (release 7.5)
Previous IDs: DUF567; Tub_2;
Type: Domain
Sequence Ontology: SO:0000417
Author: Waterfield DI , Finn RD , Eberhardt R
Number in seed: 15
Number in full: 5243
Average length of the domain: 162.7 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 80.84 %

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 24.5 24.5
Trusted cut-off 24.5 24.5
Noise cut-off 24.4 24.4
Model length: 187
Family (HMM) version: 15
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

Selections

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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 LOR domain has been found. There are 2 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.

Protein Predicted structure External Information
A0A0P0VCE9 View 3D Structure Click here
A0A0P0WAL6 View 3D Structure Click here
A0A0R0F7U7 View 3D Structure Click here
A0A0R0FMD8 View 3D Structure Click here
A0A0R0FMF0 View 3D Structure Click here
A0A0R0FMF5 View 3D Structure Click here
A0A0R0FSV4 View 3D Structure Click here
A0A0R0FV78 View 3D Structure Click here
A0A0R0KF36 View 3D Structure Click here
A0A0R0L576 View 3D Structure Click here
A0A175VZ71 View 3D Structure Click here
A0A1D6E9R9 View 3D Structure Click here
A0A1D6EIW7 View 3D Structure Click here
A0A1D6HW87 View 3D Structure Click here
A0A1D6K2P4 View 3D Structure Click here
A0A1D6L9A8 View 3D Structure Click here
A0A1D6M2U7 View 3D Structure Click here
A0A1D6N2A4 View 3D Structure Click here
A0A1D6N2A5 View 3D Structure Click here
A0A1D6NM38 View 3D Structure Click here
A0A1D6NQL9 View 3D Structure Click here
A0A1D6NQM0 View 3D Structure Click here
A0A1D6PIZ8 View 3D Structure Click here
A0A1D6QGP8 View 3D Structure Click here
A0A1D6QGP9 View 3D Structure Click here
A0A1P8AT59 View 3D Structure Click here
A0A1P8AWJ7 View 3D Structure Click here
A0MFH4 View 3D Structure Click here
A0MFL4 View 3D Structure Click here
B3H5L1 View 3D Structure Click here
B4FTB7 View 3D Structure Click here
B6SS88 View 3D Structure Click here
B6SU53 View 3D Structure Click here
B6SUE0 View 3D Structure Click here
B6SUW7 View 3D Structure Click here
B9G937 View 3D Structure Click here
C4IYU6 View 3D Structure Click here
C6T3J7 View 3D Structure Click here
C6T4D8 View 3D Structure Click here
C6T4M9 View 3D Structure Click here