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4  structures 873  species 0  interactions 3048  sequences 67  architectures

Family: RRM_2 (PF04059)

Summary: RNA recognition motif 2

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.

RNA recognition motif 2 Provide feedback

No Pfam abstract.

Literature references

  1. Jeffares DC, Phillips MJ, Moore S, Veit B; , Dev Genes Evol 2004; [Epub ahead of print]: A description of the Mei2-like protein family; structure, phylogenetic distribution and biological context. PUBMED:14986133 EPMC:14986133


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007201

This RNA recognition motif 2 is found in meiosis protein mei2 and mei2-like proteins [ PUBMED:14986133 ]. It is found C-terminal to the RNA-binding region RNP-1 ( INTERPRO ).

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 RRM (CL0221), which has the following description:

This clan contains families that are related to the RNA recognition motif domains. However, not all these families are RNA binding.

The clan contains the following 33 members:

BRAP2 Calcipressin DbpA DUF1743 DUF1866 DUF4523 GlcNAc-1_reg GUCT MARF1_RRM1 Nup35_RRM Nup35_RRM_2 PHM7_cyt Ret2_MD RL RNA_bind RRM_1 RRM_2 RRM_3 RRM_5 RRM_7 RRM_8 RRM_9 RRM_occluded RRM_Rrp7 SET_assoc Smg4_UPF3 Spo7_2_N Tap-RNA_bind Transposase_22 U1snRNP70_N xRRM XS YlmH_RBD

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
(4)
Full
(3048)
Representative proteomes UniProt
(5243)
RP15
(632)
RP35
(1766)
RP55
(2603)
RP75
(3352)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(4)
Full
(3048)
Representative proteomes UniProt
(5243)
RP15
(632)
RP35
(1766)
RP55
(2603)
RP75
(3352)
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
(4)
Full
(3048)
Representative proteomes UniProt
(5243)
RP15
(632)
RP35
(1766)
RP55
(2603)
RP75
(3352)
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_4981 (release 7.3);
Previous IDs: rrm_2;
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Finn RD
Number in seed: 4
Number in full: 3048
Average length of the domain: 92.40 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 14.11 %

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 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 97
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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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The tree shows the occurrence of this domain across different species. 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 RRM_2 domain has been found. There are 4 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
A0A0R0IF05 View 3D Structure Click here
A0A0R0JYR4 View 3D Structure Click here
A0A0R0KGZ6 View 3D Structure Click here
A0A1D6ETQ7 View 3D Structure Click here
A0A1D6H984 View 3D Structure Click here
A0A1D6J661 View 3D Structure Click here
A0A1D6LIK7 View 3D Structure Click here
A0A1D6LJ43 View 3D Structure Click here
A0A1D6N407 View 3D Structure Click here
A0A1D6Q2D4 View 3D Structure Click here
A0A368ULM4 View 3D Structure Click here
B0G157 View 3D Structure Click here
C6KT70 View 3D Structure Click here
F4JBE2 View 3D Structure Click here
F4K9I2 View 3D Structure Click here
I1LW38 View 3D Structure Click here
I1MHW2 View 3D Structure Click here
I1MYL9 View 3D Structure Click here
K7KVF7 View 3D Structure Click here
K7L8W6 View 3D Structure Click here
K7LA02 View 3D Structure Click here
K7LCN4 View 3D Structure Click here
K7LP66 View 3D Structure Click here
K7LSW9 View 3D Structure Click here
K7M7G1 View 3D Structure Click here
K7MR64 View 3D Structure Click here
K7US77 View 3D Structure Click here
K7VTA8 View 3D Structure Click here
O65001 View 3D Structure Click here
P08965 View 3D Structure Click here
Q0JGS5 View 3D Structure Click here
Q4PT05 View 3D Structure Click here
Q54X23 View 3D Structure Click here
Q64M78 View 3D Structure Click here
Q652K6 View 3D Structure Click here
Q6EQX3 View 3D Structure Click here
Q6ET49 View 3D Structure Click here
Q6ZI17 View 3D Structure Click here
Q75M35 View 3D Structure Click here
Q8VWF5 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;