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94  structures 9406  species 0  interactions 34125  sequences 578  architectures

Family: ResIII (PF04851)

Summary: Type III restriction enzyme, res subunit

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.

Type III restriction enzyme, res subunit Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006935

This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases ( EC ), the Res subunit of type III endonucleases ( EC ), and the B subunit of excinuclease ABC (uvrB) [ PUBMED:11178902 , PUBMED:9628345 , PUBMED:16125908 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite 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 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
(52)
Full
(34125)
Representative proteomes UniProt
(153814)
RP15
(5944)
RP35
(17251)
RP55
(33396)
RP75
(54680)
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
(52)
Full
(34125)
Representative proteomes UniProt
(153814)
RP15
(5944)
RP35
(17251)
RP55
(33396)
RP75
(54680)
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
(52)
Full
(34125)
Representative proteomes UniProt
(153814)
RP15
(5944)
RP35
(17251)
RP55
(33396)
RP75
(54680)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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_4631 (release 7.6)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Mifsud W
Number in seed: 52
Number in full: 34125
Average length of the domain: 163.30 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 20.09 %

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 22.5 22.5
Trusted cut-off 22.5 22.5
Noise cut-off 22.4 22.4
Model length: 171
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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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 ResIII domain has been found. There are 94 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
A0A0G2K7F0 View 3D Structure Click here
A0A0P0XZP0 View 3D Structure Click here
A0A0R0IZL9 View 3D Structure Click here
A0A1D6JA16 View 3D Structure Click here
A0A1D6NF15 View 3D Structure Click here
A0A1D6P239 View 3D Structure Click here
A0A1D6QLQ7 View 3D Structure Click here
A0A1D8PSC6 View 3D Structure Click here
A4I4B1 View 3D Structure Click here
A4I6A0 View 3D Structure Click here
A4I8L0 View 3D Structure Click here
D3ZD46 View 3D Structure Click here
D4ADT5 View 3D Structure Click here
E9PU15 View 3D Structure Click here
F1QUY3 View 3D Structure Click here
F1R4B9 View 3D Structure Click here
G3V6W5 View 3D Structure Click here
G5EDI8 View 3D Structure Click here
I1K6G2 View 3D Structure Click here
I1KPD4 View 3D Structure Click here
I3XHK1 View 3D Structure Click here
K7KH72 View 3D Structure Click here
K7KIB7 View 3D Structure Click here
K7LBG6 View 3D Structure Click here
K7N0F5 View 3D Structure Click here
O00835 View 3D Structure Click here
O13768 View 3D Structure Click here
O50435 View 3D Structure Click here
O53470 View 3D Structure Click here
O53873 View 3D Structure Click here
P08956 View 3D Structure Click here
P0A8F8 View 3D Structure Click here
P19447 View 3D Structure Click here
P33919 View 3D Structure Click here
P34529 View 3D Structure Click here
P40562 View 3D Structure Click here
P49135 View 3D Structure Click here
P76257 View 3D Structure Click here
P9WFC7 View 3D Structure Click here
P9WL21 View 3D Structure Click here
Q00578 View 3D Structure Click here
Q02870 View 3D Structure Click here
Q06683 View 3D Structure Click here
Q09884 View 3D Structure Click here
Q0JK78 View 3D Structure Click here
Q1MTR1 View 3D Structure Click here
Q2FVC3 View 3D Structure Click here
Q2G050 View 3D Structure Click here
Q2G057 View 3D Structure Click here
Q2G266 View 3D Structure Click here
Q38861 View 3D Structure Click here
Q4CVA8 View 3D Structure Click here
Q4D326 View 3D Structure Click here
Q4D5K3 View 3D Structure Click here
Q4D8C5 View 3D Structure Click here
Q4DHR0 View 3D Structure Click here
Q4G005 View 3D Structure Click here
Q54EH7 View 3D Structure Click here
Q54H25 View 3D Structure Click here
Q54UI6 View 3D Structure Click here
Q54UP1 View 3D Structure Click here
Q58352 View 3D Structure Click here
Q59PU5 View 3D Structure Click here
Q59PU6 View 3D Structure Click here
Q5A1A0 View 3D Structure Click here
Q5N870 View 3D Structure Click here
Q60287 View 3D Structure Click here
Q6Q899 View 3D Structure Click here
Q7ZVV1 View 3D Structure Click here
Q86L44 View 3D Structure Click here
Q8BGE5 View 3D Structure Click here
Q8I2H7 View 3D Structure Click here
Q8IJ31 View 3D Structure Click here
Q8IYD8 View 3D Structure Click here
Q8R418 View 3D Structure Click here
Q8R5F7 View 3D Structure Click here
Q8T145 View 3D Structure Click here
Q95PZ4 View 3D Structure Click here
Q96C10 View 3D Structure Click here
Q99J87 View 3D Structure Click here
Q9BYX4 View 3D Structure Click here
Q9FUG4 View 3D Structure Click here
Q9HE09 View 3D Structure Click here
Q9SP32 View 3D Structure Click here
Q9UPY3 View 3D Structure Click here
Q9UT23 View 3D Structure Click here
Q9VDA0 View 3D Structure Click here