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177  structures 1748  species 0  interactions 8585  sequences 169  architectures

Family: Rad51 (PF08423)

Summary: Rad51

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Rad51 Provide feedback

Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein.

Literature references

  1. Abe K, Osakabe K, Nakayama S, Endo M, Tagiri A, Todoriki S, Ichikawa H, Toki S; , Plant Physiol. 2005;139:896-908.: Arabidopsis RAD51C gene is important for homologous recombination in meiosis and mitosis. PUBMED:16169964 EPMC:16169964


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013632

This domain is found at the C terminus of DNA repair and recombination protein Rad51, and eukaryotic and archaeal Rad51-like proteins. It is critical for DNA binding [ PUBMED:15908697 ]. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.

Unlike eubacteria, several archaeal species have two recA/RAD51-like genes, called RadA and RadB. Among eukaryotes, yeast contain four RAD51-like genes (RAD51, DMC1, RAD55/rhp55, and RAD57/rhp57). In vertebrate animals and plants, there are different RAD51-like genes: RAD51, RAD51B, RAD51C, RAD51D, DMC1, XRCC2, and XRCC3 [ PUBMED:16798872 ].

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 P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 243 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp bpMoxR Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF5906 DUF6079 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB Mur_ligase_M MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 OPA1_C ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom Spore_III_AA Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6N Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YqeC Zeta_toxin Zot

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
(22)
Full
(8585)
Representative proteomes UniProt
(19734)
RP15
(1702)
RP35
(4031)
RP55
(7017)
RP75
(9600)
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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
(22)
Full
(8585)
Representative proteomes UniProt
(19734)
RP15
(1702)
RP35
(4031)
RP55
(7017)
RP75
(9600)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(22)
Full
(8585)
Representative proteomes UniProt
(19734)
RP15
(1702)
RP35
(4031)
RP55
(7017)
RP75
(9600)
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_684 (release 17.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Wood V
Number in seed: 22
Number in full: 8585
Average length of the domain: 222.70 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 67.93 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.2 20.2
Trusted cut-off 20.2 20.2
Noise cut-off 20.1 20.1
Model length: 255
Family (HMM) version: 13
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 Rad51 domain has been found. There are 177 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
A0A075DNI2 View 3D Structure Click here
A0A0G2JTF1 View 3D Structure Click here
A0A0R0HH67 View 3D Structure Click here
A0A0R0HH88 View 3D Structure Click here
A0A0R0HPS8 View 3D Structure Click here
A0A0R0KKW8 View 3D Structure Click here
A0A1D6EZG3 View 3D Structure Click here
A0A1D6FVE8 View 3D Structure Click here
A0A1D6H580 View 3D Structure Click here
A0A1D6H580 View 3D Structure Click here
A0A1D6HAQ9 View 3D Structure Click here
A0A1D6IL54 View 3D Structure Click here
A0A1D6J046 View 3D Structure Click here
A0A1D6LIT8 View 3D Structure Click here
A0A1D6N769 View 3D Structure Click here
A0A1D6NQ57 View 3D Structure Click here
A0A1D6Q3Q1 View 3D Structure Click here
A0A1D8PFE4 View 3D Structure Click here
A0A1D8PI62 View 3D Structure Click here
A1Z7R8 View 3D Structure Click here
A4HUT5 View 3D Structure Click here
A4I3C9 View 3D Structure Click here
A4I499 View 3D Structure Click here
A4I499 View 3D Structure Click here
A4IC25 View 3D Structure Click here
B3DIR0 View 3D Structure Click here
B4FBZ5 View 3D Structure Click here
B5DF04 View 3D Structure Click here
B5DFH5 View 3D Structure Click here
B6TPY8 View 3D Structure Click here
D3ZJ85 View 3D Structure Click here
D3ZPC8 View 3D Structure Click here
D4A5N4 View 3D Structure Click here
E9AHR7 View 3D Structure Click here
E9AHR7 View 3D Structure Click here
F1Q9N3 View 3D Structure Click here
F1QJ27 View 3D Structure Click here
F1QQC9 View 3D Structure Click here
F1R474 View 3D Structure Click here
G3V6U0 View 3D Structure Click here
I1LPM0 View 3D Structure Click here
I1LYB2 View 3D Structure Click here
I1MDL7 View 3D Structure Click here
I1MS33 View 3D Structure Click here
I1N544 View 3D Structure Click here
K7N3K1 View 3D Structure Click here
O15315 View 3D Structure Click here
O35719 View 3D Structure Click here
O42634 View 3D Structure Click here
O43502 View 3D Structure Click here
O43542 View 3D Structure Click here
O43543 View 3D Structure Click here
O55230 View 3D Structure Click here
O75771 View 3D Structure Click here
O77135 View 3D Structure Click here
P25301 View 3D Structure Click here
P25453 View 3D Structure Click here
P25454 View 3D Structure Click here
P34348 View 3D Structure Click here
P36601 View 3D Structure Click here
P38953 View 3D Structure Click here
P94102 View 3D Structure Click here
Q06609 View 3D Structure Click here
Q08297 View 3D Structure Click here
Q14565 View 3D Structure Click here
Q1ZXF0 View 3D Structure Click here
Q27297 View 3D Structure Click here
Q39009 View 3D Structure Click here
Q49593 View 3D Structure Click here
Q4CWC1 View 3D Structure Click here
Q4CYE3 View 3D Structure Click here
Q4CYK4 View 3D Structure Click here
Q4D5E1 View 3D Structure Click here
Q4DWR3 View 3D Structure Click here
Q4DWR3 View 3D Structure Click here
Q4DWX4 View 3D Structure Click here
Q4E2R1 View 3D Structure Click here
Q4E2R1 View 3D Structure Click here
Q4E4H2 View 3D Structure Click here
Q54PJ7 View 3D Structure Click here
Q54QU4 View 3D Structure Click here
Q557E6 View 3D Structure Click here
Q57702 View 3D Structure Click here
Q59UY8 View 3D Structure Click here
Q5TYR1 View 3D Structure Click here
Q5TZD9 View 3D Structure Click here
Q60F40 View 3D Structure Click here
Q61880 View 3D Structure Click here
Q67EU8 View 3D Structure Click here
Q6YU07 View 3D Structure Click here
Q7GBF7 View 3D Structure Click here
Q7GBF8 View 3D Structure Click here
Q8GXF0 View 3D Structure Click here
Q8I1P4 View 3D Structure Click here
Q8IB05 View 3D Structure Click here
Q8IIS8 View 3D Structure Click here
Q8RV34 View 3D Structure Click here
Q8SBB9 View 3D Structure Click here
Q8SZ30 View 3D Structure Click here
Q924H5 View 3D Structure Click here
Q95Q25 View 3D Structure Click here
Q96449 View 3D Structure Click here
Q9AWX8 View 3D Structure Click here
Q9CX47 View 3D Structure Click here
Q9CXE6 View 3D Structure Click here
Q9FKM5 View 3D Structure Click here
Q9LQQ2 View 3D Structure Click here
Q9SK02 View 3D Structure Click here
Q9UUL2 View 3D Structure Click here
Q9XED7 View 3D Structure Click here