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41  structures 6827  species 0  interactions 11037  sequences 122  architectures

Family: DNA_mis_repair (PF01119)

Summary: DNA mismatch repair protein, C-terminal domain

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

This is the Wikipedia entry entitled "DNA mismatch repair". More...

DNA mismatch repair Edit Wikipedia article

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

DNA mismatch repair protein, C-terminal domain Provide feedback

This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013507

This domain is found in MutL and homologues and is characterized by a ribosomal protein S5 domain 2-like fold [ PUBMED:26249686 ].

The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [ PUBMED:14527292 ].

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 S5 (CL0329), which has the following description:

This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.

The clan contains the following 18 members:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N

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
(113)
Full
(11037)
Representative proteomes UniProt
(40895)
RP15
(1837)
RP35
(5314)
RP55
(10098)
RP75
(15937)
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
(113)
Full
(11037)
Representative proteomes UniProt
(40895)
RP15
(1837)
RP35
(5314)
RP55
(10098)
RP75
(15937)
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
(113)
Full
(11037)
Representative proteomes UniProt
(40895)
RP15
(1837)
RP35
(5314)
RP55
(10098)
RP75
(15937)
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: SCOP
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A , Griffiths-Jones SR
Number in seed: 113
Number in full: 11037
Average length of the domain: 119.30 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 16.29 %

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 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 119
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 DNA_mis_repair domain has been found. There are 41 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
A0A1D6EUN3 View 3D Structure Click here
A0A1D6Q3Y5 View 3D Structure Click here
A0A1D8PII6 View 3D Structure Click here
A0A1Y7VMP7 View 3D Structure Click here
A1Z7C1 View 3D Structure Click here
A1ZA03 View 3D Structure Click here
A4I0Y1 View 3D Structure Click here
A4IB67 View 3D Structure Click here
B0S640 View 3D Structure Click here
B1H246 View 3D Structure Click here
B8A6F5 View 3D Structure Click here
D4ADG4 View 3D Structure Click here
E7F558 View 3D Structure Click here
E9QGN2 View 3D Structure Click here
G5EFG5 View 3D Structure Click here
I1JFI1 View 3D Structure Click here
I1JZC3 View 3D Structure Click here
K7K439 View 3D Structure Click here
K7LGX1 View 3D Structure Click here
K7W1B0 View 3D Structure Click here
P14242 View 3D Structure Click here
P23367 View 3D Structure Click here
P38920 View 3D Structure Click here
P40692 View 3D Structure Click here
P54277 View 3D Structure Click here
P54278 View 3D Structure Click here
P54279 View 3D Structure Click here
P54280 View 3D Structure Click here
P97679 View 3D Structure Click here
Q07980 View 3D Structure Click here
Q4DG46 View 3D Structure Click here
Q4DI77 View 3D Structure Click here
Q4DJF3 View 3D Structure Click here
Q54KD8 View 3D Structure Click here
Q54QA0 View 3D Structure Click here
Q54QI0 View 3D Structure Click here
Q59SL0 View 3D Structure Click here
Q5JN46 View 3D Structure Click here
Q69L72 View 3D Structure Click here
Q8IBJ3 View 3D Structure Click here
Q8IIJ0 View 3D Structure Click here
Q8K119 View 3D Structure Click here
Q93T05 View 3D Structure Click here
Q941I6 View 3D Structure Click here
Q9JK91 View 3D Structure Click here
Q9P7W6 View 3D Structure Click here
Q9UHC1 View 3D Structure Click here
Q9XU10 View 3D Structure Click here
Q9ZRV4 View 3D Structure Click here